Publications

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• Fukushima, K. (2023) ‘A decaploid pitcher plant genome reveals a novel role for recessive subgenomes’, Nature Plants, 9(12), 1950–1951, available: https://doi.org/10.1038/s41477-023-01563-1.
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  Genomic polyploidy is prevalent in the plant kingdom, giving rise to dominant and recessive subgenomes. We show that the recessive subgenomes of the pitcher plant Nepenthes gracilis had a crucial role in the acquisition of novel genes with species-specific function such as dioecy and carnivory.

  @article{fukushima2023decaploid, abstract = {Genomic polyploidy is prevalent in the plant kingdom, giving rise to dominant and recessive subgenomes. We show that the recessive subgenomes of the pitcher plant Nepenthes gracilis had a crucial role in the acquisition of novel genes with species-specific function such as dioecy and carnivory.}, author = {Fukushima, Kenji}, journal = {Nature Plants}, keywords = {myown}, month = 12, number = 12, pages = {1950–1951}, title = {A decaploid pitcher plant genome reveals a novel role for recessive subgenomes}, volume = 9, year = 2023 }

  %0 Journal Article %1 fukushima2023decaploid %A Fukushima, Kenji %D 2023 %J Nature Plants %N 12 %P 1950--1951 %R 10.1038/s41477-023-01563-1 %T A decaploid pitcher plant genome reveals a novel role for recessive subgenomes %U https://doi.org/10.1038/s41477-023-01563-1 %V 9 %X Genomic polyploidy is prevalent in the plant kingdom, giving rise to dominant and recessive subgenomes. We show that the recessive subgenomes of the pitcher plant Nepenthes gracilis had a crucial role in the acquisition of novel genes with species-specific function such as dioecy and carnivory.
• Fukushima, K. and Pollock, D.D. (2023) ‘Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence’, Nature Ecology & Evolution, 7, 155–170, available: https://doi.org/https://doi.org/10.1038/s41559-022-01932-7.
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  @article{noauthororeditor, author = {Fukushima, Kenji and Pollock, David D.}, journal = {Nature Ecology & Evolution}, keywords = {myown}, month = {02}, pages = {155–170}, title = {Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence}, volume = 7, year = 2023 }

  %0 Journal Article %1 noauthororeditor %A Fukushima, Kenji %A Pollock, David D. %D 2023 %J Nature Ecology & Evolution %P 155–170 %R https://doi.org/10.1038/s41559-022-01932-7 %T Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence %U https://www.nature.com/articles/s41559-022-01932-7 %V 7
• Suetsugu, K., Fukushima, K., Makino, T., Ikematsu, S., Sakamoto, T., and Kimura, S. (2023) ‘Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid Gastrodia’, New Phytologist, 237(1), 323–338, available: https://doi.org/https://doi.org/10.1111/nph.18495.
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  @article{noauthororeditor, author = {Suetsugu, Kenji and Fukushima, Kenji and Makino, Takashi and Ikematsu, Shuka and Sakamoto, Tomoaki and Kimura, Seisuke}, journal = {New Phytologist}, keywords = {myown}, month = {01}, number = 1, pages = {323-338}, title = {Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid Gastrodia}, volume = 237, year = 2023 }

  %0 Journal Article %1 noauthororeditor %A Suetsugu, Kenji %A Fukushima, Kenji %A Makino, Takashi %A Ikematsu, Shuka %A Sakamoto, Tomoaki %A Kimura, Seisuke %D 2023 %J New Phytologist %N 1 %P 323-338 %R https://doi.org/10.1111/nph.18495 %T Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid Gastrodia %U https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.18495 %V 237
• Montero, H. and Fukushima, K. (2023) ‘Non-prey biotic interactions in carnivorous plants’, Current Biology, 33(11), R497-R500, available: https://doi.org/https://doi.org/10.1016/j.cub.2023.01.053.
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  Summary Carnivorous plants often spark broad interest due to their specialized adaptations for trapping and consuming animals. These notable organisms not only fix carbon through photosynthesis, but they also obtain essential nutrients such as nitrogen and phosphate from their captured prey. In typical angiosperms, interactions with animals are usually confined to such processes as pollination and herbivory, but another layer of complexity in these interactions is added for carnivorous plants. Here, we introduce carnivorous plants and their associated organisms — ranging from their prey to their symbionts — and highlight biotic interactions beyond carnivory to discuss how the ‘default’ interactions typical for flowering plants have changed in the case of the carnivorous plants (Figure 1).

  @article{MONTERO2023R497, abstract = {Summary Carnivorous plants often spark broad interest due to their specialized adaptations for trapping and consuming animals. These notable organisms not only fix carbon through photosynthesis, but they also obtain essential nutrients such as nitrogen and phosphate from their captured prey. In typical angiosperms, interactions with animals are usually confined to such processes as pollination and herbivory, but another layer of complexity in these interactions is added for carnivorous plants. Here, we introduce carnivorous plants and their associated organisms — ranging from their prey to their symbionts — and highlight biotic interactions beyond carnivory to discuss how the ‘default’ interactions typical for flowering plants have changed in the case of the carnivorous plants (Figure 1).}, author = {Montero, Héctor and Fukushima, Kenji}, journal = {Current Biology}, keywords = {myown}, number = 11, pages = {R497-R500}, title = {Non-prey biotic interactions in carnivorous plants}, volume = 33, year = 2023 }

  %0 Journal Article %1 MONTERO2023R497 %A Montero, Héctor %A Fukushima, Kenji %D 2023 %J Current Biology %N 11 %P R497-R500 %R https://doi.org/10.1016/j.cub.2023.01.053 %T Non-prey biotic interactions in carnivorous plants %U https://www.sciencedirect.com/science/article/pii/S0960982223000878 %V 33 %X Summary Carnivorous plants often spark broad interest due to their specialized adaptations for trapping and consuming animals. These notable organisms not only fix carbon through photosynthesis, but they also obtain essential nutrients such as nitrogen and phosphate from their captured prey. In typical angiosperms, interactions with animals are usually confined to such processes as pollination and herbivory, but another layer of complexity in these interactions is added for carnivorous plants. Here, we introduce carnivorous plants and their associated organisms — ranging from their prey to their symbionts — and highlight biotic interactions beyond carnivory to discuss how the ‘default’ interactions typical for flowering plants have changed in the case of the carnivorous plants (Figure 1).
• Saul, F., Scharmann, M., Wakatake, T., Rajaraman, S., Marques, A., Freund, M., Bringmann, G., Channon, L., Becker, D., Carroll, E., Low, Y.W., Lindqvist, C., Gilbert, K.J., Renner, T., Masuda, S., Richter, M., Vogg, G., Shirasu, K., Michael, T.P., Hedrich, R., Albert, V.A., and Fukushima, K. (2023) ‘Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis’, Nature Plants, 9(12), 2000–2015, available: https://doi.org/10.1038/s41477-023-01562-2.
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  Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.

  @article{Saul2023, abstract = {Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.}, author = {Saul, Franziska and Scharmann, Mathias and Wakatake, Takanori and Rajaraman, Sitaram and Marques, Andr{\'e} and Freund, Matthias and Bringmann, Gerhard and Channon, Louisa and Becker, Dirk and Carroll, Emily and Low, Yee Wen and Lindqvist, Charlotte and Gilbert, Kadeem J. and Renner, Tanya and Masuda, Sachiko and Richter, Michaela and Vogg, Gerd and Shirasu, Ken and Michael, Todd P. and Hedrich, Rainer and Albert, Victor A. and Fukushima, Kenji}, journal = {Nature Plants}, keywords = {myown}, month = 12, number = 12, pages = {2000–2015}, title = {Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis}, volume = 9, year = 2023 }

  %0 Journal Article %1 Saul2023 %A Saul, Franziska %A Scharmann, Mathias %A Wakatake, Takanori %A Rajaraman, Sitaram %A Marques, Andr{é} %A Freund, Matthias %A Bringmann, Gerhard %A Channon, Louisa %A Becker, Dirk %A Carroll, Emily %A Low, Yee Wen %A Lindqvist, Charlotte %A Gilbert, Kadeem J. %A Renner, Tanya %A Masuda, Sachiko %A Richter, Michaela %A Vogg, Gerd %A Shirasu, Ken %A Michael, Todd P. %A Hedrich, Rainer %A Albert, Victor A. %A Fukushima, Kenji %D 2023 %J Nature Plants %N 12 %P 2000--2015 %R 10.1038/s41477-023-01562-2 %T Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis %U https://doi.org/10.1038/s41477-023-01562-2 %V 9 %X Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.

• Freund, M., Graus, D., Fleischmann, A., Gilbert, K.J., Lin, Q., Renner, T., Stigloher, C., Albert, V.A., Hedrich, R., and Fukushima, K. (2022) ‘The digestive systems of carnivorous plants’, Plant Physiology, 190(1), 44–59, available: https://doi.org/https://doi.org/10.1093/plphys/kiac232.
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  @article{freund2022digestive, author = {Freund, Matthias and Graus, Dorothea and Fleischmann, Andreas and Gilbert, Kadeem J. and Lin, Qianshi and Renner, Tanya and Stigloher, Christian and Albert, Victor A. and Hedrich, Rainer and Fukushima, Kenji}, journal = {Plant Physiology}, keywords = {myown}, month = {08}, number = 1, pages = {44-59}, title = {The digestive systems of carnivorous plants}, volume = 190, year = 2022 }

  %0 Journal Article %1 freund2022digestive %A Freund, Matthias %A Graus, Dorothea %A Fleischmann, Andreas %A Gilbert, Kadeem J. %A Lin, Qianshi %A Renner, Tanya %A Stigloher, Christian %A Albert, Victor A. %A Hedrich, Rainer %A Fukushima, Kenji %D 2022 %J Plant Physiology %N 1 %P 44-59 %R https://doi.org/10.1093/plphys/kiac232 %T The digestive systems of carnivorous plants %U https://academic.oup.com/plphys/article/190/1/44/6590657 %V 190
• Naito, K., Wakatake, T., Shibata, T.F., Iseki, K., Shigenobu, S., Takahashi, Y., Ogiso-Tanaka, E., Muto, C., Teruya, K., Shiroma, A., Shimoji, M., Satou, K., Hirano, T., Nagano, A.J., Tomooka, N., Hasebe, M., Fukushima, K., and Sakai, H. (2022) ‘Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance’, bioRxiv, available: https://doi.org/10.1101/2022.03.28.486085.
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  Harnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna, family Fabaceae, consists of many species of such kind, as they are often adapted to harsh environments including marine beach, arid sandy soil, acidic soil, limestone karst and marshes. Here we report long-read assemblies of 12 Vigna species, achieving 95\% or higher BUSCO scores. The comparative analyses discovered a new class of WUSCHEL-related homeobox (WOX) transcription factor superfamily that are incorporated into LTR retrotransposons and have dramatically amplified in some species of the genus Vigna. Except WOX transcription factors, however, gene contents are highly conserved among Vigna species with few copy number variations. On the other hand, transcriptome data provided some insights that transcriptional alterations played more important roles in evolution of stress tolerance in the genus Vigna. The whole genome sequences presented in this study will facilitate understanding genetic mechanisms of stress tolerance and application for developing new crops that are adapted to unfavorable environments.Competing Interest StatementThe authors have declared no competing interest.

  @article{Naito2022.03.28.486085, abstract = {Harnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna, family Fabaceae, consists of many species of such kind, as they are often adapted to harsh environments including marine beach, arid sandy soil, acidic soil, limestone karst and marshes. Here we report long-read assemblies of 12 Vigna species, achieving 95\% or higher BUSCO scores. The comparative analyses discovered a new class of WUSCHEL-related homeobox (WOX) transcription factor superfamily that are incorporated into LTR retrotransposons and have dramatically amplified in some species of the genus Vigna. Except WOX transcription factors, however, gene contents are highly conserved among Vigna species with few copy number variations. On the other hand, transcriptome data provided some insights that transcriptional alterations played more important roles in evolution of stress tolerance in the genus Vigna. The whole genome sequences presented in this study will facilitate understanding genetic mechanisms of stress tolerance and application for developing new crops that are adapted to unfavorable environments.Competing Interest StatementThe authors have declared no competing interest.}, author = {Naito, Ken and Wakatake, Takanori and Shibata, Tomoko F. and Iseki, Kohtaro and Shigenobu, Shuji and Takahashi, Yu and Ogiso-Tanaka, Eri and Muto, Chiaki and Teruya, Kuniko and Shiroma, Akino and Shimoji, Makiko and Satou, Kazuhito and Hirano, Takashi and Nagano, Atsushi J. and Tomooka, Norihiko and Hasebe, Mitsuyasu and Fukushima, Kenji and Sakai, Hiroaki}, journal = {bioRxiv}, keywords = {Vigna}, publisher = {Cold Spring Harbor Laboratory}, title = {Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance}, year = 2022 }

  %0 Journal Article %1 Naito2022.03.28.486085 %A Naito, Ken %A Wakatake, Takanori %A Shibata, Tomoko F. %A Iseki, Kohtaro %A Shigenobu, Shuji %A Takahashi, Yu %A Ogiso-Tanaka, Eri %A Muto, Chiaki %A Teruya, Kuniko %A Shiroma, Akino %A Shimoji, Makiko %A Satou, Kazuhito %A Hirano, Takashi %A Nagano, Atsushi J. %A Tomooka, Norihiko %A Hasebe, Mitsuyasu %A Fukushima, Kenji %A Sakai, Hiroaki %D 2022 %I Cold Spring Harbor Laboratory %J bioRxiv %R 10.1101/2022.03.28.486085 %T Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance %U https://www.biorxiv.org/content/early/2022/03/29/2022.03.28.486085 %X Harnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna, family Fabaceae, consists of many species of such kind, as they are often adapted to harsh environments including marine beach, arid sandy soil, acidic soil, limestone karst and marshes. Here we report long-read assemblies of 12 Vigna species, achieving 95\% or higher BUSCO scores. The comparative analyses discovered a new class of WUSCHEL-related homeobox (WOX) transcription factor superfamily that are incorporated into LTR retrotransposons and have dramatically amplified in some species of the genus Vigna. Except WOX transcription factors, however, gene contents are highly conserved among Vigna species with few copy number variations. On the other hand, transcriptome data provided some insights that transcriptional alterations played more important roles in evolution of stress tolerance in the genus Vigna. The whole genome sequences presented in this study will facilitate understanding genetic mechanisms of stress tolerance and application for developing new crops that are adapted to unfavorable environments.Competing Interest StatementThe authors have declared no competing interest.

• Winkelmüller, T.M., Entila, F., Anver, S., Piasecka, A., Song, B., Dahms, E., Sakakibara, H., Gan, X., Kułak, K., Sawikowska, A., Krajewski, P., Tsiantis, M., Garrido-Oter, R., Fukushima, K., Schulze-Lefert, P., Laurent, S., Bednarek, P., and Tsuda, K. (2021) ‘Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species’, The Plant Cell, 33, 1863–1887, available: https://doi.org/https://doi.org/10.1093/plcell/koab073.
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  Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Here, by employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species to investigate PTI responses, we identified a set of genes that commonly respond to the MAMP flg22 and genes that exhibit species-specific expression signatures. Variation in flg22-triggered transcriptome responses across Brassicaceae species was incongruent with their phylogeny, while expression changes were strongly conserved within A. thaliana. We found the enrichment of WRKY transcription factor binding sites in the 5′-regulatory regions of conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene expression patterns during PTI. Our findings advance our understanding of the evolution of the transcriptome during biotic stress.

  @article{noauthororeditor, abstract = {Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Here, by employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species to investigate PTI responses, we identified a set of genes that commonly respond to the MAMP flg22 and genes that exhibit species-specific expression signatures. Variation in flg22-triggered transcriptome responses across Brassicaceae species was incongruent with their phylogeny, while expression changes were strongly conserved within A. thaliana. We found the enrichment of WRKY transcription factor binding sites in the 5′-regulatory regions of conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene expression patterns during PTI. Our findings advance our understanding of the evolution of the transcriptome during biotic stress.}, author = {Winkelmüller, Thomas M and Entila, Frederickson and Anver, Shajahan and Piasecka, Anna and Song, Baoxing and Dahms, Eik and Sakakibara, Hitoshi and Gan, Xiangchao and Kułak, Karolina and Sawikowska, Aneta and Krajewski, Paweł and Tsiantis, Miltos and Garrido-Oter, Ruben and Fukushima, Kenji and Schulze-Lefert, Paul and Laurent, Stefan and Bednarek, Paweł and Tsuda, Kenichi}, journal = {The Plant Cell}, keywords = {plants}, pages = {1863-1887}, title = {Gene expression evolution in pattern-triggered immunity within <i>Arabidopsis thaliana</i> and across Brassicaceae species}, volume = 33, year = 2021 }

  %0 Journal Article %1 noauthororeditor %A Winkelmüller, Thomas M %A Entila, Frederickson %A Anver, Shajahan %A Piasecka, Anna %A Song, Baoxing %A Dahms, Eik %A Sakakibara, Hitoshi %A Gan, Xiangchao %A Kułak, Karolina %A Sawikowska, Aneta %A Krajewski, Paweł %A Tsiantis, Miltos %A Garrido-Oter, Ruben %A Fukushima, Kenji %A Schulze-Lefert, Paul %A Laurent, Stefan %A Bednarek, Paweł %A Tsuda, Kenichi %D 2021 %J The Plant Cell %P 1863-1887 %R https://doi.org/10.1093/plcell/koab073 %T Gene expression evolution in pattern-triggered immunity within <i>Arabidopsis thaliana</i> and across Brassicaceae species %V 33 %X Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Here, by employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species to investigate PTI responses, we identified a set of genes that commonly respond to the MAMP flg22 and genes that exhibit species-specific expression signatures. Variation in flg22-triggered transcriptome responses across Brassicaceae species was incongruent with their phylogeny, while expression changes were strongly conserved within A. thaliana. We found the enrichment of WRKY transcription factor binding sites in the 5′-regulatory regions of conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene expression patterns during PTI. Our findings advance our understanding of the evolution of the transcriptome during biotic stress.
• Hedrich, R. and Fukushima, K. (2021) ‘On the origin of carnivory: Molecular physiology and evolution of plants on an animal diet’, Annual Review of Plant Biology, 72, 133–153, available: https://doi.org/10.1146/annurev-arplant-080620-010429.
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  @article{hedrich2021origin, author = {Hedrich, Rainer and Fukushima, Kenji}, journal = {Annual Review of Plant Biology}, keywords = {myown}, pages = {133-153}, title = {On the origin of carnivory: Molecular physiology and evolution of plants on an animal diet}, volume = 72, year = 2021 }

  %0 Journal Article %1 hedrich2021origin %A Hedrich, Rainer %A Fukushima, Kenji %D 2021 %J Annual Review of Plant Biology %P 133-153 %R 10.1146/annurev-arplant-080620-010429 %T On the origin of carnivory: Molecular physiology and evolution of plants on an animal diet %U https://www.annualreviews.org/doi/10.1146/annurev-arplant-080620-010429 %V 72
• Fukushima, K., Narukawa, H., Palfalvi, G., and Hasebe, M. (2021) ‘A discordance of seasonally covarying cues uncovers misregulated phenotypes in the heterophyllous pitcher plant Cephalotus follicularis’, Proceedings of the Royal Society B, 288(1943), 10.1098/rspb.2020.2568, available: https://doi.org/10.1098/rspb.2020.2568.
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  Organisms withstand normal ranges of environmental fluctuations by producing a set of phenotypes genetically programmed as a reaction norm; however, extreme conditions can expose a misregulation of phenotypes called a hidden reaction norm. Although an environment consists of multiple factors, how combinations of these factors influence a reaction norm is not well understood. To elucidate the combinatorial effects of environmental factors, we studied the leaf shape plasticity of the carnivorous pitcher plant Cephalotus follicularis. Clonally propagated plants were subjected to 12-week-long growth experiments in different conditions controlled by growth chambers. Here, we show that the dimorphic response of forming a photosynthetic flat leaf or an insect-trapping pitcher leaf is regulated by two covarying environmental cues: temperature and photoperiod. Even within the normal ranges of temperature and photoperiod, unusual combinations of the two induced the production of malformed leaves that were rarely observed under the environmentally typical combinations. We identified such cases in combinations of a summer temperature with a short-to-neutral day length, whose average frequency in the natural Cephalotus habitats corresponded to a once-in-a-lifetime event for this perennial species. Our results suggest that even if individual cues are within the range of natural fluctuations, a hidden reaction norm can be exposed under their discordant combinations. We anticipate that climate change may challenge organismal responses through not only extreme cues but also through uncommon combinations of benign cues.

  @article{noauthororeditor, abstract = {Organisms withstand normal ranges of environmental fluctuations by producing a set of phenotypes genetically programmed as a reaction norm; however, extreme conditions can expose a misregulation of phenotypes called a hidden reaction norm. Although an environment consists of multiple factors, how combinations of these factors influence a reaction norm is not well understood. To elucidate the combinatorial effects of environmental factors, we studied the leaf shape plasticity of the carnivorous pitcher plant Cephalotus follicularis. Clonally propagated plants were subjected to 12-week-long growth experiments in different conditions controlled by growth chambers. Here, we show that the dimorphic response of forming a photosynthetic flat leaf or an insect-trapping pitcher leaf is regulated by two covarying environmental cues: temperature and photoperiod. Even within the normal ranges of temperature and photoperiod, unusual combinations of the two induced the production of malformed leaves that were rarely observed under the environmentally typical combinations. We identified such cases in combinations of a summer temperature with a short-to-neutral day length, whose average frequency in the natural Cephalotus habitats corresponded to a once-in-a-lifetime event for this perennial species. Our results suggest that even if individual cues are within the range of natural fluctuations, a hidden reaction norm can be exposed under their discordant combinations. We anticipate that climate change may challenge organismal responses through not only extreme cues but also through uncommon combinations of benign cues.}, author = {Fukushima, Kenji and Narukawa, Hideki and Palfalvi, Gergo and Hasebe, Mitsuyasu}, journal = {Proceedings of the Royal Society B}, keywords = {myown}, number = 1943, pages = {10.1098/rspb.2020.2568}, title = {A discordance of seasonally covarying cues uncovers misregulated phenotypes in the heterophyllous pitcher plant Cephalotus follicularis}, volume = 288, year = 2021 }

  %0 Journal Article %1 noauthororeditor %A Fukushima, Kenji %A Narukawa, Hideki %A Palfalvi, Gergo %A Hasebe, Mitsuyasu %D 2021 %J Proceedings of the Royal Society B %N 1943 %P 10.1098/rspb.2020.2568 %R 10.1098/rspb.2020.2568 %T A discordance of seasonally covarying cues uncovers misregulated phenotypes in the heterophyllous pitcher plant Cephalotus follicularis %U https://royalsocietypublishing.org/doi/10.1098/rspb.2020.2568 %V 288 %X Organisms withstand normal ranges of environmental fluctuations by producing a set of phenotypes genetically programmed as a reaction norm; however, extreme conditions can expose a misregulation of phenotypes called a hidden reaction norm. Although an environment consists of multiple factors, how combinations of these factors influence a reaction norm is not well understood. To elucidate the combinatorial effects of environmental factors, we studied the leaf shape plasticity of the carnivorous pitcher plant Cephalotus follicularis. Clonally propagated plants were subjected to 12-week-long growth experiments in different conditions controlled by growth chambers. Here, we show that the dimorphic response of forming a photosynthetic flat leaf or an insect-trapping pitcher leaf is regulated by two covarying environmental cues: temperature and photoperiod. Even within the normal ranges of temperature and photoperiod, unusual combinations of the two induced the production of malformed leaves that were rarely observed under the environmentally typical combinations. We identified such cases in combinations of a summer temperature with a short-to-neutral day length, whose average frequency in the natural Cephalotus habitats corresponded to a once-in-a-lifetime event for this perennial species. Our results suggest that even if individual cues are within the range of natural fluctuations, a hidden reaction norm can be exposed under their discordant combinations. We anticipate that climate change may challenge organismal responses through not only extreme cues but also through uncommon combinations of benign cues.

• Palfalvi, G., Hackl, T., Terhoeven, N., Shibata, T.F., Nishiyama, T., Ankenbrand, M., Becker, D., Förster, F., Freund, M., Iosip, A., Kreuzer, I., Saul, F., Kamida, C., Fukushima, K., Shigenobu, S., Tamada, Y., Adamec, L., Hoshi, Y., Ueda, K., Winkelmann, T., Fuchs, J., Schubert, I., Schwacke, R., Al-Rasheid, K., Schultz, J., Hasebe, M., and Hedrich, R. (2020) ‘Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory’, Current Biology, 30(12), 2312 – 2320.e5, available: https://doi.org/https://doi.org/10.1016/j.cub.2020.04.051.
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  Summary Most plants grow and develop by taking up nutrients from the soil while continuously under threat from foraging animals. Carnivorous plants have turned the tables by capturing and consuming nutrient-rich animal prey, enabling them to thrive in nutrient-poor soil. To better understand the evolution of botanical carnivory, we compared the draft genome of the Venus flytrap (Dionaea muscipula) with that of its aquatic sister, the waterwheel plant Aldrovanda vesiculosa, and the sundew Drosera spatulata. We identified an early whole-genome duplication in the family as source for carnivory-associated genes. Recruitment of genes to the trap from the root especially was a major mechanism in the evolution of carnivory, supported by family-specific duplications. Still, these genomes belong to the gene poorest land plants sequenced thus far, suggesting reduction of selective pressure on different processes, including non-carnivorous nutrient acquisition. Our results show how non-carnivorous plants evolved into the most skillful green hunters on the planet.

  @article{PALFALVI20202312, abstract = {Summary Most plants grow and develop by taking up nutrients from the soil while continuously under threat from foraging animals. Carnivorous plants have turned the tables by capturing and consuming nutrient-rich animal prey, enabling them to thrive in nutrient-poor soil. To better understand the evolution of botanical carnivory, we compared the draft genome of the Venus flytrap (Dionaea muscipula) with that of its aquatic sister, the waterwheel plant Aldrovanda vesiculosa, and the sundew Drosera spatulata. We identified an early whole-genome duplication in the family as source for carnivory-associated genes. Recruitment of genes to the trap from the root especially was a major mechanism in the evolution of carnivory, supported by family-specific duplications. Still, these genomes belong to the gene poorest land plants sequenced thus far, suggesting reduction of selective pressure on different processes, including non-carnivorous nutrient acquisition. Our results show how non-carnivorous plants evolved into the most skillful green hunters on the planet.}, author = {Palfalvi, Gergo and Hackl, Thomas and Terhoeven, Niklas and Shibata, Tomoko F. and Nishiyama, Tomoaki and Ankenbrand, Markus and Becker, Dirk and Förster, Frank and Freund, Matthias and Iosip, Anda and Kreuzer, Ines and Saul, Franziska and Kamida, Chiharu and Fukushima, Kenji and Shigenobu, Shuji and Tamada, Yosuke and Adamec, Lubomir and Hoshi, Yoshikazu and Ueda, Kunihiko and Winkelmann, Traud and Fuchs, Jörg and Schubert, Ingo and Schwacke, Rainer and Al-Rasheid, Khaled and Schultz, Jörg and Hasebe, Mitsuyasu and Hedrich, Rainer}, journal = {Current Biology}, keywords = {myown}, number = 12, pages = {2312 - 2320.e5}, title = {Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory}, volume = 30, year = 2020 }

  %0 Journal Article %1 PALFALVI20202312 %A Palfalvi, Gergo %A Hackl, Thomas %A Terhoeven, Niklas %A Shibata, Tomoko F. %A Nishiyama, Tomoaki %A Ankenbrand, Markus %A Becker, Dirk %A Förster, Frank %A Freund, Matthias %A Iosip, Anda %A Kreuzer, Ines %A Saul, Franziska %A Kamida, Chiharu %A Fukushima, Kenji %A Shigenobu, Shuji %A Tamada, Yosuke %A Adamec, Lubomir %A Hoshi, Yoshikazu %A Ueda, Kunihiko %A Winkelmann, Traud %A Fuchs, Jörg %A Schubert, Ingo %A Schwacke, Rainer %A Al-Rasheid, Khaled %A Schultz, Jörg %A Hasebe, Mitsuyasu %A Hedrich, Rainer %D 2020 %J Current Biology %N 12 %P 2312 - 2320.e5 %R https://doi.org/10.1016/j.cub.2020.04.051 %T Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory %U http://www.sciencedirect.com/science/article/pii/S0960982220305674 %V 30 %X Summary Most plants grow and develop by taking up nutrients from the soil while continuously under threat from foraging animals. Carnivorous plants have turned the tables by capturing and consuming nutrient-rich animal prey, enabling them to thrive in nutrient-poor soil. To better understand the evolution of botanical carnivory, we compared the draft genome of the Venus flytrap (Dionaea muscipula) with that of its aquatic sister, the waterwheel plant Aldrovanda vesiculosa, and the sundew Drosera spatulata. We identified an early whole-genome duplication in the family as source for carnivory-associated genes. Recruitment of genes to the trap from the root especially was a major mechanism in the evolution of carnivory, supported by family-specific duplications. Still, these genomes belong to the gene poorest land plants sequenced thus far, suggesting reduction of selective pressure on different processes, including non-carnivorous nutrient acquisition. Our results show how non-carnivorous plants evolved into the most skillful green hunters on the planet.
• Suda, H., Mano, H., Toyota, M., Fukushima, K., Mimura, T., Tsutsui, I., Hedrich, R., Tamada, Y., and Hasebe, M. (2020) ‘Calcium dynamics during trap closure visualized in transgenic Venus flytrap’, Nature Plants, 6(10), 1219–1224, available: https://doi.org/10.1038/s41477-020-00773-1.
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  The leaves of the carnivorous plant Venus flytrap, Dionaea muscipula (Dionaea) close rapidly to capture insect prey. The closure response usually requires two successive mechanical stimuli to sensory hairs on the leaf blade within approximately 30 s (refs. 1–4). An unknown biological system in Dionaea is thought to memorize the first stimulus and transduce the signal from the sensory hair to the leaf blade2. Here, we link signal memory to calcium dynamics using transgenic Dionaea expressing a Ca2+ sensor. Stimulation of a sensory hair caused an increase in cytosolic Ca2+ concentration ([Ca2+]cyt) starting in the sensory hair and spreading to the leaf blade. A second stimulus increased [Ca2+]cyt to an even higher level, meeting a threshold that is correlated to the leaf blade closure. Because [Ca2+]cyt gradually decreased after the first stimulus, the [Ca2+]cyt increase induced by the second stimulus was insufficient to meet the putative threshold for movement after about 30 s. The Ca2+ wave triggered by mechanical stimulation moved an order of magnitude faster than that induced by wounding in petioles of Arabidopsis thaliana5 and Dionaea. The capacity for rapid movement has evolved repeatedly in flowering plants. This study opens a path to investigate the role of Ca2+ in plant movement mechanisms and their evolution.

  @article{suda2020calcium, abstract = {The leaves of the carnivorous plant Venus flytrap, Dionaea muscipula (Dionaea) close rapidly to capture insect prey. The closure response usually requires two successive mechanical stimuli to sensory hairs on the leaf blade within approximately 30 s (refs. 1–4). An unknown biological system in Dionaea is thought to memorize the first stimulus and transduce the signal from the sensory hair to the leaf blade2. Here, we link signal memory to calcium dynamics using transgenic Dionaea expressing a Ca2+ sensor. Stimulation of a sensory hair caused an increase in cytosolic Ca2+ concentration ([Ca2+]cyt) starting in the sensory hair and spreading to the leaf blade. A second stimulus increased [Ca2+]cyt to an even higher level, meeting a threshold that is correlated to the leaf blade closure. Because [Ca2+]cyt gradually decreased after the first stimulus, the [Ca2+]cyt increase induced by the second stimulus was insufficient to meet the putative threshold for movement after about 30 s. The Ca2+ wave triggered by mechanical stimulation moved an order of magnitude faster than that induced by wounding in petioles of Arabidopsis thaliana5 and Dionaea. The capacity for rapid movement has evolved repeatedly in flowering plants. This study opens a path to investigate the role of Ca2+ in plant movement mechanisms and their evolution.}, author = {Suda, Hiraku and Mano, Hiroaki and Toyota, Masatsugu and Fukushima, Kenji and Mimura, Tetsuro and Tsutsui, Izuo and Hedrich, Rainer and Tamada, Yosuke and Hasebe, Mitsuyasu}, journal = {Nature Plants}, keywords = {publication}, number = 10, pages = {1219–1224}, title = {Calcium dynamics during trap closure visualized in transgenic Venus flytrap}, volume = 6, year = 2020 }

  %0 Journal Article %1 suda2020calcium %A Suda, Hiraku %A Mano, Hiroaki %A Toyota, Masatsugu %A Fukushima, Kenji %A Mimura, Tetsuro %A Tsutsui, Izuo %A Hedrich, Rainer %A Tamada, Yosuke %A Hasebe, Mitsuyasu %D 2020 %J Nature Plants %N 10 %P 1219--1224 %R 10.1038/s41477-020-00773-1 %T Calcium dynamics during trap closure visualized in transgenic Venus flytrap %U https://doi.org/10.1038/s41477-020-00773-1 %V 6 %X The leaves of the carnivorous plant Venus flytrap, Dionaea muscipula (Dionaea) close rapidly to capture insect prey. The closure response usually requires two successive mechanical stimuli to sensory hairs on the leaf blade within approximately 30 s (refs. 1–4). An unknown biological system in Dionaea is thought to memorize the first stimulus and transduce the signal from the sensory hair to the leaf blade2. Here, we link signal memory to calcium dynamics using transgenic Dionaea expressing a Ca2+ sensor. Stimulation of a sensory hair caused an increase in cytosolic Ca2+ concentration ([Ca2+]cyt) starting in the sensory hair and spreading to the leaf blade. A second stimulus increased [Ca2+]cyt to an even higher level, meeting a threshold that is correlated to the leaf blade closure. Because [Ca2+]cyt gradually decreased after the first stimulus, the [Ca2+]cyt increase induced by the second stimulus was insufficient to meet the putative threshold for movement after about 30 s. The Ca2+ wave triggered by mechanical stimulation moved an order of magnitude faster than that induced by wounding in petioles of Arabidopsis thaliana5 and Dionaea. The capacity for rapid movement has evolved repeatedly in flowering plants. This study opens a path to investigate the role of Ca2+ in plant movement mechanisms and their evolution.
• Fukushima, K. and Pollock, D.D. (2020) ‘Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution’, Nature Communications, 11(1), 4459-, available: https://doi.org/10.1038/s41467-020-18090-8.
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  The origins of multicellular physiology are tied to evolution of gene expression. Genes can shift expression as organisms evolve, but how ancestral expression influences altered descendant expression is not well understood. To examine this, we amalgamate 1,903 RNA-seq datasets from 182 research projects, including 6 organs in 21 vertebrate species. Quality control eliminates project-specific biases, and expression shifts are reconstructed using gene-family-wise phylogenetic Ornstein–Uhlenbeck models. Expression shifts following gene duplication result in more drastic changes in expression properties than shifts without gene duplication. The expression properties are tightly coupled with protein evolutionary rate, depending on whether and how gene duplication occurred. Fluxes in expression patterns among organs are nonrandom, forming modular connections that are reshaped by gene duplication. Thus, if expression shifts, ancestral expression in some organs induces a strong propensity for expression in particular organs in descendants. Regardless of whether the shifts are adaptive or not, this supports a major role for what might be termed preadaptive pathways of gene expression evolution.

  @article{fukushima2020amalgamated, abstract = {The origins of multicellular physiology are tied to evolution of gene expression. Genes can shift expression as organisms evolve, but how ancestral expression influences altered descendant expression is not well understood. To examine this, we amalgamate 1,903 RNA-seq datasets from 182 research projects, including 6 organs in 21 vertebrate species. Quality control eliminates project-specific biases, and expression shifts are reconstructed using gene-family-wise phylogenetic Ornstein–Uhlenbeck models. Expression shifts following gene duplication result in more drastic changes in expression properties than shifts without gene duplication. The expression properties are tightly coupled with protein evolutionary rate, depending on whether and how gene duplication occurred. Fluxes in expression patterns among organs are nonrandom, forming modular connections that are reshaped by gene duplication. Thus, if expression shifts, ancestral expression in some organs induces a strong propensity for expression in particular organs in descendants. Regardless of whether the shifts are adaptive or not, this supports a major role for what might be termed preadaptive pathways of gene expression evolution.}, author = {Fukushima, Kenji and Pollock, David D.}, journal = {Nature Communications}, keywords = {myown}, number = 1, pages = {4459–}, title = {Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution}, volume = 11, year = 2020 }

  %0 Journal Article %1 fukushima2020amalgamated %A Fukushima, Kenji %A Pollock, David D. %D 2020 %J Nature Communications %N 1 %P 4459-- %R 10.1038/s41467-020-18090-8 %T Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution %U https://doi.org/10.1038/s41467-020-18090-8 %V 11 %X The origins of multicellular physiology are tied to evolution of gene expression. Genes can shift expression as organisms evolve, but how ancestral expression influences altered descendant expression is not well understood. To examine this, we amalgamate 1,903 RNA-seq datasets from 182 research projects, including 6 organs in 21 vertebrate species. Quality control eliminates project-specific biases, and expression shifts are reconstructed using gene-family-wise phylogenetic Ornstein–Uhlenbeck models. Expression shifts following gene duplication result in more drastic changes in expression properties than shifts without gene duplication. The expression properties are tightly coupled with protein evolutionary rate, depending on whether and how gene duplication occurred. Fluxes in expression patterns among organs are nonrandom, forming modular connections that are reshaped by gene duplication. Thus, if expression shifts, ancestral expression in some organs induces a strong propensity for expression in particular organs in descendants. Regardless of whether the shifts are adaptive or not, this supports a major role for what might be termed preadaptive pathways of gene expression evolution.
• Dreyer, I., Sussmilch, F.C., Fukushima, K., Riadi, G., Becker, D., Schultz, J., and Hedrich, R. (2020) ‘How to Grow a Tree: Plant Voltage-Dependent Cation Channels in the Spotlight of Evolution’, Trends in Plant Science, available: https://doi.org/https://doi.org/10.1016/j.tplants.2020.07.011.
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  Phylogenetic analysis can be a powerful tool for generating hypotheses regarding the evolution of physiological processes. Here, we provide an updated view of the evolution of the main cation channels in plant electrical signalling: the Shaker family of voltage-gated potassium channels and the two-pore cation (K+) channel (TPC1) family. Strikingly, the TPC1 family followed the same conservative evolutionary path as one particular subfamily of Shaker channels (Kout) and remained highly invariant after terrestrialisation, suggesting that electrical signalling was, and remains, key to survival on land. We note that phylogenetic analyses can have pitfalls, which may lead to erroneous conclusions. To avoid these in the future, we suggest guidelines for analyses of ion channel evolution in plants.

  @article{DREYER2020, abstract = {Phylogenetic analysis can be a powerful tool for generating hypotheses regarding the evolution of physiological processes. Here, we provide an updated view of the evolution of the main cation channels in plant electrical signalling: the Shaker family of voltage-gated potassium channels and the two-pore cation (K+) channel (TPC1) family. Strikingly, the TPC1 family followed the same conservative evolutionary path as one particular subfamily of Shaker channels (Kout) and remained highly invariant after terrestrialisation, suggesting that electrical signalling was, and remains, key to survival on land. We note that phylogenetic analyses can have pitfalls, which may lead to erroneous conclusions. To avoid these in the future, we suggest guidelines for analyses of ion channel evolution in plants.}, author = {Dreyer, Ingo and Sussmilch, Frances C. and Fukushima, Kenji and Riadi, Gonzalo and Becker, Dirk and Schultz, Jörg and Hedrich, Rainer}, journal = {Trends in Plant Science}, keywords = {myown}, title = {How to Grow a Tree: Plant Voltage-Dependent Cation Channels in the Spotlight of Evolution}, year = 2020 }

  %0 Journal Article %1 DREYER2020 %A Dreyer, Ingo %A Sussmilch, Frances C. %A Fukushima, Kenji %A Riadi, Gonzalo %A Becker, Dirk %A Schultz, Jörg %A Hedrich, Rainer %D 2020 %J Trends in Plant Science %R https://doi.org/10.1016/j.tplants.2020.07.011 %T How to Grow a Tree: Plant Voltage-Dependent Cation Channels in the Spotlight of Evolution %U http://www.sciencedirect.com/science/article/pii/S1360138520302417 %X Phylogenetic analysis can be a powerful tool for generating hypotheses regarding the evolution of physiological processes. Here, we provide an updated view of the evolution of the main cation channels in plant electrical signalling: the Shaker family of voltage-gated potassium channels and the two-pore cation (K+) channel (TPC1) family. Strikingly, the TPC1 family followed the same conservative evolutionary path as one particular subfamily of Shaker channels (Kout) and remained highly invariant after terrestrialisation, suggesting that electrical signalling was, and remains, key to survival on land. We note that phylogenetic analyses can have pitfalls, which may lead to erroneous conclusions. To avoid these in the future, we suggest guidelines for analyses of ion channel evolution in plants.

• Zhang, Y., Zheng, L., Zheng, Y., Zhou, C., Huang, P., Xiao, X., Zhao, Y., Hao, X., Hu, Z., Chen, Q., Li, H., Wang, X., Fukushima, K., Wang, G., and Li, C. (2019) ‘Assembly and annotation of a draft genome of the medicinal plant Polygonum cuspidatum’, Frontiers in Plant Science, 10, 1274, available: https://doi.org/10.3389/fpls.2019.01274.
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  Polygonum cuspidatum (Japanese knotweed, also known as Huzhang in Chinese), a plant that produces bioactive components such as stilbenes and quinones, has long been recognized as important in traditional Chinese herbal medicine. To better understand the biological features of this plant and to gain genetic insight into the biosynthesis of its natural products, we assembled a draft genome of P. cuspidatum using Illumina sequencing technology. The draft genome is ca. 2.56 Gb long, with 71.54% of the genome annotated as transposable elements. Integrated gene prediction suggested that the P. cuspidatum genome encodes 55,075 functional genes, including 6,776 gene families that are conserved in the five eudicot species examined and 2,386 that are unique to P. cuspidatum. Among the functional genes identified, 4,753 are predicted to encode transcription factors. We traced the gene duplication history of P. cuspidatum and determined that it has undergone two whole-genome duplication events about 65 and 6.6 million years ago. Roots are considered the primary medicinal tissue and transcriptome analysis identified 2,173 genes that were expressed at higher levels in roots compared to aboveground tissues. Detailed phylogenetic analysis demonstrated expansion of the gene family encoding stilbene synthase and chalcone synthase enzymes in the phenylpropanoid metabolic pathway, which is associated with the biosynthesis of resveratrol, a pharmacologically important stilbene. Analysis of the draft genome identified 7 abscisic acid and water deficit stress-induced protein-coding genes and 14 cysteine-rich transmembrane module genes predicted to be involved in stress responses. The draft de novo genome assembly produced in this study represents a valuable resource for the molecular characterization of medicinal compounds in P. cuspidatum, the improvement of this important medicinal plant, and the exploration of its abiotic stress resistance.

  @article{zhang2019assembly, abstract = {Polygonum cuspidatum (Japanese knotweed, also known as Huzhang in Chinese), a plant that produces bioactive components such as stilbenes and quinones, has long been recognized as important in traditional Chinese herbal medicine. To better understand the biological features of this plant and to gain genetic insight into the biosynthesis of its natural products, we assembled a draft genome of P. cuspidatum using Illumina sequencing technology. The draft genome is ca. 2.56 Gb long, with 71.54% of the genome annotated as transposable elements. Integrated gene prediction suggested that the P. cuspidatum genome encodes 55,075 functional genes, including 6,776 gene families that are conserved in the five eudicot species examined and 2,386 that are unique to P. cuspidatum. Among the functional genes identified, 4,753 are predicted to encode transcription factors. We traced the gene duplication history of P. cuspidatum and determined that it has undergone two whole-genome duplication events about 65 and 6.6 million years ago. Roots are considered the primary medicinal tissue and transcriptome analysis identified 2,173 genes that were expressed at higher levels in roots compared to aboveground tissues. Detailed phylogenetic analysis demonstrated expansion of the gene family encoding stilbene synthase and chalcone synthase enzymes in the phenylpropanoid metabolic pathway, which is associated with the biosynthesis of resveratrol, a pharmacologically important stilbene. Analysis of the draft genome identified 7 abscisic acid and water deficit stress-induced protein-coding genes and 14 cysteine-rich transmembrane module genes predicted to be involved in stress responses. The draft de novo genome assembly produced in this study represents a valuable resource for the molecular characterization of medicinal compounds in P. cuspidatum, the improvement of this important medicinal plant, and the exploration of its abiotic stress resistance.}, author = {Zhang, Yonghong and Zheng, Lanlan and Zheng, Yan and Zhou, Chao and Huang, Ping and Xiao, Xiao and Zhao, Yongheng and Hao, Xincai and Hu, Zhubing and Chen, Qinhua and Li, Hongliang and Wang, Xuanbin and Fukushima, Kenji and Wang, Guodong and Li, Chen}, journal = {Frontiers in Plant Science}, keywords = {imported}, pages = 1274, publisher = {Frontiers}, title = {Assembly and annotation of a draft genome of the medicinal plant Polygonum cuspidatum}, type = {article}, volume = 10, year = 2019 }

  %0 Journal Article %1 zhang2019assembly %A Zhang, Yonghong %A Zheng, Lanlan %A Zheng, Yan %A Zhou, Chao %A Huang, Ping %A Xiao, Xiao %A Zhao, Yongheng %A Hao, Xincai %A Hu, Zhubing %A Chen, Qinhua %A Li, Hongliang %A Wang, Xuanbin %A Fukushima, Kenji %A Wang, Guodong %A Li, Chen %D 2019 %I Frontiers %J Frontiers in Plant Science %P 1274 %R 10.3389/fpls.2019.01274 %T Assembly and annotation of a draft genome of the medicinal plant Polygonum cuspidatum %U https://www.frontiersin.org/articles/10.3389/fpls.2019.01274/full %V 10 %X Polygonum cuspidatum (Japanese knotweed, also known as Huzhang in Chinese), a plant that produces bioactive components such as stilbenes and quinones, has long been recognized as important in traditional Chinese herbal medicine. To better understand the biological features of this plant and to gain genetic insight into the biosynthesis of its natural products, we assembled a draft genome of P. cuspidatum using Illumina sequencing technology. The draft genome is ca. 2.56 Gb long, with 71.54% of the genome annotated as transposable elements. Integrated gene prediction suggested that the P. cuspidatum genome encodes 55,075 functional genes, including 6,776 gene families that are conserved in the five eudicot species examined and 2,386 that are unique to P. cuspidatum. Among the functional genes identified, 4,753 are predicted to encode transcription factors. We traced the gene duplication history of P. cuspidatum and determined that it has undergone two whole-genome duplication events about 65 and 6.6 million years ago. Roots are considered the primary medicinal tissue and transcriptome analysis identified 2,173 genes that were expressed at higher levels in roots compared to aboveground tissues. Detailed phylogenetic analysis demonstrated expansion of the gene family encoding stilbene synthase and chalcone synthase enzymes in the phenylpropanoid metabolic pathway, which is associated with the biosynthesis of resveratrol, a pharmacologically important stilbene. Analysis of the draft genome identified 7 abscisic acid and water deficit stress-induced protein-coding genes and 14 cysteine-rich transmembrane module genes predicted to be involved in stress responses. The draft de novo genome assembly produced in this study represents a valuable resource for the molecular characterization of medicinal compounds in P. cuspidatum, the improvement of this important medicinal plant, and the exploration of its abiotic stress resistance.

• Pollard, S., Fukushima, K., Wang, Z.O., Castoe, T.A., and Pollock, D. (2018) ‘{Markov katana: a novel method for Bayesian resampling of parameter space applied to phylogenetic trees}’, bioRxiv, 250951, available: https://doi.org/10.1101/250951.
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  Phylogenetic inference requires a means to search phylogenetic tree space. This is usually achieved using progressive algorithms that propose and test small alterations in the current tree topology and branch lengths. Current programs search tree topology space using branch-swapping algorithms, but proposals do not discriminate well between swaps likely to succeed or fail. When applied to datasets with many taxa, the huge number of possible topologies slows these programs dramatically. To overcome this, we developed a novel statistical approach for proposal generation in Bayesian analysis, and evaluated its applicability for the problem of searching phylogenetic tree space. The general idea of the approach, which we call 'Markov katana', is to make proposals based on a heuristic algorithm using bootstrapped subsets of the data. Such proposals induce an unintended sampling distribution that must be determined and removed to generate posterior estimates, but the cost of this extra step can in principle be small compared to the added value of more efficient parameter exploration in Markov chain Monte Carlo analyses. Our prototype application uses the simple neighbor joining distance heuristic on data subsets to propose new reasonably likely phylogenetic trees (including topologies and branch lengths). The evolutionary model used to generate distances in our prototype was far simpler than the more complex model used to evaluate the likelihood of phylogenies based on the full dataset. This prototype implementation indicates that the Markov katana approach could be easily incorporated into existing phylogenetic search programs and may prove a useful alternative in conjunction with existing methods. The general features of this statistical approach may also prove useful in disciplines other than phylogenetics. We demonstrate that this method can be used to efficiently estimate a Bayesian posterior.

  @article{Pollard2018, abstract = {Phylogenetic inference requires a means to search phylogenetic tree space. This is usually achieved using progressive algorithms that propose and test small alterations in the current tree topology and branch lengths. Current programs search tree topology space using branch-swapping algorithms, but proposals do not discriminate well between swaps likely to succeed or fail. When applied to datasets with many taxa, the huge number of possible topologies slows these programs dramatically. To overcome this, we developed a novel statistical approach for proposal generation in Bayesian analysis, and evaluated its applicability for the problem of searching phylogenetic tree space. The general idea of the approach, which we call 'Markov katana', is to make proposals based on a heuristic algorithm using bootstrapped subsets of the data. Such proposals induce an unintended sampling distribution that must be determined and removed to generate posterior estimates, but the cost of this extra step can in principle be small compared to the added value of more efficient parameter exploration in Markov chain Monte Carlo analyses. Our prototype application uses the simple neighbor joining distance heuristic on data subsets to propose new reasonably likely phylogenetic trees (including topologies and branch lengths). The evolutionary model used to generate distances in our prototype was far simpler than the more complex model used to evaluate the likelihood of phylogenies based on the full dataset. This prototype implementation indicates that the Markov katana approach could be easily incorporated into existing phylogenetic search programs and may prove a useful alternative in conjunction with existing methods. The general features of this statistical approach may also prove useful in disciplines other than phylogenetics. We demonstrate that this method can be used to efficiently estimate a Bayesian posterior.}, author = {Pollard, Stephen and Fukushima, Kenji and Wang, Zhengyuan O and Castoe, Todd A and Pollock, David}, journal = {bioRxiv}, keywords = {imported}, month = {01}, pages = 250951, publisher = {Cold Spring Harbor Laboratory}, title = {{Markov katana: a novel method for Bayesian resampling of parameter space applied to phylogenetic trees}}, year = 2018 }

  %0 Journal Article %1 Pollard2018 %A Pollard, Stephen %A Fukushima, Kenji %A Wang, Zhengyuan O %A Castoe, Todd A %A Pollock, David %D 2018 %I Cold Spring Harbor Laboratory %J bioRxiv %P 250951 %R 10.1101/250951 %T {Markov katana: a novel method for Bayesian resampling of parameter space applied to phylogenetic trees} %U https://www.biorxiv.org/content/early/2018/01/24/250951 %X Phylogenetic inference requires a means to search phylogenetic tree space. This is usually achieved using progressive algorithms that propose and test small alterations in the current tree topology and branch lengths. Current programs search tree topology space using branch-swapping algorithms, but proposals do not discriminate well between swaps likely to succeed or fail. When applied to datasets with many taxa, the huge number of possible topologies slows these programs dramatically. To overcome this, we developed a novel statistical approach for proposal generation in Bayesian analysis, and evaluated its applicability for the problem of searching phylogenetic tree space. The general idea of the approach, which we call 'Markov katana', is to make proposals based on a heuristic algorithm using bootstrapped subsets of the data. Such proposals induce an unintended sampling distribution that must be determined and removed to generate posterior estimates, but the cost of this extra step can in principle be small compared to the added value of more efficient parameter exploration in Markov chain Monte Carlo analyses. Our prototype application uses the simple neighbor joining distance heuristic on data subsets to propose new reasonably likely phylogenetic trees (including topologies and branch lengths). The evolutionary model used to generate distances in our prototype was far simpler than the more complex model used to evaluate the likelihood of phylogenies based on the full dataset. This prototype implementation indicates that the Markov katana approach could be easily incorporated into existing phylogenetic search programs and may prove a useful alternative in conjunction with existing methods. The general features of this statistical approach may also prove useful in disciplines other than phylogenetics. We demonstrate that this method can be used to efficiently estimate a Bayesian posterior.
• Renner, T., Lan, T., Farr, K.M., Ibarra-Laclette, E., Herrera-Esrella, L., Schuster, S.C., Hasebe, M., Fukushima, K., and Albert, V.A. (2018) ‘{Carnivorous plant genomes}’, in Ellison, A. and Adamec, L., eds., Carnivorous Plants: Physiology, Ecology, and Evolution, Oxford University Press, 135–152, available: https://global.oup.com/academic/product/carnivorous-plants-9780198779841.
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  @incollection{Renner2018, author = {Renner, Tanya and Lan, Tianying and Farr, Kimberly M. and Ibarra-Laclette, Enrique and Herrera-Esrella, Luis and Schuster, Stephan C and Hasebe, Mitsuyasu and Fukushima, Kenji and Albert, Victor A}, booktitle = {Carnivorous plants: Physiology, ecology, and evolution}, editor = {Ellison, Aaron and Adamec, Lubom{\'{i}}r}, keywords = {imported}, pages = {135–152}, publisher = {Oxford University Press}, title = {{Carnivorous plant genomes}}, year = 2018 }

  %0 Book Section %1 Renner2018 %A Renner, Tanya %A Lan, Tianying %A Farr, Kimberly M. %A Ibarra-Laclette, Enrique %A Herrera-Esrella, Luis %A Schuster, Stephan C %A Hasebe, Mitsuyasu %A Fukushima, Kenji %A Albert, Victor A %B Carnivorous plants: Physiology, ecology, and evolution %D 2018 %E Ellison, Aaron %E Adamec, Lubom{{í}}r %I Oxford University Press %P 135--152 %T {Carnivorous plant genomes} %U https://global.oup.com/academic/product/carnivorous-plants-9780198779841 %@ 9780198779841

• Fukushima, K., Fang, X., Alvarez-Ponce, D., Cai, H., Carretero-Paulet, L., Chen, C., Chang, T.-H., Farr, K.M., Fujita, T., Hiwatashi, Y., Hoshi, Y., Imai, T., Kasahara, M., Librado, P., Mao, L., Mori, H., Nishiyama, T., Nozawa, M., P{{á}}lfalvi, G., Pollard, S.T., Rozas, J., S{{á}}nchez-Gracia, A., Sankoff, D., Shibata, T.F., Shigenobu, S., Sumikawa, N., Uzawa, T., Xie, M., Zheng, C., Pollock, D.D., Albert, V.A., Li, S., and Hasebe, M. (2017) ‘Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory’, Nature Ecology {\&} Evolution, 1(3), 0059, available: https://doi.org/10.1038/s41559-016-0059.
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  Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption. Analysis of digestive fluid proteins from C. follicularis and three other carnivorous plants with independent carnivorous origins revealed repeated co-options of stress-responsive protein lineages coupled with convergent amino acid substitutions to acquire digestive physiology. These results imply constraints on the available routes to evolve plant carnivory.

  @article{Fukushima2017, abstract = {Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption. Analysis of digestive fluid proteins from C. follicularis and three other carnivorous plants with independent carnivorous origins revealed repeated co-options of stress-responsive protein lineages coupled with convergent amino acid substitutions to acquire digestive physiology. These results imply constraints on the available routes to evolve plant carnivory.}, author = {Fukushima, Kenji and Fang, Xiaodong and Alvarez-Ponce, David and Cai, Huimin and Carretero-Paulet, Lorenzo and Chen, Cui and Chang, Tien-Hao and Farr, Kimberly M. and Fujita, Tomomichi and Hiwatashi, Yuji and Hoshi, Yoshikazu and Imai, Takamasa and Kasahara, Masahiro and Librado, Pablo and Mao, Likai and Mori, Hitoshi and Nishiyama, Tomoaki and Nozawa, Masafumi and P{\'{a}}lfalvi, Gergő and Pollard, Stephen T. and Rozas, Julio and S{\'{a}}nchez-Gracia, Alejandro and Sankoff, David and Shibata, Tomoko F. and Shigenobu, Shuji and Sumikawa, Naomi and Uzawa, Taketoshi and Xie, Meiying and Zheng, Chunfang and Pollock, David D. and Albert, Victor A. and Li, Shuaicheng and Hasebe, Mitsuyasu}, journal = {Nature Ecology {\&} Evolution}, keywords = {imported}, month = {02}, number = 3, pages = {0059}, publisher = {Nature Publishing Group}, title = {Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory}, volume = 1, year = 2017 }

  %0 Journal Article %1 Fukushima2017 %A Fukushima, Kenji %A Fang, Xiaodong %A Alvarez-Ponce, David %A Cai, Huimin %A Carretero-Paulet, Lorenzo %A Chen, Cui %A Chang, Tien-Hao %A Farr, Kimberly M. %A Fujita, Tomomichi %A Hiwatashi, Yuji %A Hoshi, Yoshikazu %A Imai, Takamasa %A Kasahara, Masahiro %A Librado, Pablo %A Mao, Likai %A Mori, Hitoshi %A Nishiyama, Tomoaki %A Nozawa, Masafumi %A P{{á}}lfalvi, Gergő %A Pollard, Stephen T. %A Rozas, Julio %A S{{á}}nchez-Gracia, Alejandro %A Sankoff, David %A Shibata, Tomoko F. %A Shigenobu, Shuji %A Sumikawa, Naomi %A Uzawa, Taketoshi %A Xie, Meiying %A Zheng, Chunfang %A Pollock, David D. %A Albert, Victor A. %A Li, Shuaicheng %A Hasebe, Mitsuyasu %D 2017 %I Nature Publishing Group %J Nature Ecology {\&} Evolution %N 3 %P 0059 %R 10.1038/s41559-016-0059 %T Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory %U http://www.nature.com/articles/s41559-016-0059 %V 1 %X Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption. Analysis of digestive fluid proteins from C. follicularis and three other carnivorous plants with independent carnivorous origins revealed repeated co-options of stress-responsive protein lineages coupled with convergent amino acid substitutions to acquire digestive physiology. These results imply constraints on the available routes to evolve plant carnivory.

• Fukushima, K., Fujita, H., Yamaguchi, T., Kawaguchi, M., Tsukaya, H., and Hasebe, M. (2015) ‘Oriented cell division shapes carnivorous pitcher leaves of Sarracenia purpurea’, Nature Communications, 6(1), 6450, available: https://doi.org/10.1038/ncomms7450.
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  The pitcher-shaped leaf of the carnivorous plant Sarracenia purpurea acts as a pitfall trap to capture small animals. Here, Fukushima et al. analyse pitcher leaf development and propose that this unusual shape evolved from ancestral planar leaves through changes in the orientation of cell division.

  @article{Fukushima2015, abstract = {The pitcher-shaped leaf of the carnivorous plant Sarracenia purpurea acts as a pitfall trap to capture small animals. Here, Fukushima et al. analyse pitcher leaf development and propose that this unusual shape evolved from ancestral planar leaves through changes in the orientation of cell division.}, author = {Fukushima, Kenji and Fujita, Hironori and Yamaguchi, Takahiro and Kawaguchi, Masayoshi and Tsukaya, Hirokazu and Hasebe, Mitsuyasu}, journal = {Nature Communications}, keywords = {Cell}, month = 12, number = 1, pages = 6450, publisher = {Nature Publishing Group}, title = {Oriented cell division shapes carnivorous pitcher leaves of Sarracenia purpurea}, volume = 6, year = 2015 }

  %0 Journal Article %1 Fukushima2015 %A Fukushima, Kenji %A Fujita, Hironori %A Yamaguchi, Takahiro %A Kawaguchi, Masayoshi %A Tsukaya, Hirokazu %A Hasebe, Mitsuyasu %D 2015 %I Nature Publishing Group %J Nature Communications %N 1 %P 6450 %R 10.1038/ncomms7450 %T Oriented cell division shapes carnivorous pitcher leaves of Sarracenia purpurea %U http://www.nature.com/articles/ncomms7450 %V 6 %X The pitcher-shaped leaf of the carnivorous plant Sarracenia purpurea acts as a pitfall trap to capture small animals. Here, Fukushima et al. analyse pitcher leaf development and propose that this unusual shape evolved from ancestral planar leaves through changes in the orientation of cell division.

• Nakayama, H., Fukushima, K., Fukuda, T., Yokoyama, J., and Kimura, S. (2014) ‘Molecular phylogeny determined using chloroplast DNA inferred a new phylogenetic relationship of Rorippa aquatica (Eaton) EJ Palmer & Steyermark (Brassicaceae)—lake cress’, American Journal of Plant Sciences, 05(01), 48–54, available: https://doi.org/10.4236/ajps.2014.51008.
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  North American lake cress, Rorippa aquatica (Eaton) EJ Palmer {\&} Steyermark (Brassicaceae), is listed as an endangered or threatened species. Lake cress shows heterophyllic changes in leaf form in response to the surrounding environment. Therefore, this species has received considerable attention from ecological and morphological perspectives. However, its phylogenetic position and taxonomic status have long been a subject of debate. To analyze the phylogenetic relationship of lake cress, we investigated chloroplast DNA sequences from 17 plant species. The results of phylogenetic reconstruction performed using trnL intron, trnG (GCC)-trnM (CAU), and psbC-trnS (UGA) indicated that lake cress is a member of Rorippa. Moreover, we found that the chromosome number of lake cress is 2n = 30. This result indicated that lake cress might have originated from aneuploidy of triploid species or via intergeneric crossing. Taken together, our results suggest an affinity between lake cress and Rorippa at the molecular level, indicating that lake cress should be treated as Rorippa aquatica (Eaton) EJ Palmer {\&} Steyermark.

  @article{Nakayama2014, abstract = {North American lake cress, Rorippa aquatica (Eaton) EJ Palmer {\&} Steyermark (Brassicaceae), is listed as an endangered or threatened species. Lake cress shows heterophyllic changes in leaf form in response to the surrounding environment. Therefore, this species has received considerable attention from ecological and morphological perspectives. However, its phylogenetic position and taxonomic status have long been a subject of debate. To analyze the phylogenetic relationship of lake cress, we investigated chloroplast DNA sequences from 17 plant species. The results of phylogenetic reconstruction performed using trnL intron, trnG (GCC)-trnM (CAU), and psbC-trnS (UGA) indicated that lake cress is a member of Rorippa. Moreover, we found that the chromosome number of lake cress is 2n = 30. This result indicated that lake cress might have originated from aneuploidy of triploid species or via intergeneric crossing. Taken together, our results suggest an affinity between lake cress and Rorippa at the molecular level, indicating that lake cress should be treated as Rorippa aquatica (Eaton) EJ Palmer {\&} Steyermark.}, author = {Nakayama, Hokuto and Fukushima, Kenji and Fukuda, Tatsuya and Yokoyama, Jun and Kimura, Seisuke}, journal = {American Journal of Plant Sciences}, keywords = {imported}, month = {01}, number = {01}, pages = {48–54}, publisher = {Scientific Research Publishing}, title = {Molecular phylogeny determined using chloroplast DNA inferred a new phylogenetic relationship of Rorippa aquatica (Eaton) EJ Palmer & Steyermark (Brassicaceae)—lake cress}, volume = {05}, year = 2014 }

  %0 Journal Article %1 Nakayama2014 %A Nakayama, Hokuto %A Fukushima, Kenji %A Fukuda, Tatsuya %A Yokoyama, Jun %A Kimura, Seisuke %D 2014 %I Scientific Research Publishing %J American Journal of Plant Sciences %N 01 %P 48--54 %R 10.4236/ajps.2014.51008 %T Molecular phylogeny determined using chloroplast DNA inferred a new phylogenetic relationship of Rorippa aquatica (Eaton) EJ Palmer & Steyermark (Brassicaceae)—lake cress %U http://www.scirp.org/journal/doi.aspx?DOI=10.4236/ajps.2014.51008 %V 05 %X North American lake cress, Rorippa aquatica (Eaton) EJ Palmer {\&} Steyermark (Brassicaceae), is listed as an endangered or threatened species. Lake cress shows heterophyllic changes in leaf form in response to the surrounding environment. Therefore, this species has received considerable attention from ecological and morphological perspectives. However, its phylogenetic position and taxonomic status have long been a subject of debate. To analyze the phylogenetic relationship of lake cress, we investigated chloroplast DNA sequences from 17 plant species. The results of phylogenetic reconstruction performed using trnL intron, trnG (GCC)-trnM (CAU), and psbC-trnS (UGA) indicated that lake cress is a member of Rorippa. Moreover, we found that the chromosome number of lake cress is 2n = 30. This result indicated that lake cress might have originated from aneuploidy of triploid species or via intergeneric crossing. Taken together, our results suggest an affinity between lake cress and Rorippa at the molecular level, indicating that lake cress should be treated as Rorippa aquatica (Eaton) EJ Palmer {\&} Steyermark.
• Fukushima, K. and Hasebe, M. (2014) ‘Adaxial–abaxial polarity: The developmental basis of leaf shape diversity’, genesis, 52(1), 1–18, available: https://doi.org/10.1002/dvg.22728.
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  Summary Leaves of flowering plants are diverse in shape. Part of this morphological diversity can be attributed to differences in spatiotemporal regulation of polarity in the upper (adaxial) and lower (abaxial) sides of developing leaves. In a leaf primordium, antagonistic interactions between polarity determinants specify the adaxial and abaxial domains in a mutually exclusive manner. The patterning of those domains is critical for leaf morphogenesis. In this review, we first summarize the gene networks regulating adaxial–abaxial polarity in conventional bifacial leaves and then discuss how patterning is modified in different leaf type categories. genesis 52:1–18, 2014. © 2013 The Authors. Genesis Published byWiley Periodicals, Inc.

  @article{doi:10.1002/dvg.22728, abstract = {Summary Leaves of flowering plants are diverse in shape. Part of this morphological diversity can be attributed to differences in spatiotemporal regulation of polarity in the upper (adaxial) and lower (abaxial) sides of developing leaves. In a leaf primordium, antagonistic interactions between polarity determinants specify the adaxial and abaxial domains in a mutually exclusive manner. The patterning of those domains is critical for leaf morphogenesis. In this review, we first summarize the gene networks regulating adaxial–abaxial polarity in conventional bifacial leaves and then discuss how patterning is modified in different leaf type categories. genesis 52:1–18, 2014. © 2013 The Authors. Genesis Published byWiley Periodicals, Inc.}, author = {Fukushima, Kenji and Hasebe, Mitsuyasu}, journal = {genesis}, keywords = {peltate}, number = 1, pages = {1-18}, title = {Adaxial–abaxial polarity: The developmental basis of leaf shape diversity}, volume = 52, year = 2014 }

  %0 Journal Article %1 doi:10.1002/dvg.22728 %A Fukushima, Kenji %A Hasebe, Mitsuyasu %D 2014 %J genesis %N 1 %P 1-18 %R 10.1002/dvg.22728 %T Adaxial–abaxial polarity: The developmental basis of leaf shape diversity %U https://onlinelibrary.wiley.com/doi/abs/10.1002/dvg.22728 %V 52 %X Summary Leaves of flowering plants are diverse in shape. Part of this morphological diversity can be attributed to differences in spatiotemporal regulation of polarity in the upper (adaxial) and lower (abaxial) sides of developing leaves. In a leaf primordium, antagonistic interactions between polarity determinants specify the adaxial and abaxial domains in a mutually exclusive manner. The patterning of those domains is critical for leaf morphogenesis. In this review, we first summarize the gene networks regulating adaxial–abaxial polarity in conventional bifacial leaves and then discuss how patterning is modified in different leaf type categories. genesis 52:1–18, 2014. © 2013 The Authors. Genesis Published byWiley Periodicals, Inc.

• Fukushima, K., Imamura, K., Nagano, K., and Hoshi, Y. (2011) ‘Contrasting patterns of the 5S and 45S rDNA evolutions in the Byblis liniflora complex (Byblidaceae)’, Journal of Plant Research, 124(2), 231–244, available: https://doi.org/10.1007/s10265-010-0366-x.
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  o clarify the evolutionary dynamics of ribosomal RNA genes (rDNAs) in the Byblis liniflora complex (Byblidaceae), we investigated the 5S and 45S rDNA genes through (1) chromosomal physical mapping by fluorescence in situ hybridization (FISH) and (2) phylogenetic analyses using the nontranscribed spacer of 5S rDNA (5S-NTS) and the internal transcribed spacer of 45S rDNA (ITS). In addition, we performed phylogenetic analyses based on rbcL and trnK intron. The complex was divided into 2 clades: B. aquatica-B. filifolia and B. guehoi-B. liniflora-B. rorida. Although members of the complex had conservative symmetric karyotypes, they were clearly differentiated on chromosomal rDNA distribution patterns. The sequence data indicated that ITS was almost homogeneous in all taxa in which two or four 45S rDNA arrays were frequently found at distal regions of chromosomes in the somatic karyotype. ITS homogenization could have been prompted by relatively distal 45S rDNA positions. In contrast, 2-12 5S rDNA arrays were mapped onto proximal/interstitial regions of chromosomes, and some paralogous 5S-NTS were found in the genomes harboring 4 or more arrays. 5S-NTS sequence type-specific FISH analysis showed sequence heterogeneity within and between some 5S rDNA arrays. Interlocus homogenization may have been hampered by their proximal location on chromosomes. Chromosomal location may have affected the contrasting evolutionary dynamics of rDNAs in the B. liniflora complex.

  @article{Fukushima2011, abstract = {o clarify the evolutionary dynamics of ribosomal RNA genes (rDNAs) in the Byblis liniflora complex (Byblidaceae), we investigated the 5S and 45S rDNA genes through (1) chromosomal physical mapping by fluorescence in situ hybridization (FISH) and (2) phylogenetic analyses using the nontranscribed spacer of 5S rDNA (5S-NTS) and the internal transcribed spacer of 45S rDNA (ITS). In addition, we performed phylogenetic analyses based on rbcL and trnK intron. The complex was divided into 2 clades: B. aquatica-B. filifolia and B. guehoi-B. liniflora-B. rorida. Although members of the complex had conservative symmetric karyotypes, they were clearly differentiated on chromosomal rDNA distribution patterns. The sequence data indicated that ITS was almost homogeneous in all taxa in which two or four 45S rDNA arrays were frequently found at distal regions of chromosomes in the somatic karyotype. ITS homogenization could have been prompted by relatively distal 45S rDNA positions. In contrast, 2-12 5S rDNA arrays were mapped onto proximal/interstitial regions of chromosomes, and some paralogous 5S-NTS were found in the genomes harboring 4 or more arrays. 5S-NTS sequence type-specific FISH analysis showed sequence heterogeneity within and between some 5S rDNA arrays. Interlocus homogenization may have been hampered by their proximal location on chromosomes. Chromosomal location may have affected the contrasting evolutionary dynamics of rDNAs in the B. liniflora complex.}, author = {Fukushima, Kenji and Imamura, Kaori and Nagano, Katsuya and Hoshi, Yoshikazu}, journal = {Journal of Plant Research}, keywords = {imported}, month = {03}, number = 2, pages = {231–244}, publisher = {Springer Japan}, title = {Contrasting patterns of the 5S and 45S rDNA evolutions in the Byblis liniflora complex (Byblidaceae)}, volume = 124, year = 2011 }

  %0 Journal Article %1 Fukushima2011 %A Fukushima, Kenji %A Imamura, Kaori %A Nagano, Katsuya %A Hoshi, Yoshikazu %D 2011 %I Springer Japan %J Journal of Plant Research %N 2 %P 231--244 %R 10.1007/s10265-010-0366-x %T Contrasting patterns of the 5S and 45S rDNA evolutions in the Byblis liniflora complex (Byblidaceae) %U http://link.springer.com/10.1007/s10265-010-0366-x %V 124 %X o clarify the evolutionary dynamics of ribosomal RNA genes (rDNAs) in the Byblis liniflora complex (Byblidaceae), we investigated the 5S and 45S rDNA genes through (1) chromosomal physical mapping by fluorescence in situ hybridization (FISH) and (2) phylogenetic analyses using the nontranscribed spacer of 5S rDNA (5S-NTS) and the internal transcribed spacer of 45S rDNA (ITS). In addition, we performed phylogenetic analyses based on rbcL and trnK intron. The complex was divided into 2 clades: B. aquatica-B. filifolia and B. guehoi-B. liniflora-B. rorida. Although members of the complex had conservative symmetric karyotypes, they were clearly differentiated on chromosomal rDNA distribution patterns. The sequence data indicated that ITS was almost homogeneous in all taxa in which two or four 45S rDNA arrays were frequently found at distal regions of chromosomes in the somatic karyotype. ITS homogenization could have been prompted by relatively distal 45S rDNA positions. In contrast, 2-12 5S rDNA arrays were mapped onto proximal/interstitial regions of chromosomes, and some paralogous 5S-NTS were found in the genomes harboring 4 or more arrays. 5S-NTS sequence type-specific FISH analysis showed sequence heterogeneity within and between some 5S rDNA arrays. Interlocus homogenization may have been hampered by their proximal location on chromosomes. Chromosomal location may have affected the contrasting evolutionary dynamics of rDNAs in the B. liniflora complex.

• Fukushima, K., Nagai, K., Hoshi, Y., Masumoto, S., Mikami, I., Takahashi, Y., Oike, H., and Kobori, M. (2009) ‘Drosera rotundifolia and Drosera tokaiensis suppress the activation of HMC-1 human mast cells’, Journal of Ethnopharmacology, 125(1), 90–96, available: https://doi.org/10.1016/j.jep.2009.06.009.
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  ETHNOPHARMACOLOGICAL RELEVANCE Several Northern Hemisphere Drosera species have been used in the therapy of respiratory tract infections as the traditional medicine Droserae Herba. AIM OF THE STUDY To determine the anti-inflammatory effects of Drosera species and to investigate a substitute material for Droserae Herba, we examined the effect of extracts of Drosera rotundifolia, Drosera tokaiensis and Drosera spatulata on activated T cell membrane (aTc-m)-induced inflammatory gene expression in HMC-1 human mast cells. MATERIALS AND METHODS Drosera rotundifolia, Drosera spatulata and Drosera tokaiensis were collected in Japan. Herbs were extracted with 80{\%} EtOH, and subsequently applied to OASIS HLB column. HMC-1 cells were treated with each Drosera column-adsorbed fraction for 15min, and subsequently added to aTc-m and incubated for 16h. Inflammatory gene and protein expressions were determined by DNA microarray, RT-PCR and Western blotting. RESULTS Drosera rotundifolia and Drosera tokaiensis fractions, but not the Drosera spatulata fraction, suppressed inflammatory gene expression induced by aTc-m in HMC-1 cells. CONCLUSIONS Drosera rotundifolia and Drosera tokaiensis suppressed activation of HMC-1 cells induced by aTc-m. Since the Drosera tokaiensis fraction was more effective than the traditionally used Drosera rotundifolia, Drosera tokaiensis is a likely substitute as a source of Droserae Herba.

  @article{Fukushima2009, abstract = {ETHNOPHARMACOLOGICAL RELEVANCE Several Northern Hemisphere Drosera species have been used in the therapy of respiratory tract infections as the traditional medicine Droserae Herba. AIM OF THE STUDY To determine the anti-inflammatory effects of Drosera species and to investigate a substitute material for Droserae Herba, we examined the effect of extracts of Drosera rotundifolia, Drosera tokaiensis and Drosera spatulata on activated T cell membrane (aTc-m)-induced inflammatory gene expression in HMC-1 human mast cells. MATERIALS AND METHODS Drosera rotundifolia, Drosera spatulata and Drosera tokaiensis were collected in Japan. Herbs were extracted with 80{\%} EtOH, and subsequently applied to OASIS HLB column. HMC-1 cells were treated with each Drosera column-adsorbed fraction for 15min, and subsequently added to aTc-m and incubated for 16h. Inflammatory gene and protein expressions were determined by DNA microarray, RT-PCR and Western blotting. RESULTS Drosera rotundifolia and Drosera tokaiensis fractions, but not the Drosera spatulata fraction, suppressed inflammatory gene expression induced by aTc-m in HMC-1 cells. CONCLUSIONS Drosera rotundifolia and Drosera tokaiensis suppressed activation of HMC-1 cells induced by aTc-m. Since the Drosera tokaiensis fraction was more effective than the traditionally used Drosera rotundifolia, Drosera tokaiensis is a likely substitute as a source of Droserae Herba.}, author = {Fukushima, Kenji and Nagai, Kanji and Hoshi, Yoshikazu and Masumoto, Saeko and Mikami, Ichiho and Takahashi, Yumiko and Oike, Hideaki and Kobori, Masuko}, journal = {Journal of Ethnopharmacology}, keywords = {imported}, number = 1, pages = {90–96}, title = {Drosera rotundifolia and Drosera tokaiensis suppress the activation of HMC-1 human mast cells}, volume = 125, year = 2009 }

  %0 Journal Article %1 Fukushima2009 %A Fukushima, Kenji %A Nagai, Kanji %A Hoshi, Yoshikazu %A Masumoto, Saeko %A Mikami, Ichiho %A Takahashi, Yumiko %A Oike, Hideaki %A Kobori, Masuko %D 2009 %J Journal of Ethnopharmacology %N 1 %P 90--96 %R 10.1016/j.jep.2009.06.009 %T Drosera rotundifolia and Drosera tokaiensis suppress the activation of HMC-1 human mast cells %U http://www.sciencedirect.com/science/article/pii/S0378874109003717 %V 125 %X ETHNOPHARMACOLOGICAL RELEVANCE Several Northern Hemisphere Drosera species have been used in the therapy of respiratory tract infections as the traditional medicine Droserae Herba. AIM OF THE STUDY To determine the anti-inflammatory effects of Drosera species and to investigate a substitute material for Droserae Herba, we examined the effect of extracts of Drosera rotundifolia, Drosera tokaiensis and Drosera spatulata on activated T cell membrane (aTc-m)-induced inflammatory gene expression in HMC-1 human mast cells. MATERIALS AND METHODS Drosera rotundifolia, Drosera spatulata and Drosera tokaiensis were collected in Japan. Herbs were extracted with 80{\%} EtOH, and subsequently applied to OASIS HLB column. HMC-1 cells were treated with each Drosera column-adsorbed fraction for 15min, and subsequently added to aTc-m and incubated for 16h. Inflammatory gene and protein expressions were determined by DNA microarray, RT-PCR and Western blotting. RESULTS Drosera rotundifolia and Drosera tokaiensis fractions, but not the Drosera spatulata fraction, suppressed inflammatory gene expression induced by aTc-m in HMC-1 cells. CONCLUSIONS Drosera rotundifolia and Drosera tokaiensis suppressed activation of HMC-1 cells induced by aTc-m. Since the Drosera tokaiensis fraction was more effective than the traditionally used Drosera rotundifolia, Drosera tokaiensis is a likely substitute as a source of Droserae Herba.

• Hoshi, Y., Shirakawa, J., Hasebe, M., Fukushima, K., and Kondo, K. (2008) ‘{Tandem repeat rDNA sequences derived from parents were stably maintained in hexaploids of Drosera spathulata complex (Droseraceae)}’, Cytologia, 73(3), 313–325, available: https://doi.org/10.1508/cytologia.73.313.
  • [ Abstract ]
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  Drosera spathulata complex, which consists of diploid, tetraploid and hexaploid populations, is widely but disjunctively distributed from eastern part of Australia throughout the South East Asian countries, to Japan. Among these populations, high morphological changing has been found in this species. To investigate intraspecific DNA polymorphism, and to infer the polyploid origin, some populations and cultivars of the Drosera spathulata complex and close related species were investigated using molecular cluster analysis with nucleotide sequences of the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL), and the internal transcribed spacer (ITS) of 18S-26S nuclear rDNA sequences (ITS). The rbcL analysis to estimate the species as maternal inheritance revealed that the highest similarity to the hexaploid sequence was found in that of the tetraploid. In contrast, the nuclear rDNA analysis clarified that the hexaploid had two types of ITS sequences: One type of the sequence showed the highest sequence similarity to ITS in D. rotundifolia L. genome, while another type of sequence showed the highest sequence similarity to ITS in the tetraploid D. spathulata Labill. genome. These results suggested that the hexaploid genome could be derived from amphiploidizaion between ancestor species of D. rotundifolia as paternal genome, and the tetraploid D. spathulata as maternal genome.

  @article{Hoshi2008, abstract = {Drosera spathulata complex, which consists of diploid, tetraploid and hexaploid populations, is widely but disjunctively distributed from eastern part of Australia throughout the South East Asian countries, to Japan. Among these populations, high morphological changing has been found in this species. To investigate intraspecific DNA polymorphism, and to infer the polyploid origin, some populations and cultivars of the Drosera spathulata complex and close related species were investigated using molecular cluster analysis with nucleotide sequences of the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL), and the internal transcribed spacer (ITS) of 18S-26S nuclear rDNA sequences (ITS). The rbcL analysis to estimate the species as maternal inheritance revealed that the highest similarity to the hexaploid sequence was found in that of the tetraploid. In contrast, the nuclear rDNA analysis clarified that the hexaploid had two types of ITS sequences: One type of the sequence showed the highest sequence similarity to ITS in D. rotundifolia L. genome, while another type of sequence showed the highest sequence similarity to ITS in the tetraploid D. spathulata Labill. genome. These results suggested that the hexaploid genome could be derived from amphiploidizaion between ancestor species of D. rotundifolia as paternal genome, and the tetraploid D. spathulata as maternal genome.}, author = {Hoshi, Yoshikazu and Shirakawa, Junichi and Hasebe, Mitsuyasu and Fukushima, Kenji and Kondo, Katsuhiko}, journal = {Cytologia}, keywords = {nucleotide}, month = {09}, number = 3, pages = {313–325}, publisher = {Japan Mendel Society, International Society of Cytology}, title = {{Tandem repeat rDNA sequences derived from parents were stably maintained in hexaploids of Drosera spathulata complex (Droseraceae)}}, volume = 73, year = 2008 }

  %0 Journal Article %1 Hoshi2008 %A Hoshi, Yoshikazu %A Shirakawa, Junichi %A Hasebe, Mitsuyasu %A Fukushima, Kenji %A Kondo, Katsuhiko %D 2008 %I Japan Mendel Society, International Society of Cytology %J Cytologia %N 3 %P 313--325 %R 10.1508/cytologia.73.313 %T {Tandem repeat rDNA sequences derived from parents were stably maintained in hexaploids of Drosera spathulata complex (Droseraceae)} %U http://joi.jlc.jst.go.jp/JST.JSTAGE/cytologia/73.313 %V 73 %X Drosera spathulata complex, which consists of diploid, tetraploid and hexaploid populations, is widely but disjunctively distributed from eastern part of Australia throughout the South East Asian countries, to Japan. Among these populations, high morphological changing has been found in this species. To investigate intraspecific DNA polymorphism, and to infer the polyploid origin, some populations and cultivars of the Drosera spathulata complex and close related species were investigated using molecular cluster analysis with nucleotide sequences of the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL), and the internal transcribed spacer (ITS) of 18S-26S nuclear rDNA sequences (ITS). The rbcL analysis to estimate the species as maternal inheritance revealed that the highest similarity to the hexaploid sequence was found in that of the tetraploid. In contrast, the nuclear rDNA analysis clarified that the hexaploid had two types of ITS sequences: One type of the sequence showed the highest sequence similarity to ITS in D. rotundifolia L. genome, while another type of sequence showed the highest sequence similarity to ITS in the tetraploid D. spathulata Labill. genome. These results suggested that the hexaploid genome could be derived from amphiploidizaion between ancestor species of D. rotundifolia as paternal genome, and the tetraploid D. spathulata as maternal genome.
• Kobori, M., Nakayama, H., Fukushima, K., Ohnishi-Kameyama, M., Ono, H., Fukushima, T., Akimoto, Y., Masumoto, S., Yukizaki, C., Hoshi, Y., Deguchi, T., and Yoshida, M. (2008) ‘{Bitter gourd suppresses lipopolysaccharide-induced inflammatory responses}’, Journal of Agricultural and Food Chemistry, 56(11), 4004–4011, available: https://doi.org/10.1021/jf800052y.
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  Bitter gourd (Momordica charantia L.) is a popular tropical vegetable in Asian countries. Previously it was shown that bitter gourd placenta extract suppressed lipopolysaccharide (LPS)-induced TNF$\alpha$ production in RAW 264.7 macrophage-like cells. Here it is shown that the butanol-soluble fraction of bitter gourd placenta extract strongly suppresses LPS-induced TNF$\alpha$ production in RAW 264.7 cells. Gene expression analysis using a fibrous DNA microarray showed that the bitter gourd butanol fraction suppressed expression of various LPS-induced inflammatory genes, such as those for TNF, IL1$\alpha$, IL1$\beta$, G1p2, and Ccl5. The butanol fraction significantly suppressed NF$\kappa$B DNA binding activity and phosphorylation of p38, JNK, and ERK MAPKs. Components in the active fraction from bitter gourd were identified as 1-$\alpha$-linolenoyl-lysophosphatidylcholine (LPC), 2-$\alpha$-linolenoyl-LPC, 1-lynoleoyl-LPC, and 2-linoleoyl-LPC. Purified 1-$\alpha$-linolenoyl-LPC and 1-linoleoyl-LPC suppressed the LPS-induced TNF$\alpha$ production of RAW 264.7 cells ...

  @article{Kobori2008, abstract = {Bitter gourd (Momordica charantia L.) is a popular tropical vegetable in Asian countries. Previously it was shown that bitter gourd placenta extract suppressed lipopolysaccharide (LPS)-induced TNF$\alpha$ production in RAW 264.7 macrophage-like cells. Here it is shown that the butanol-soluble fraction of bitter gourd placenta extract strongly suppresses LPS-induced TNF$\alpha$ production in RAW 264.7 cells. Gene expression analysis using a fibrous DNA microarray showed that the bitter gourd butanol fraction suppressed expression of various LPS-induced inflammatory genes, such as those for TNF, IL1$\alpha$, IL1$\beta$, G1p2, and Ccl5. The butanol fraction significantly suppressed NF$\kappa$B DNA binding activity and phosphorylation of p38, JNK, and ERK MAPKs. Components in the active fraction from bitter gourd were identified as 1-$\alpha$-linolenoyl-lysophosphatidylcholine (LPC), 2-$\alpha$-linolenoyl-LPC, 1-lynoleoyl-LPC, and 2-linoleoyl-LPC. Purified 1-$\alpha$-linolenoyl-LPC and 1-linoleoyl-LPC suppressed the LPS-induced TNF$\alpha$ production of RAW 264.7 cells ...}, author = {Kobori, Masuko and Nakayama, Hirosuke and Fukushima, Kenji and Ohnishi-Kameyama, Mayumi and Ono, Hiroshi and Fukushima, Tatsunobu and Akimoto, Yukari and Masumoto, Saeko and Yukizaki, Chizuko and Hoshi, Yoshikazu and Deguchi, Tomoaki and Yoshida, Mitsuru}, journal = {Journal of Agricultural and Food Chemistry}, keywords = {Bitter}, month = {06}, number = 11, pages = {4004–4011}, publisher = {American Chemical Society}, title = {{Bitter gourd suppresses lipopolysaccharide-induced inflammatory responses}}, volume = 56, year = 2008 }

  %0 Journal Article %1 Kobori2008 %A Kobori, Masuko %A Nakayama, Hirosuke %A Fukushima, Kenji %A Ohnishi-Kameyama, Mayumi %A Ono, Hiroshi %A Fukushima, Tatsunobu %A Akimoto, Yukari %A Masumoto, Saeko %A Yukizaki, Chizuko %A Hoshi, Yoshikazu %A Deguchi, Tomoaki %A Yoshida, Mitsuru %D 2008 %I American Chemical Society %J Journal of Agricultural and Food Chemistry %N 11 %P 4004--4011 %R 10.1021/jf800052y %T {Bitter gourd suppresses lipopolysaccharide-induced inflammatory responses} %U http://pubs.acs.org/doi/abs/10.1021/jf800052y %V 56 %X Bitter gourd (Momordica charantia L.) is a popular tropical vegetable in Asian countries. Previously it was shown that bitter gourd placenta extract suppressed lipopolysaccharide (LPS)-induced TNF$\alpha$ production in RAW 264.7 macrophage-like cells. Here it is shown that the butanol-soluble fraction of bitter gourd placenta extract strongly suppresses LPS-induced TNF$\alpha$ production in RAW 264.7 cells. Gene expression analysis using a fibrous DNA microarray showed that the bitter gourd butanol fraction suppressed expression of various LPS-induced inflammatory genes, such as those for TNF, IL1$\alpha$, IL1$\beta$, G1p2, and Ccl5. The butanol fraction significantly suppressed NF$\kappa$B DNA binding activity and phosphorylation of p38, JNK, and ERK MAPKs. Components in the active fraction from bitter gourd were identified as 1-$\alpha$-linolenoyl-lysophosphatidylcholine (LPC), 2-$\alpha$-linolenoyl-LPC, 1-lynoleoyl-LPC, and 2-linoleoyl-LPC. Purified 1-$\alpha$-linolenoyl-LPC and 1-linoleoyl-LPC suppressed the LPS-induced TNF$\alpha$ production of RAW 264.7 cells ...
• Fukushima, K., Nagano, K., and Hoshi, Y. (2008) ‘Somatic chromosome differentiation in three species of the Byblis liniflora complex (Byblidaceae)’, Chromosome Botany, 3(3/4), 95–99, available: https://doi.org/10.3199/iscb.3.95.
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  We conducted chromosomal characterizations of three species in the Byblis liniflora complex using sequential fluorescent staining with chromomycin A3 (CMA) and 4',6-diamidino-2-phenylindole (DAPI), and fluorescence in situ hybridization method. Byblis filifolia and B. rorida had the diploidal chromosome number of 2n=16, while B. liniflora had the tetraploidal chromosome number of 2n=32. All chromosomes of three species were median-centromeric. The primary constrictions, which contain centromeric regions, showed slightly CMA-positive stainability. Two CMA-positive DAPI-negative segments were observed on two chromosomes of the diploids B. rorida and B. filifolia, and the tetraploid B. liniflora. The 45S rDNA signals were detected on two chromosomes of the diploid and the tetraploid species, respectively. The positions of the 45S rDNA were corresponded to CMA-positive DAPI-negative segments.

  @article{Fukushima2008, abstract = {We conducted chromosomal characterizations of three species in the Byblis liniflora complex using sequential fluorescent staining with chromomycin A3 (CMA) and 4',6-diamidino-2-phenylindole (DAPI), and fluorescence in situ hybridization method. Byblis filifolia and B. rorida had the diploidal chromosome number of 2n=16, while B. liniflora had the tetraploidal chromosome number of 2n=32. All chromosomes of three species were median-centromeric. The primary constrictions, which contain centromeric regions, showed slightly CMA-positive stainability. Two CMA-positive DAPI-negative segments were observed on two chromosomes of the diploids B. rorida and B. filifolia, and the tetraploid B. liniflora. The 45S rDNA signals were detected on two chromosomes of the diploid and the tetraploid species, respectively. The positions of the 45S rDNA were corresponded to CMA-positive DAPI-negative segments.}, author = {Fukushima, Kenji and Nagano, Katsuya and Hoshi, Yoshikazu}, journal = {Chromosome Botany}, keywords = {45S}, number = {3/4}, pages = {95–99}, publisher = {International Society of Chromosome Botany}, title = {Somatic chromosome differentiation in three species of the Byblis liniflora complex (Byblidaceae)}, volume = 3, year = 2008 }

  %0 Journal Article %1 Fukushima2008 %A Fukushima, Kenji %A Nagano, Katsuya %A Hoshi, Yoshikazu %D 2008 %I International Society of Chromosome Botany %J Chromosome Botany %N 3/4 %P 95--99 %R 10.3199/iscb.3.95 %T Somatic chromosome differentiation in three species of the Byblis liniflora complex (Byblidaceae) %U http://joi.jlc.jst.go.jp/JST.JSTAGE/iscb/3.95 %V 3 %X We conducted chromosomal characterizations of three species in the Byblis liniflora complex using sequential fluorescent staining with chromomycin A3 (CMA) and 4',6-diamidino-2-phenylindole (DAPI), and fluorescence in situ hybridization method. Byblis filifolia and B. rorida had the diploidal chromosome number of 2n=16, while B. liniflora had the tetraploidal chromosome number of 2n=32. All chromosomes of three species were median-centromeric. The primary constrictions, which contain centromeric regions, showed slightly CMA-positive stainability. Two CMA-positive DAPI-negative segments were observed on two chromosomes of the diploids B. rorida and B. filifolia, and the tetraploid B. liniflora. The 45S rDNA signals were detected on two chromosomes of the diploid and the tetraploid species, respectively. The positions of the 45S rDNA were corresponded to CMA-positive DAPI-negative segments.

• Hoshi, Y., Fukushima, K., and Nagano, K. (2007) ‘A comparative study of karyotypes in two species of Byblis (Byblidaceae)’, Chromosome Botany, 2(1), 39–43, available: https://doi.org/10.3199/iscb.2.39.
  • [ Abstract ]
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  Byblis filifolia and B. liniflora had the diploidal and the tetraploidal chromosome numbers of 2n=16 and 32, respectively. In condensation behavior from prophase to metaphase, most chromosomes of both species had early condensing segments at the proximal regions. At prometaphase and early-metaphase, all chromosomes except for some small sized chromosomes had decondense segments at the distal regions in both arms. At mid-metaphase, well-spread chromosomes were quite rare to obtain, because all chromosomes at mid-metaphase stage were quite sticky nature, but not earlier stages of metaphase and prophase. The metaphase chromosomes in both species showed a gradual decrease in size from the largest to the smallest. In B. filifolia, total chromosome length at early-metaphase was 40.5 μm, while total chromosome length at mid-metaphase was 23.3 μm. In contrast, B. liniflora showed total chromosome length of 106.1 μm at early-metaphase, and 54.0 μm at mid-metaphase. To compare to the same stage of metaphase, the total length in B. liniflora was nearly twice as long as that of B. filifolia. Two sat-chromosomes were observed in both species.

  @article{Hoshi2007, abstract = {Byblis filifolia and B. liniflora had the diploidal and the tetraploidal chromosome numbers of 2n=16 and 32, respectively. In condensation behavior from prophase to metaphase, most chromosomes of both species had early condensing segments at the proximal regions. At prometaphase and early-metaphase, all chromosomes except for some small sized chromosomes had decondense segments at the distal regions in both arms. At mid-metaphase, well-spread chromosomes were quite rare to obtain, because all chromosomes at mid-metaphase stage were quite sticky nature, but not earlier stages of metaphase and prophase. The metaphase chromosomes in both species showed a gradual decrease in size from the largest to the smallest. In B. filifolia, total chromosome length at early-metaphase was 40.5 μm, while total chromosome length at mid-metaphase was 23.3 μm. In contrast, B. liniflora showed total chromosome length of 106.1 μm at early-metaphase, and 54.0 μm at mid-metaphase. To compare to the same stage of metaphase, the total length in B. liniflora was nearly twice as long as that of B. filifolia. Two sat-chromosomes were observed in both species.}, author = {Hoshi, Yoshikazu and Fukushima, Kenji and Nagano, Katsuya}, journal = {Chromosome Botany}, keywords = {Byblidaceae,Byblis,Chromosome,Karyotype}, number = 1, pages = {39–43}, publisher = {International Society of Chromosome Botany}, title = {A comparative study of karyotypes in two species of Byblis (Byblidaceae)}, volume = 2, year = 2007 }

  %0 Journal Article %1 Hoshi2007 %A Hoshi, Yoshikazu %A Fukushima, Kenji %A Nagano, Katsuya %D 2007 %I International Society of Chromosome Botany %J Chromosome Botany %N 1 %P 39--43 %R 10.3199/iscb.2.39 %T A comparative study of karyotypes in two species of Byblis (Byblidaceae) %U http://joi.jlc.jst.go.jp/JST.JSTAGE/iscb/2.39 %V 2 %X Byblis filifolia and B. liniflora had the diploidal and the tetraploidal chromosome numbers of 2n=16 and 32, respectively. In condensation behavior from prophase to metaphase, most chromosomes of both species had early condensing segments at the proximal regions. At prometaphase and early-metaphase, all chromosomes except for some small sized chromosomes had decondense segments at the distal regions in both arms. At mid-metaphase, well-spread chromosomes were quite rare to obtain, because all chromosomes at mid-metaphase stage were quite sticky nature, but not earlier stages of metaphase and prophase. The metaphase chromosomes in both species showed a gradual decrease in size from the largest to the smallest. In B. filifolia, total chromosome length at early-metaphase was 40.5 μm, while total chromosome length at mid-metaphase was 23.3 μm. In contrast, B. liniflora showed total chromosome length of 106.1 μm at early-metaphase, and 54.0 μm at mid-metaphase. To compare to the same stage of metaphase, the total length in B. liniflora was nearly twice as long as that of B. filifolia. Two sat-chromosomes were observed in both species.