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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 studies.Poplars,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental adaptability.In 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 adaptation.Through 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 regions.Further 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 divergence.We have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration formation.Finally,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 fields.To address this chal-lenge,environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice cultivation.However,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 WsT.Polysome profiling-coupled transcriptome sequencing(polysome-seq)analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR activity.molecular,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 WST.Intriguingly,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 allocation.We 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 region.Collectively,these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and NUE.Our 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 signaling.The 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 species.The 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 protease.The perception of^(1)O_(2)via Trp643 oxidation and subsequent EX1 proteolysis facilitate chloroplast-to-nucleus retrograde signaling.In 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 degradation.Consistent 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 EX2.Intriguingly,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 plants.Although many Resistance to Phytophthora infestans(Rpi)genes effective against potato late blight have been cloned,few have been cloned against other Phytophthora species.Most Rpi genes encode nucleotide-binding domain,leucine-rich repeat-containing(NLR)immune receptor proteins that recognize RXLR(Arg-X-Leu-Arg)effectors.However,whether NLR proteins can recognize RXLR effectors from multiple Phytophthora species has rarely been investigated.Here,we identified a new RXLR-WY effector AVRamr3 from P.infestans that is recognized by Rpi-amr3 from a wild Solanaceae species Solanum americanum.Rpi-amr3 associates with AVRamr3 in planta.AVRamr3 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 P.parasitica and P.palmivora.Rpi-amr3 is thus the first characterized resistance gene that acts against P.parasitica or P.palmivora.These 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 species.Emerging evidence indicates that calcium may play an important role in the regulation of flowering time.However,the underlying molecular mechanisms remain unclear.In 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 time.The knockdown of CPK32 results in an obvious late flowering phenotype and dramatically enhanced FL C transcription.CPK32 interacts with FCA,and phosphorylates the serine592of FCA in a Ca2+-dependent manner.Moreover,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 transition.The 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 plants.Flower 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 cv.Green 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 understood.Here 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 co-profiling.The 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 temperature.The 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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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 cells.Although 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 SOG1.Here,we report the roles of the Arabidopsis E2FA and EF2B transcription factors,two well-characterized regulators of DNA replication,in plant response to replication stress.Through 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 DDR.Analysis 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.Conversely,SOG1 aids in overcoming the replication defects of E2FA/E2FB-deficient plants.Collectively,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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How Sugars Might Coordinate Chloroplast and Nuclear Gene Expression during Acclimation to High Light Intensities

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molecular plant 2014年第7期7卷 1121-1137页

作者： Rainer E. Haiusler Luisa Heinrichs Jessica Schmitz Ulf-Ingo Flugge Department of Botany II Cologne Biocenter University of Cologne ZuIpicherstr. 47b 50674 Cologne Germany present address: plant molecular physiology and biotechnology Heinrich-Heine-University Universitatsstrasse 1 40225 D~sseldorfGermany

The concept of retrograde control of nuclear gene expression assumes the generation of signals inside the chloroplasts, which are either released from or sensed inside of the organelle. In both cases, downstream signaling path- ways lead eventually to a differential regulation of nuclear gene expression and the production of proteins required in the chloroplast. This concept appears reasonable as the majority of the over 3000 predicted plastidial proteins are encoded by nuclear genes. Hence, the nucleus needs information on the status of the chloroplasts, such as during acclimation responses, which trigger massive changes in the protein composition of the thylakoid membrane and in the stroma. Here, we propose an additional control mechanism of nuclear- and plastome-encoded photosynthesis genes, taking advantage of pathways involved in sugar- or hormonal signaling. Sugars are major end products of photosynthesis and their con- tents respond very sensitively to changes in light intensities. Based on recent findings, we ask the question as to whether the carbohydrate status outside the chloroplast can be directly sensed within the chloroplast stroma. Sugars might syn- chronize the responsiveness of both genomes and thereby help to coordinate the expression of piastome- and nuclear- encoded photosynthesis genes in concert with other, more specific retrograde signals.

关键词： acclimation--physiological assimilate allocation/partitioning carbohydrate metabolism molecular physiology membrane proteins Arabidopsis.

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The Role of Phosphorylation in Redox Regulation of Photosynthesis Genes psaA and psbA during Photosynthetic Acclimation of Mustard

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molecular plant 2009年第3期2卷 416-429页

作者： Sebastian Steiner Lars Dietzel Yvonne Schroter Vidal Fey Raik Wagner Thomas Pfannschmidt Junior Research Group 'plant acclimation to environmental changes: Protein analysis by MS' at the Institute of General Botany and plant physiology Department of Plant Physiology Friedrich-Schiller-University of Jena Dornburger Str. 159 07743 Jena Germany present address: VTT Technical research Center of Finland Medical Biotechnology Turku Finland present address: Department of Chemistry Bioenergetics University of Umea Sweden

The long-term response （LTR） to light-quality gradients improves performance and survival of plants in dense stands. It involves redox-controlled transcriptional regulation of the plastome-encoded genes psaAB （encoding the P700 apoproteins of photosystem I） and psbA （encoding the D1 protein of photosystem II） and requires the action of plastidlocalized kinases. To study the potential impact of phosphorylation events on plastid gene expression during the LTR, we analyzed mustard seedlings acclimated to light sources favoring either photosystem I or photosystem II. Primer extension analyses of psaA transcripts indicate that the redox regulation occurs at the principal bacterial promoters, suggesting that the plastid encoded RNA polymerase （PEP） is the target for redox signals. Chloroplast protein fractions containing PEP and other DNA-binding proteins were purified from mustard via heparin-Sepharose chromatography. The biochemical properties of these fractions were analyzed with special emphasis on promoter recognition and specificity, phosphorylation state, and kinase activity. The results demonstrate that the LTR involves the action of small DNA-binding proteins; three of them exhibit specific changes in the phosphorylation state. Auto-phosphorylation assays, in addition, exhibit large differences in the activity of endogenous kinase activities. Chloroplast run-on transcription experiments with the kinase inhibitor H7 and the reductant DTT indicate that phosphorylation events are essential for the mediation of redox signals toward psaA and psbA transcription initiation, but require the synergistic action of a thiol redox signal. The data support the idea that redox signals from the thylakoid membrane are linked to gene expression via phosphorylation events; however, this mediation appears to require a complex network of interacting proteins rather than a simple phosphorelay.

关键词： Light-quality acclimation redox control protein phosphorylation chloroplast transcription Sinapis alba.

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