Nature Plants最新文献

{"title":"The unconventional resistance protein PTR recognizes the Magnaporthe oryzae effector AVR-Pita in an allele-specific manner","authors":"Gui Xiao, Nutthalak Laksanavilat, Stella Cesari, Karine Lambou, Maël Baudin, Ahmad Jalilian, Mary Jeanie Telebanco-Yanoria, Veronique Chalvon, Isabelle Meusnier, Elisabeth Fournier, Didier Tharreau, Bo Zhou, Jun Wu, Thomas Kroj","doi":"10.1038/s41477-024-01694-z","DOIUrl":"10.1038/s41477-024-01694-z","url":null,"abstract":"Blast disease caused by the fungus Magnaporthe oryzae is one of the most devastating rice diseases. Disease resistance genes such as Pi-ta or Pi-ta2 are critical in protecting rice production from blast. Published work reports that Pi-ta codes for a nucleotide-binding and leucine-rich repeat domain protein (NLR) that recognizes the fungal protease-like effector AVR-Pita by direct binding. However, this model was challenged by the recent discovery that Pi-ta2 resistance, which also relies on AVR-Pita detection, is conferred by the unconventional resistance gene Ptr, which codes for a membrane protein with a cytoplasmic armadillo repeat domain. Here, using NLR Pi-ta and Ptr RNAi knockdown and CRISPR/Cas9 knockout mutant rice lines, we found that AVR-Pita recognition relies solely on Ptr and that the NLR Pi-ta has no role in it, indicating that it is not the Pi-ta resistance gene. Different alleles of Ptr confer different recognition specificities. The A allele of Ptr (PtrA) detects all natural sequence variants of the effector and confers Pi-ta2 resistance, while the B allele of Ptr (PtrB) recognizes a restricted set of AVR-Pita alleles and, thereby, confers Pi-ta resistance. Analysis of the natural diversity in AVR-Pita and of mutant and transgenic strains identified one specific polymorphism in the effector sequence that controls escape from PtrB-mediated resistance. Taken together, our work establishes that the M. oryzae effector AVR-Pita is detected in an allele-specific manner by the unconventional rice resistance protein Ptr and that the NLR Pi-ta has no function in Pi-ta resistance and the recognition of AVR-Pita. The rice protein Ptr defends against blast disease by detecting the effector AVR-Pita in an allele-specific manner. The immune receptor Pi-ta proved to have no function in this process, contrary to what was previously reported.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141246238","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}

{"title":"Modulation of histone acetylation enables fully mechanized hybrid rice breeding","authors":"Ke Huang, Yuexing Wang, Yingjie Li, Baolan Zhang, Limin Zhang, Penggen Duan, Ran Xu, Dekai Wang, Lijie Liu, Guozheng Zhang, Hao Zhang, Chenjie Wang, Nian Guo, Jianqin Hao, Yuehua Luo, Xudong Zhu, Yunhai Li","doi":"10.1038/s41477-024-01720-0","DOIUrl":"10.1038/s41477-024-01720-0","url":null,"abstract":"Hybrid rice has achieved high grain yield and greatly contributes to food security, but the manual-labour-intensive hybrid seed production process limits fully mechanized hybrid rice breeding. For next-generation hybrid seed production, the use of small-grain male sterile lines to mechanically separate small hybrid seeds from mixed harvest is promising. However, it is difficult to find ideal grain-size genes for breeding ideal small-grain male sterile lines without penalties in the number of hybrid seeds and hybrid rice yield. Here we report that the use of small-grain alleles of the ideal grain-size gene GSE3 in male sterile lines enables fully mechanized hybrid seed production and dramatically increases hybrid seed number in three-line and two-line hybrid rice systems. The GSE3 gene encodes a histone acetyltransferase that binds histones and influences histone acetylation levels. GSE3 is recruited by the transcription factor GS2 to the promoters of their co-regulated grain-size genes and influences the histone acetylation status of their co-regulated genes. Field trials demonstrate that genome editing of GSE3 can be used to immediately improve current elite male sterile lines of hybrid rice for fully mechanized hybrid rice breeding, providing a new perspective for mechanized hybrid breeding in other crops. The manual-labour-intensive hybrid seed production process is a limiting step for fully mechanized hybrid rice breeding. This work demonstrates that the use of ideal small-grain alleles of GSE3 enables fully mechanized hybrid rice breeding.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141236035","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}

{"title":"Designing a synthetic moss genome using GenoDesigner","authors":"Wenfei Yu, Shuo Zhang, Shijun Zhao, Lian-ge Chen, Jie Cao, Hao Ye, Jianbin Yan, Qiao Zhao, Beixin Mo, Ying Wang, Yuling Jiao, Yingxin Ma, Xiaoluo Huang, Wenfeng Qian, Junbiao Dai","doi":"10.1038/s41477-024-01693-0","DOIUrl":"10.1038/s41477-024-01693-0","url":null,"abstract":"The de novo synthesis of genomes has made unprecedented progress and achieved milestones, particularly in bacteria and yeast. However, the process of synthesizing a multicellular plant genome has not progressed at the same pace, due to the complexity of multicellular plant genomes, technical difficulties associated with large genome size and structure, and the intricacies of gene regulation and expression in plants. Here we outline the bottom-up design principles for the de novo synthesis of the Physcomitrium patens (that is, earthmoss) genome. To facilitate international collaboration and accessibility, we have developed and launched a public online design platform called GenoDesigner. This platform offers an intuitive graphical interface enabling users to efficiently manipulate extensive genome sequences, even up to the gigabase level. This tool is poised to greatly expedite the synthesis of the P. patens genome, offering an essential reference and roadmap for the synthesis of plant genomes. The authors present the design principles of a synthetic earthmoss (Physcomitrium patens) genome. To aid future genome design projects, they also develop GenoDesigner, a software package that provides users with an intuitive graphical interface to efficiently manipulate genomic sequences.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141235893","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}

{"title":"MpMLO1 controls sperm discharge in liverwort","authors":"Meng-Xing Cao, Shi-Zhen Li, Hong-Ju Li","doi":"10.1038/s41477-024-01703-1","DOIUrl":"10.1038/s41477-024-01703-1","url":null,"abstract":"In bryophytes, sexual reproduction necessitates the release of motile sperm cells from a gametophyte into the environment. Since 1856, this process, particularly in liverworts, has been known to depend on water. However, the molecular mechanism underlying this phenomenon has remained elusive. Here we identify the plasma membrane protein MpMLO1 in Marchantia polymorpha, a model liverwort, as critical for sperm discharge from antheridia. The MpMLO1-expressing tip cells among the sperm-wrapping jacket cells undergo programmed cell death upon antheridium maturation to facilitate sperm discharge after the application of water and even hypertonic solutions. The absence of MpMLO1 leads to reduced cytoplasmic Ca2+ levels in tip cells, preventing cell death and consequently sperm discharge. Our findings reveal that MpMLO1-mediated programmed cell death in antheridial tip cells, regulated by cytosolic Ca2+ dynamics, is essential for sperm release, elucidating a key mechanism in bryophyte sexual reproduction and providing insights into terrestrial plant evolution. In Marchantia polymorpha, sperm cells are released from the antheridium into the surroundings. The process is facilitated by MpMLO1, which initiates Ca2+-dependent programmed cell death of tip jacket cells of the mature antheridium, enabling water to enter and ultimately resulting in the bursting of the antheridium and the discharge of sperm.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141236040","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}

{"title":"A family of maternally expressed auxin response factors trigger endosperm cellularization","authors":"","doi":"10.1038/s41477-024-01707-x","DOIUrl":"10.1038/s41477-024-01707-x","url":null,"abstract":"The endosperm is a seed tissue that supports the embryo. In most flowering plant species, the endosperm starts as a coenocyte that cellularizes after a defined number of mitotic divisions. We show that endosperm cellularization is under antagonistic parental control mediated by a family of maternally expressed auxin response factors.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141182509","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}

{"title":"Genome resources for three modern cotton lines guide future breeding efforts","authors":"Avinash Sreedasyam, John T. Lovell, Sujan Mamidi, Sameer Khanal, Jerry W. Jenkins, Christopher Plott, Kempton B. Bryan, Zhigang Li, Shengqiang Shu, Joseph Carlson, David Goodstein, Luis De Santiago, Ryan C. Kirkbride, Sebastian Calleja, Todd Campbell, Jenny C. Koebernick, Jane K. Dever, Jodi A. Scheffler, Duke Pauli, Johnie N. Jenkins, Jack C. McCarty, Melissa Williams, LoriBeth Boston, Jenell Webber, Joshua A. Udall, Z. Jeffrey Chen, Fred Bourland, Warwick N. Stiller, Christopher A. Saski, Jane Grimwood, Peng W. Chee, Don C. Jones, Jeremy Schmutz","doi":"10.1038/s41477-024-01713-z","DOIUrl":"10.1038/s41477-024-01713-z","url":null,"abstract":"Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’ and ‘CSX8308’) and updating the ‘TM-1’ cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from ‘Pima’ cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability. Analyses of three newly sequenced modern cultivar cotton genomes revealed sequence and structural variation alongside traces of ancient and ongoing introgressions. Moreover, transcriptome analysis pointed at unique fibre quality traits of cultivars.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01713-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141177739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure of plant photosystem I in a native assembly state defines PsaF as a regulatory checkpoint","authors":"Andreas Naschberger, Mariia Fadeeva, Daniel Klaiman, Anna Borovikova-Sheinker, Ido Caspy, Nathan Nelson, Alexey Amunts","doi":"10.1038/s41477-024-01699-8","DOIUrl":"10.1038/s41477-024-01699-8","url":null,"abstract":"Plant photosystem I (PSI) consists of at least 13 nuclear-encoded and 4 chloroplast-encoded subunits that together act as a sunlight-driven oxidoreductase. Here we report the structure of a PSI assembly intermediate that we isolated from greening oat seedlings. The assembly intermediate shows an absence of at least eight subunits, including PsaF and LHCI, and lacks photoreduction activity. The data show that PsaF is a regulatory checkpoint that promotes the assembly of LHCI, effectively coupling biogenesis to function. This study reports the structure of a photosystem I assembly intermediate isolated from greening oat seedlings. It defines PsaF as a regulatory checkpoint promoting the association of LHCI that couples biogenesis to function.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01699-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141177502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parental conflict driven regulation of endosperm cellularization by a family of Auxin Response Factors","authors":"N. Butel, Y. Qiu, W. Xu, J. Santos-González, C. Köhler","doi":"10.1038/s41477-024-01706-y","DOIUrl":"10.1038/s41477-024-01706-y","url":null,"abstract":"The endosperm is a reproductive tissue supporting embryo development. In most flowering plants, the initial divisions of endosperm nuclei are not succeeded by cellularization; this process occurs only after a specific number of mitotic cycles have taken place. The timing of cellularization significantly influences seed viability and size. Previous research implicated auxin as a key factor in initiating nuclear divisions and determining the timing of cellularization. Here we uncover the involvement of a family of clustered auxin response factors (cARFs) as dosage-sensitive regulators of endosperm cellularization. cARFs, maternally expressed and paternally silenced, are shown to induce cellularization, thereby restricting seed growth. Our findings align with the predictions of the parental conflict theory, suggesting that cARFs represent major molecular targets in this conflict. We further demonstrate a recurring amplification of cARFs in the Brassicaceae, suggesting an evolutionary response to parental conflict by reinforcing maternal control over endosperm cellularization. Our study highlights that antagonistic parental control on endosperm cellularization converges on auxin biosynthesis and signalling. In most flowering plants, early divisions of endosperm nuclei are not succeeded by cellularization. This study uncovered a family of clustered auxin response factors as dosage-sensitive, maternally expressed regulators of endosperm cellularization.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01706-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number","authors":"Carolin Krämer, Christian R. Boehm, Jinghan Liu, Michael Kien Yin Ting, Alexander P. Hertle, Joachim Forner, Stephanie Ruf, Mark A. Schöttler, Reimo Zoschke, Ralph Bock","doi":"10.1038/s41477-024-01709-9","DOIUrl":"10.1038/s41477-024-01709-9","url":null,"abstract":"The chloroplast genomes of most plants and algae contain a large inverted repeat (IR) region that separates two single-copy regions and harbours the ribosomal RNA operon. We have addressed the functional importance of the IR region by removing an entire copy of the 25.3-kb IR from the tobacco plastid genome. Using plastid transformation and subsequent selectable marker gene elimination, we precisely excised the IR, thus generating plants with a substantially reduced plastid genome size. We show that the lack of the IR results in a mildly reduced plastid ribosome number, suggesting a gene dosage benefit from the duplicated presence of the ribosomal RNA operon. Moreover, the IR deletion plants contain an increased number of plastid genomes, suggesting that genome copy number is regulated by measuring total plastid DNA content rather than by counting genomes. Together, our findings (1) demonstrate that the IR can enhance the translation capacity of the plastid, (2) reveal the relationship between genome size and genome copy number, and (3) provide a simplified plastid genome structure that will facilitate future synthetic biology applications. Removing the large inverted repeat region from the chloroplast genome revealed a gene dosage benefit for the ribosomal RNA operon. The reduced genome size resulted in increased genome copy numbers and offers potential for synthetic biology.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01709-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141156641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Raison d’être of the plastid repeat","authors":"Jeffrey P. Mower","doi":"10.1038/s41477-024-01710-2","DOIUrl":"10.1038/s41477-024-01710-2","url":null,"abstract":"Creation of a plastid genome without an inverted repeat in Nicotiana tabacum reveals a role for the inverted repeat in gene dosage and the regulation of replication by total DNA content rather than copy number.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141156670","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}