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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

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molecular plant 2024年第5期17卷 725-746页

作者： Tingting Shi Xinxin Zhang Yukang Hou Changfu Jia Xuming Dan Yulin Zhang Yuanzhong Jiang Qiang Lai Jiajun Feng Jianju Feng Tao Ma Jiali Wu Shuyu Liu Lei Zhang Zhiqin Long Liyang Chen Nathaniel R.Street Par K.Ingvarsson Jianquan Liu Tongming Yin Jing Wang Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengduSichuanChina College of Horticulture and Forestry Tarim UniversityAlar 843300China Umea plant Science Centre Department of Plant PhysiologyUmea UniversityUmeaVasterbottenSweden Linnean Centre for plant Biology Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural SciencesUppsalaSweden The Key Laboratory of Tree Genetics and biotechnology of Jiangsu Province and Education Department of China Nanjing Forestry UniversityNanjingJiangsuChina

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary ***,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental *** this study,we present a genus-level super-pangenome comprising 19 Populus genomes,revealing the likely pivotal role of private genes in facilitating local environmental and climate *** the integration of pangenomes with transcriptomes,methylomes,and chromatin accessibility mapping,we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures,notably CG methylation in gene-body *** comparative genomic analyses have enabled the identification of 142202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive *** have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration ***,we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome(http://***).Together,the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

关键词： Populus pangenomes whole-genome duplication structural variation genome evolution

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Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

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molecular plant 2024年第2期17卷 240-257页

作者： Wei Li Jiaqi Liu Zeqi Li Ruiqiang Ye Wenzhen Chen Yuqing Huang Yue Yuan Yi Zhang Huayi Hu Peng Zheng Zhongming Fang Zeng Tao Shiyong Song Ronghui Pan Jian Zhang Jumim Tu Jen Sheen Hao Du State Key Laboratory of Rice Biology College of Agriculture and BiotechnologyZhejiang UniversityYu-Hang-Tang Road No.866Hangzhou 310058China ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang UniversityHangzhou 311215China Hainan Institute of Zhejiang University Sanya 572025China National Key Laboratory of plant molecular Genetics CASCenter for Excellence in Molecular Plant SciencesShanghai lnstitute of Plant Physiology and EcologyChineseAcademy of SciencesShanghai 200032China Key Laboratory of plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education) College of Agricultural SciencesGuizhouUniversityGuiyang 550025China State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 311400China Department of molecular Biology and Center for Computational and Integrative Biology Massachusetts General Hospitaland Department of GeneticsHarvard Medical SchoolBostonMA02114USA

Rice production accounts for approximately half of the freshwater resources utilized in agriculture,result-ing in greenhouse gas emissions such as methane(CH4)from flooded paddy *** address this chal-lenge,environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice ***,the implementation of water-saving treatments(WsTs)in paddy-field rice has been associated with a substantial yield loss of up to 50%as well as a reduction in nitrogen use efficiency(NUE).In this study,we discovered that the target of rapamycin(TOR)signaling pathway is compromised in rice under *** profiling-coupled transcriptome sequencing(polysome-seq)analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR ***,biochemical,and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under ***,ammonium exhibited a greater ability to alleviate growth constraints under WsT by enhancing TOR signaling,which simultaneously promoted uptake and utilization of ammonium and nitrogen *** further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5'untranslated ***,these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and *** study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.

关键词： target of rapamycin TOR water-saving rice low-carbon agriculture drought nitrogen use efficiency NUE

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EXECUTER2 modulates the EXECUTER1 signalosome through its singlet oxygen-dependent oxidation

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molecular plant 2022年第3期15卷 438-453页

作者： Vivek Dogra Rahul Mohan Singh Mengping Li Mingyue Li Somesh Singh Chanhong Kim Shanghai Center for plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China University of the Chinese Academy of Sciences Beijing 100049China present address:biotechnology Division CSIR-Institute of Himalayan Bioresource TechnologyPalampur 176061India

Oxidative post-translational modifications of specific chloroplast proteins contribute to the initiation of retrograde *** Arabidopsis thaliana EXECUTER1(EX1)protein,a chloroplast-localized singlet oxygen(^(1)O_(2))sensor,undergoes tryptophan(Trp)643 oxidation by^(1)O_(2),a chloroplast-derived and light-dependent reactive oxygen *** indole side chain of Trp is vulnerable to^(1)O_(2),leading to the generation of oxidized Trp variants and priming EX1 for degradation by a membrane-bound FtsH *** perception of^(1)O_(2)via Trp643 oxidation and subsequent EX1 proteolysis facilitate chloroplast-to-nucleus retrograde *** this study,we discovered that the EX1-like protein EX2 also undergoes^(1)O_(2)-dependent Trp530 oxidation and FtsH-dependent turnover,which attenuates^(1)O_(2)signaling by decelerating EX1-Trp643 oxidation and subsequent EX1 *** with this finding,the loss of EX2 function reinforces EX1-dependent retrograde signaling by accelerating EX1-Trp643 oxidation and subsequent EX1 proteolysis,whereas overexpression of EX2 produces molecular phenotypes opposite to those observed in the loss-of-function mutants of ***,phylogenetic analysis suggests that EX2 may have emerged evolutionarily to attenuate the sensitivity of EX1 toward^(1)O_(2).Collectively,these results suggest that EX2 functions as a negative regulator of the EX1 signalosome through its own^(1)O_(2)-dependent oxidation,providing a new mechanistic insight into the regulation of EX1-mediated^(1)O_(2)signaling.

关键词： EXECUTER1 EXECUTER2 singlet oxygen retrograde signaling Trp oxidation FtsH protease

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A potato late blight resistance gene protects against multiple Phytophthora species by recognizing a broadly conserved RXLR-WY effector

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molecular plant 2022年第9期15卷 1457-1469页

作者： Xiao Lin Andrea Olave-Achury Robert Heal Marina Pais Kamil Witek Hee-Kyung Ahn He Zhao Shivani Bhanvadia Hari S.Karki Tianqiao Song Chih-hang Wu Hiroaki Adachi Sophien Kamoun Vivianne G.A.A.Vleeshouwers Jonathan D.G.Jones The Sainsbury Laboratory University of East AngliaNorwich Research ParkNR47UH NorwichUK Wageningen UR plant Breeding Wageningen University and ResearchDroevendaalsesteeg 16708 PB WageningenThe Netherlands present address:Institute of plant Protection Jiangsu Academy of Agricultural SciencesNanjing 210014P.R.China present address:Institute of plant and Microbial Biology Academia SinicaTaipei 11529 Taiwan present address:Laboratory of Crop Evolution Graduate School of AgricultureKyoto UniversityMozumeMukoKyoto 617-0001Japan present address:Lipman Family Farms 21106 Six Ls Farm RdEsteroFloridaUnited States

Species of the genus Phytophthora,the plant killer,cause disease and reduce yields in many crop *** many Resistance to Phytophthora infestans(Rpi)genes effective against potato late blight have been cloned,few have been cloned against other Phytophthora *** Rpi genes encode nucleotide-binding domain,leucine-rich repeat-containing(NLR)immune receptor proteins that recognize RXLR(Arg-X-Leu-Arg)***,whether NLR proteins can recognize RXLR effectors from multiple Phytophthora species has rarely been ***,we identified a new RXLR-WY effector AVRamr3 from *** that is recognized by Rpi-amr3 from a wild Solanaceae species Solanum ***-amr3 associates with AVRamr3 in ***3 is broadly conserved in many different Phytophthora species,and the recognition of AVRamr3 homologs by Rpi-amr3 activates resistance against multiple Phytophthora pathogens,including the tobacco black shank disease and cacao black pod disease pathogens *** and ***-amr3 is thus the first characterized resistance gene that acts against *** or *** findings suggest a novel path to redeploy known R genes against different important plant pathogens.

关键词： Rpi-amr3 AVRamr3 potato late blight Phytophthora disease RXLR-WY effector Solanum americanum

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Calcium-dependent protein kinase CPK32 mediates calcium signaling in regulating Arabidopsis flowering time

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National Science Review 2022年第1期9卷 56-65页

作者： Xidong Li Limei Chen Li Yao Junjie Zou Jie Hao Weihua Wu State Key Laboratory of plant physiology and Biochemistry College of Biological Sciences China Agricultural University Center for Crop Functional Genomics and molecular Breeding China Agricultural University Syngenta biotechnology China Co. Ltd. biotechnology Research Institute Chinese Academy of Agricultural Sciences

Appropriate flowering time is critical for the reproductive success of plant *** evidence indicates that calcium may play an important role in the regulation of flowering ***,the underlying molecular mechanisms remain *** this study,we demonstrate that calcium-dependent protein kinase 32(CPK32) regulates flowering time by affecting the alternative polyadenylation of FLOWERING CONTROL LOCUS A(FCA) and altering the transcription of FLO WERING LOCUS C(FLC),a central repressor of flowering *** knockdown of CPK32 results in an obvious late flowering phenotype and dramatically enhanced FL C ***32 interacts with FCA,and phosphorylates the serine592of FCA in a Ca2+-dependent ***,the ratio of abundance of the FCA transcripts(FCA-D and FCA-P) changes significantly in the cpk32 mutant,which subsequently affects FLC expression and consequently regulates floral *** present evidence demonstrates that CPK32 modulates flowering time by regulating FCA alternative polyadenylation and consequent FL C expression.

关键词： calcium signaling CPK32 FCA FLC flowering time

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Warming‑induced changes of broccoli head to cauliflower‑like curd in Brassica oleracea are regulated by DNA methylation as revealed by methylome and transcriptome co‑profiling

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molecular Horticulture 2022年第1期2卷 318-332页

作者： Zilei Yao Lu Yuan Ke Liu Tingjin Wang Bin Liu Yan Zhao Susheng Gan Liping Chen Department of Horticulture College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China plant Biology Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA present address:College of Agronomy and biotechnology Yunnan Agricultural UniversityKunming 650201China

Increasingly warming temperature impacts on all aspects of growth and development in *** development is a complex process that is very sensitive to ambient temperature,and warming temperatures often lead to abnor-mal flower development and remarkably reduce the quality and yield of inflorescent vegetables and many other crops,which can be exemplified by Brassica oleracea *** Harmony F1,a broccoli cultivar,whose floral develop-ment is ceased at inflorescence meristem(at 28℃)or floral primordium stage(at 22℃),forming a cauliflower-like curd(28℃)or intermediate curd(22℃)instead of normal broccoli head at 16℃.However,the underlying molecular regulatory mechanisms are not well *** we report that warming temperature(28℃ or 22℃)induced hypermethylation of the genome,especially the promoter regions of such sets of genes as ribosome biogenesis-related and others,leading to the suppression of the apex-highly-expressed distinctive genes,subsequently resulting in the abnormal floral development,as revealed by methylome and transcriptome *** regulation of warming-induced abnormal floral development in broccoli was further verified by the fact that the DNA methylation inhibitor 5-azacytidine(5-azaC)released the expression of genes from the warming temperature-induced suppres-sion,and restored the broccoli development to normalcy at warming *** research provided new approaches to breeding broccoli and other crops for growing in wider or warmer temperature zones.

关键词： Brassica oleracea DNA methylation Floral development cessation Global warming Heat stress

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Theplant cytosolic m^(6)A RNA methylome stabilizes photosynthesis in the cold

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plant Communications 2023年第6期4卷 70-84页

作者： Alexandre Magno Vicente Nikolay Manavski Paul Torben Rohn Lisa-Marie Schmid Antoni Garcia-Molina Dario Leister Charlotte Seydel Leo Bellin Torsten Möhlmann Gregor Ammann Stefanie Kaiser Jörg Meurer plant molecular Biology Faculty of BiologyLudwig-Maximilians-University MunichGroßhaderner Street 2-482152 Planegg-MartinsriedGermany plant Development Faculty of BiologyLudwig-Maximilians-University MunichGroßhaderner Street 2-482152 Planegg-MartinsriedGermany plant physiology Faculty of BiologyUniversity of KaiserslauternErwin-Schröodinger-Street767663 KaiserslauternGermany Pharmaceutical Chemistry Goethe University FrankfurtMax-von-Laue-Str.960438 Frankfurt am MainGermany present address:Loewe Biochemica GmbH Möuhlweg 2a82054 SauerlachGermany present address:Center for Research in Agricultural Genomics 08193

The sessile lifestyle of plants requires an immediate response to environmental stressors that affect photosynthesis,growth,and crop ***,we showed that three abiotic perturbations—heat,cold,and high light—triggered considerable changes in the expression signatures of 42 epitranscriptomic factors(writers,erasers,and readers)with putative chloroplast-associated functions that formed clusters of commonly expressed genes in *** expression changes under all conditions were reversible upon deacclimation,identifying epitranscriptomic players as modulators in acclimation *** dysfunctions,particularly those induced by the oxidative stress-inducing norflurazon in a largely GENOME UNCOUPLED-independent manner,triggered retrograde signals to remodel chloroplastassociated epitranscriptomic expression patterns.N6-methyladenosine(m^(6)A)is known as the most prevalent RNA modification and impacts numerous developmental and physiological functions in living *** cold treatment,expression of components of the primary nuclear m^(6)A methyltransferase complex was upregulated,accompanied by a significant increase in cellular m^(6)A mRNA *** the cold,the presence of FIP37,a core component of the writer complex,played an important role in positive regulation of thylakoid structure,photosynthetic functions,and accumulation of photosystemⅠ,the Cytb6f complex,cyclic electron transport proteins,and Curvature Thylakoid1 but not that of photosystemⅡcomponents and the chloroplast ATP *** of FIP37 affected abundance,polysomal loading,and translation of cytosolic transcripts related to photosynthesis in the cold,suggesting m^(6)Adependent translational regulation of chloroplast *** summary,we identified multifaceted roles of the cellular m^(6)A RNA methylome in coping with cold;these were predominantly associated with chloroplasts and served to stabilize photosynthesis.

关键词： m^(6)A RNA methylation cold acclimation stress response Arabidopsis thaliana photosynthesis chloroplast

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Calcineurin-B-Like Protein CBL9 Interacts with Target Kinase CIPK3 in the Regulation of ABA Response in Seed Germination

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molecular plant 2008年第2期1卷 238-248页

作者： Girdhar K. Pandey John J. Grant Yong Hwa Cheong Beom-Gi Kim Le Gong Li Sheng Luan Department of plant and Microbial Biology University of California Berkeley CA 94720 USA Department of plant molecular Biology University of Delhi South Campus Benito Juarez Road New Delhi-110021 India present address: Department of Bio-Environmental Science Sunchon National University Suncheon Jeonnam 540-742 Korea present address: Department of molecular physiology and Biochemistry National institute of Agricultural Biotechnology Suwon 441-707 Korea

Calcium plays a vital role as a second messenger in many signaling pathways in plants. The calcineurin B-like proteins （CBLs） represent a family of plant calcium-binding proteins that function in calcium signaling by interacting with their interacting protein kinases （CIPKs）. In our previous study, we have reported a role for one of the CBLs （CBL9） and one of the CIPKs （CIPK3） in ABA signaling. Here, we have shown that CBL9 and CIPK3 physically and functionally interact with each other in regulating the ABA responses. The CBL9 and CIPK3 proteins interacted with each other in the yeast two- hybrid system and when expressed in plant cells. The double mutant cbl9cipk3 showed the similar hypersensitive response to ABA as observed in single mutants （cbl9 or cipk3）. The constitutively active form of CIPK3 genetically complemented the cbl9 mutant, indicating that CIPK3 function downstream of CBL9. Based on these findings, we conclude that CBL9 and CIPK3 act together in the same pathway for regulating ABA responses.

关键词： ABA calcium CBL CIPK osmotic stress signal transduction.

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Distinctive and complementary roles of E2F transcription factors during plant replication stress responses

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molecular plant 2023年第8期16卷 1269-1282页

作者： Maherun Nisa Thomas Eekhout Clara Bergis Jose-Antonio Pedroza-Garcia Xiaoning He Christelle Mazubert Ilse Vercauteren Toon Cools Rim Brik-Chaouche Jeannine Drouin-Wahbi Layla Chmaiss David Latrasse Catherine Bergounioux Klaas Vandepoele Moussa Benhamed Lieven De Veylder Cécile Raynaud Universite Paris-Saclay CNRSINRAEUniversite EvryInstitute of Plant Sciences Paris-Saclay(IPS2)91190 Gif-sur-YvetteFrance Universite de Paris Cite CNRSINRAEInstitute of Plant Sciences Paris-Saclay(IPS2)91190 Gif-sur-YvetteFrance Department of plant biotechnology and Bioinformatics Ghent University9052 GhentBelgium Center for plant Systems Biology VIB9052 GhentBelgium present address:plant molecular and Cellular Biology Laboratory Salk Institute for Biological StudiesLa JollaCA 92037USA

Survival of living organisms is fully dependent on their maintenance of genome integrity,being permanently threatened by replication stress in proliferating *** the plant DNA damage response(DDR)regulator SOG1 has been demonstrated to cope with replication defects,accumulating evidence points to other pathways functioning independent of ***,we report the roles of the Arabidopsis E2FA and EF2B transcription factors,two well-characterized regulators of DNA replication,in plant response to replication *** a combination of reverse genetics and chromatin immunoprecipitation approaches,we show that E2FA and E2FB share many target genes with SOG1,providing evidence for their involvement in the *** of double-and triple-mutant combinations revealed that E2FB,rather than E2FA,plays the most prominent role in sustaining plant growth in the presence of replication defects,either operating antagonistically or synergistically with ***,SOG1 aids in overcoming the replication defects of E2FA/E2FB-deficient ***,our data reveal a complex transcriptional network controlling the replication stress response in which E2Fs and SOG1 act as key regulatory factors.

关键词： replication stress E2F SOG1 cell cycle Arabidopsis

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The boys are back in town: Rethinking the function of ribosomal DNA repeats in the genomic era

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molecular plant 2023年第3期16卷 514-516页

作者： Francesca B.Lopez Peter C.McKeown Antoine Fort Galina Brychkova Charles Spillane Genetics and biotechnology Laboratory Plant&AgriBiosciences Research Centre(PABC)Ryan InstituteUniversity of GalwayH91 REW4 GalwayIreland present address:Department of plant Biology and Genome Center University of CaliforniaDavisUC Davis Genome CenterDavisCA 95616USA

Next-generation sequencing technological advances,affording high-throughput,scalable,and fast assemblies,have enabled genome editing techniques that allow us to remove,insert,and modify genes for rapid and precise fun... 详细信息

关键词： remove precise function

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