Heterochromatic condensates (chromocenters) are critical for maintaining the silencing of heterochromatin. It is therefore puzzling that the presence of chromocenters is variable across plant species. Here we reveal that variations in the plant heterochromatin protein ADCP1 confer a diversity in chromocenter formation via phase separation. ADCP1 physically interacts with the high mobility group protein HMGA to form a complex and mediates heterochromatin condensation by multivalent interactions. The loss of intrinsically disordered regions (IDRs) in ADCP1 homologues during evolution has led to the absence of prominent chromocenter formation in various plant species, and introduction of IDR-containing ADCP1 with HMGA promotes heterochromatin condensation and retrotransposon silencing. Moreover, plants in the Cucurbitaceae group have evolved an IDR-containing chimaera of ADCP1 and HMGA, which remarkably enables formation of chromocenters. Together, our work uncovers a coevolved mechanism of phase separation in packing heterochromatin and silencing retrotransposons. The researchers have uncovered that the phase separation ability of plant heterochromatin protein ADCP1 variants defines the formation of heterochromatic condensates (chromocenters) in different plant species.
{"title":"Evolutional heterochromatin condensation delineates chromocenter formation and retrotransposon silencing in plants","authors":"Weifeng Zhang, Lingling Cheng, Kuan Li, Leiming Xie, Jinyao Ji, Xue Lei, Anjie Jiang, Chunlai Chen, Haitao Li, Pilong Li, Qianwen Sun","doi":"10.1038/s41477-024-01746-4","DOIUrl":"10.1038/s41477-024-01746-4","url":null,"abstract":"Heterochromatic condensates (chromocenters) are critical for maintaining the silencing of heterochromatin. It is therefore puzzling that the presence of chromocenters is variable across plant species. Here we reveal that variations in the plant heterochromatin protein ADCP1 confer a diversity in chromocenter formation via phase separation. ADCP1 physically interacts with the high mobility group protein HMGA to form a complex and mediates heterochromatin condensation by multivalent interactions. The loss of intrinsically disordered regions (IDRs) in ADCP1 homologues during evolution has led to the absence of prominent chromocenter formation in various plant species, and introduction of IDR-containing ADCP1 with HMGA promotes heterochromatin condensation and retrotransposon silencing. Moreover, plants in the Cucurbitaceae group have evolved an IDR-containing chimaera of ADCP1 and HMGA, which remarkably enables formation of chromocenters. Together, our work uncovers a coevolved mechanism of phase separation in packing heterochromatin and silencing retrotransposons. The researchers have uncovered that the phase separation ability of plant heterochromatin protein ADCP1 variants defines the formation of heterochromatic condensates (chromocenters) in different plant species.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-15DOI: 10.1038/s41477-024-01726-8
Yichen You, Jinren Yu, Zelong Nie, Danxiao Peng, Russell L. Barrett, Romer Narindra Rabarijaona, Yangjun Lai, Yujie Zhao, Viet-Cuong Dang, Youhua Chen, Zhiduan Chen, Jun Wen, Limin Lu
Faced with environmental changes, plants may either move to track their ancestral niches or evolve to adapt to new niches. Vitaceae, the grape family, has evolved diverse adaptive traits facilitating a global expansion in wide-ranging habitats, making it ideal for investigating transition between move and evolve strategies and exploring the underlying mechanisms. Here we inferred the patterns of biogeographic diversification and trait evolution in Vitaceae based on a robust phylogeny with dense sampling including 495 species (~52% of Vitaceae species). Vitaceae probably originated from Asia—the diversity centre of extant genera and the major source of dispersals. Boundaries of the Eocene, Oligocene and Miocene were identified as turning points in shifting strategies. A significant decrease in move strategy was identified during the Oligocene, followed by increases in move and evolve. After the Miocene, evolve began to dominate, during which increased niche opportunities and key trait innovations played important roles. This study reveals the transition of move and evolve strategies and their interaction with niche opportunity and trait innovation throughout the diversification of the grape family—a globally distributed plant group originated in the Cretaceous.
{"title":"Transition of survival strategies under global climate shifts in the grape family","authors":"Yichen You, Jinren Yu, Zelong Nie, Danxiao Peng, Russell L. Barrett, Romer Narindra Rabarijaona, Yangjun Lai, Yujie Zhao, Viet-Cuong Dang, Youhua Chen, Zhiduan Chen, Jun Wen, Limin Lu","doi":"10.1038/s41477-024-01726-8","DOIUrl":"10.1038/s41477-024-01726-8","url":null,"abstract":"Faced with environmental changes, plants may either move to track their ancestral niches or evolve to adapt to new niches. Vitaceae, the grape family, has evolved diverse adaptive traits facilitating a global expansion in wide-ranging habitats, making it ideal for investigating transition between move and evolve strategies and exploring the underlying mechanisms. Here we inferred the patterns of biogeographic diversification and trait evolution in Vitaceae based on a robust phylogeny with dense sampling including 495 species (~52% of Vitaceae species). Vitaceae probably originated from Asia—the diversity centre of extant genera and the major source of dispersals. Boundaries of the Eocene, Oligocene and Miocene were identified as turning points in shifting strategies. A significant decrease in move strategy was identified during the Oligocene, followed by increases in move and evolve. After the Miocene, evolve began to dominate, during which increased niche opportunities and key trait innovations played important roles. This study reveals the transition of move and evolve strategies and their interaction with niche opportunity and trait innovation throughout the diversification of the grape family—a globally distributed plant group originated in the Cretaceous.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141618201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15,000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry. We identify tissue-specific and tissue-enriched proteins that are linked to the functional specificity of individual tissues. Proteogenomic comparison of rice and Arabidopsis reveals conserved proteome expression, which differs from mammals in that there is a strong separation of species rather than tissues. Notably, profiling of N6-methyladenosine (m6A) across the rice major tissues shows that m6A at untranslated regions is negatively correlated with protein abundance and contributes to the discordance between RNA and protein levels. We also demonstrate that our data are valuable for identifying novel genes required for regulating m6A methylation. Taken together, this study provides a paradigm for further research into rice proteogenome. This proteomic landscape study reveals proteins associated with the functional specificity of rice tissues, and further multi-omics analysis shows that N6-methyladenosine in untranslated regions is negatively correlated with protein abundance.
{"title":"Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of N6-methyladenosine","authors":"Shang-Tong Li, Yunzhuo Ke, Yunke Zhu, Tian-Yi Zhu, Huanwei Huang, Linxia Li, Zhiyang Hou, Xuemin Zhang, Yaping Li, Chaofan Liu, Xiulan Li, Mengjia Xie, Lianqi Zhou, Chen Meng, Faming Wang, Xiaofeng Gu, Bing Yang, Hao Yu, Zhe Liang","doi":"10.1038/s41477-024-01745-5","DOIUrl":"10.1038/s41477-024-01745-5","url":null,"abstract":"Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15,000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry. We identify tissue-specific and tissue-enriched proteins that are linked to the functional specificity of individual tissues. Proteogenomic comparison of rice and Arabidopsis reveals conserved proteome expression, which differs from mammals in that there is a strong separation of species rather than tissues. Notably, profiling of N6-methyladenosine (m6A) across the rice major tissues shows that m6A at untranslated regions is negatively correlated with protein abundance and contributes to the discordance between RNA and protein levels. We also demonstrate that our data are valuable for identifying novel genes required for regulating m6A methylation. Taken together, this study provides a paradigm for further research into rice proteogenome. This proteomic landscape study reveals proteins associated with the functional specificity of rice tissues, and further multi-omics analysis shows that N6-methyladenosine in untranslated regions is negatively correlated with protein abundance.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141597400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-05DOI: 10.1038/s41477-024-01752-6
Raphael Trösch
{"title":"A peptide signal for wound healing","authors":"Raphael Trösch","doi":"10.1038/s41477-024-01752-6","DOIUrl":"10.1038/s41477-024-01752-6","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141538198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-04DOI: 10.1038/s41477-024-01739-3
Pierre Martre, Sibylle Dueri, Jose Rafael Guarin, Frank Ewert, Heidi Webber, Daniel Calderini, Gemma Molero, Matthew Reynolds, Daniel Miralles, Guillermo Garcia, Hamish Brown, Mike George, Rob Craigie, Jean-Pierre Cohan, Jean-Charles Deswarte, Gustavo Slafer, Francesco Giunta, Davide Cammarano, Roberto Ferrise, Thomas Gaiser, Yujing Gao, Zvi Hochman, Gerrit Hoogenboom, Leslie A. Hunt, Kurt C. Kersebaum, Claas Nendel, Gloria Padovan, Alex C. Ruane, Amit Kumar Srivastava, Tommaso Stella, Iwan Supit, Peter Thorburn, Enli Wang, Joost Wolf, Chuang Zhao, Zhigan Zhao, Senthold Asseng
Increasing global food demand will require more food production1 without further exceeding the planetary boundaries2 while simultaneously adapting to climate change3. We used an ensemble of wheat simulation models with improved sink and source traits from the highest-yielding wheat genotypes4 to quantify potential yield gains and associated nitrogen requirements. This was explored for current and climate change scenarios across representative sites of major world wheat producing regions. The improved sink and source traits increased yield by 16% with current nitrogen fertilizer applications under both current climate and mid-century climate change scenarios. To achieve the full yield potential—a 52% increase in global average yield under a mid-century high warming climate scenario (RCP8.5), fertilizer use would need to increase fourfold over current use, which would unavoidably lead to higher environmental impacts from wheat production. Our results show the need to improve soil nitrogen availability and nitrogen use efficiency, along with yield potential. Martre et al. found that to achieve the full yield potential of improved wheat varieties, nitrogen fertilizer use would need to increase fourfold over current use, which would unavoidably increase the environmental impacts of wheat production.
{"title":"Global needs for nitrogen fertilizer to improve wheat yield under climate change","authors":"Pierre Martre, Sibylle Dueri, Jose Rafael Guarin, Frank Ewert, Heidi Webber, Daniel Calderini, Gemma Molero, Matthew Reynolds, Daniel Miralles, Guillermo Garcia, Hamish Brown, Mike George, Rob Craigie, Jean-Pierre Cohan, Jean-Charles Deswarte, Gustavo Slafer, Francesco Giunta, Davide Cammarano, Roberto Ferrise, Thomas Gaiser, Yujing Gao, Zvi Hochman, Gerrit Hoogenboom, Leslie A. Hunt, Kurt C. Kersebaum, Claas Nendel, Gloria Padovan, Alex C. Ruane, Amit Kumar Srivastava, Tommaso Stella, Iwan Supit, Peter Thorburn, Enli Wang, Joost Wolf, Chuang Zhao, Zhigan Zhao, Senthold Asseng","doi":"10.1038/s41477-024-01739-3","DOIUrl":"10.1038/s41477-024-01739-3","url":null,"abstract":"Increasing global food demand will require more food production1 without further exceeding the planetary boundaries2 while simultaneously adapting to climate change3. We used an ensemble of wheat simulation models with improved sink and source traits from the highest-yielding wheat genotypes4 to quantify potential yield gains and associated nitrogen requirements. This was explored for current and climate change scenarios across representative sites of major world wheat producing regions. The improved sink and source traits increased yield by 16% with current nitrogen fertilizer applications under both current climate and mid-century climate change scenarios. To achieve the full yield potential—a 52% increase in global average yield under a mid-century high warming climate scenario (RCP8.5), fertilizer use would need to increase fourfold over current use, which would unavoidably lead to higher environmental impacts from wheat production. Our results show the need to improve soil nitrogen availability and nitrogen use efficiency, along with yield potential. Martre et al. found that to achieve the full yield potential of improved wheat varieties, nitrogen fertilizer use would need to increase fourfold over current use, which would unavoidably increase the environmental impacts of wheat production.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141521476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-03DOI: 10.1038/s41477-024-01730-y
Desiccation tolerance evolved multiple times across the land plants for survival in water-limited habitats. We find that desiccation tolerance evolved convergently in grasses by independent duplication of the same gene family and activation of conserved, ancestral protective pathways.
{"title":"Comparison of resurrection grasses reveals convergent evolution of desiccation tolerance","authors":"","doi":"10.1038/s41477-024-01730-y","DOIUrl":"10.1038/s41477-024-01730-y","url":null,"abstract":"Desiccation tolerance evolved multiple times across the land plants for survival in water-limited habitats. We find that desiccation tolerance evolved convergently in grasses by independent duplication of the same gene family and activation of conserved, ancestral protective pathways.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141495871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-02DOI: 10.1038/s41477-024-01728-6
Degradome sequencing of semi-active DCL1 mutants separates true miRNAs from DCL1-independent small RNAs in Arabidopsis thaliana and illustrates the processing pattern of 147 pri-miRNAs. In parallel, DMS-MaPseq decodes the in vivo secondary structures of pri-miRNAs, enabling a better understanding of cleavage modes and of the impact of DCL1 cofactors on cleavage.
{"title":"Exploring the landscape of miRNA production and the structural rules that shape it","authors":"","doi":"10.1038/s41477-024-01728-6","DOIUrl":"10.1038/s41477-024-01728-6","url":null,"abstract":"Degradome sequencing of semi-active DCL1 mutants separates true miRNAs from DCL1-independent small RNAs in Arabidopsis thaliana and illustrates the processing pattern of 147 pri-miRNAs. In parallel, DMS-MaPseq decodes the in vivo secondary structures of pri-miRNAs, enabling a better understanding of cleavage modes and of the impact of DCL1 cofactors on cleavage.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141489626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01DOI: 10.1038/s41477-024-01717-9
Fabiany Herrera, Mónica R. Carvalho, Gregory W. Stull, Carlos Jaramillo, Steven R. Manchester
The remarkably diverse plant communities of the Neotropics are the result of diversification driven by multiple biotic (for example, speciation, extinction and dispersal) and abiotic (for example, climatic and tectonic) processes. However, in the absence of a well-preserved, thoroughly sampled and critically assessed fossil record, the associated processes of dispersal and extinction are poorly understood. We report an exceptional case study documenting patterns of extinction in the grape family (Vitaceae Juss.) on the basis of fossil seeds discovered in four Neotropical palaeofloras dated between 60 and 19 Ma. These include a new species that provides the earliest evidence of Vitaceae in the Western Hemisphere. Eight additional species reveal the former presence of major clades of the family that are currently absent from the Neotropics and elucidate previously unknown dispersal events. Our results indicate that regional extinction and dispersal have substantially impacted the evolutionary history of Vitaceae in the Neotropics. They also suggest that while the Neotropics have been dynamic centres of diversification through the Cenozoic, extant Neotropical botanical diversity has also been shaped by extensive extinction over the past 66 million years. Fossil seeds (60 to 20 million years old) from Colombia, Panama and Perú show previously unrecognized patterns of diversity and local extinctions of grapes in the New World. These also support a tentative origin of Vitis in the New World.
{"title":"Cenozoic seeds of Vitaceae reveal a deep history of extinction and dispersal in the Neotropics","authors":"Fabiany Herrera, Mónica R. Carvalho, Gregory W. Stull, Carlos Jaramillo, Steven R. Manchester","doi":"10.1038/s41477-024-01717-9","DOIUrl":"10.1038/s41477-024-01717-9","url":null,"abstract":"The remarkably diverse plant communities of the Neotropics are the result of diversification driven by multiple biotic (for example, speciation, extinction and dispersal) and abiotic (for example, climatic and tectonic) processes. However, in the absence of a well-preserved, thoroughly sampled and critically assessed fossil record, the associated processes of dispersal and extinction are poorly understood. We report an exceptional case study documenting patterns of extinction in the grape family (Vitaceae Juss.) on the basis of fossil seeds discovered in four Neotropical palaeofloras dated between 60 and 19 Ma. These include a new species that provides the earliest evidence of Vitaceae in the Western Hemisphere. Eight additional species reveal the former presence of major clades of the family that are currently absent from the Neotropics and elucidate previously unknown dispersal events. Our results indicate that regional extinction and dispersal have substantially impacted the evolutionary history of Vitaceae in the Neotropics. They also suggest that while the Neotropics have been dynamic centres of diversification through the Cenozoic, extant Neotropical botanical diversity has also been shaped by extensive extinction over the past 66 million years. Fossil seeds (60 to 20 million years old) from Colombia, Panama and Perú show previously unrecognized patterns of diversity and local extinctions of grapes in the New World. These also support a tentative origin of Vitis in the New World.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141475323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01DOI: 10.1038/s41477-024-01735-7
Jorge Assis, Ester A. Serrão, Eliza Fragkopoulou, Térence Legrand, Lidiane Gouvêa, Miguel B. Araújo
{"title":"Misconception of model transferability precludes estimates of seagrass community reorganization in a changing climate","authors":"Jorge Assis, Ester A. Serrão, Eliza Fragkopoulou, Térence Legrand, Lidiane Gouvêa, Miguel B. Araújo","doi":"10.1038/s41477-024-01735-7","DOIUrl":"10.1038/s41477-024-01735-7","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141475130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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