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Bacterial diacetyl suppresses abiotic stress-induced senescence in Arabidopsis

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Journal of Integrative plant biology 2022年第6期64卷 1135-1139页

作者： Sunil K.Singh Yazhou Sun Yu Yang Ziwei Zuo Xiaoxuan Wu Chuyang Shao Li Peng Paul W.Paré Huiming Zhang Shanghai center for plant Stress biology Center for Excellence in Molecular Plant Sciencesthe Chinese Academy of SciencesShanghai 201602China University of Chinese Academy of Sciences Beijing 100049China Department of Chemistry and Biochemistry Texas Tech UniversityLubbock 79409TexasUSA

Premature plant senescence induced by abiotic stresses is a major cause of agricultural losses worldwide. Tools for suppressing stress-induced plant senescence are limited. Here, we report that diacetyl, a natural compound emitted by the plantbeneficial bacterium Bacillus amyloliquefaciens,suppresses abscisic acid-mediated foliar senescence in Arabidopsis thaliana under various abiotic stress conditions. Our results establish diacetyl as an effective protector against stressinduced plant senescence and reveal a molecular mechanism for bacteria-enhanced plant stress resistance.

关键词： ABA diacetyl microbial volatile leaf senescence

Bioinformaticians wrestling with the big biomedical data

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Journal of Genetics and Genomics 2017年第5期44卷 223-225页

作者： Yu Xue Xiu-Jie Wang MOE Key Laboratory of Molecular Biophysics College of Life Science and Technology and the Collaborative Innovation Center for Brain ScienceHuazhong University of Science and Technology The State Key Laboratory of plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of Sciences

Database plays a critical role throughout the history of the development of bioinformatics and *** 1980s,a number of databases such as GenBank（NCBI Resource Coordinators,2017）,European Nucleotide Archive（ENA）（Toribio et al,2017）,and DNA Data Bank of Japan（DDBJ）（Mashima et al.,2017）were established and have still acted as major data resources for maintaining nucleotide sequences and other types of biological data until today.

关键词： biomedical Nucleotide bioinformatics today maintaining http throughout metastasis until threaten

A meta-analysis of experimental warming effects on woody plant growth and photosynthesis in forests

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Journal of Forestry Research 2018年第3期29卷 721-727页

作者： Yongge Yuan Litao Ge Haishui Yang Weizheng Ren Natural history Research center Shanghai Natural History MuseumBranch of Shanghai Science and Technology MuseumShanghaiChina National Audit Office of the People’s Republic of China BeijingChina College of Agriculture Nanjing Agricultural UniversityNanjingChina College of life Sciences Zhejiang UniversityHangzhouChina

Increasing field experiments have been conducted in forests to better understand the response of plant growth and photosynthesis to climatic warming. However,it is still unknown whether there is a general pattern in relation to how and to what extent warming impacts woody plants in forests. In this study, a meta-analysis was conducted to investigate the warming effects. When temperatures increased between 0.3 and 10 ℃, specific leaf area(SLA) was significantly increased by 5.9%, plant height by 7.8%, biomass by 21.9%, foliar calcium(Ca) and manganese(Mn) concentrations by 20.7% and 39.6% and net photosynthetic rate(Pn) by 9.9%. Enhanced growth and Pn may have a relationship with changing SLA, efficiency of PSⅡ(photosystem Ⅱ), photosynthetic pigment concentrations and foliar nutrients. The results will be useful to understand the underlying mechanisms of forests responding to global warming.

关键词： Forest Global warming Meta-analysis Photosynthesis plant growth

Specifying the role of BAK1-interacting receptor-like kinase 3 in brassinosteroid signaling

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Journal of Integrative plant biology 2020年第4期62卷 456-469页

作者： Ruth Groβeholz Anna Feldman-Salit Friederike Wanke Sarina Schulze Nina Glockner Birgit Kemmerling Klaus Harter Ursula Kummer Centre for Organismal Studies/Bio Quant Heidelberg University69120 HeidelbergGermany center for plant Molecular biology(ZMBP) University Tübingen72076 TubingenGermany

Brassinosteroids(BR) are involved in the control of several developmental processes ranging from root elongation to senescence and adaptation to environmental cues. Thus, BR perception and signaling have to be precisely regulated. One regulator is BRI1-associated kinase 1(BAK1)-interacting receptor-like kinase 3(BIR3). In the absence of BR, BIR3 forms complexes with BR insensitive 1(BRI1) and ***, the biophysical and energetic requirements for complex formation in the absence of the ligand have yet to be determined. Using computational modeling, we simulated the potential complexes between the cytoplasmic domains of BAK1, BRI1 and BIR3. Our calculations and experimental data confirm the interaction of BIR3 Rewith BAK1 and BRI1, with the BAK1 BIR3 interaction clearly favored. Furthermore, we demonstrate that BIR3 and BRI1 share the same interaction site with BAK1. This suggests a competition between BIR3 and BRI1 for binding to BAK1, which results in preferential binding of BIR3 to BAK1 in the absence of the ligand thereby preventing the active participation of BAK1 in BR signaling. Our model also suggests that BAK1 and BRI1 can interact even while BAK1 is in complex with BIR3 at an additional binding site of BAK1 that does not allow active BR signaling.

关键词： BAK1 interaction interacting

Phylogenomic conflict analyses in the apple genus Malus *** widespread hybridization and allopolyploidy driving diversification,with insights into the complex biogeographic history in the Northern Hemisphere

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Journal of Integrative plant biology 2022年第5期64卷 1020-1043页

作者： Bin-Bin Liu Chen Ren Myounghai Kwak Richard GJHodel Chao Xu Jian He Wen-Bin Zhou Chien-Hsun Huang Hong Ma Guan-Ze Qian De-Yuan Hong Jun Wen State Key Laboratory of Systematic and Evolutionary Botany Institute of Botanythe Chinese Academy of SciencesBeijing 100093China Department of Botany National Museum of Natural HistorySmithsonian InstitutionPO Box 37012Washington 20013–7012DCUSA Key Laboratory of plant Resources Conservation and Sustainable Utilization South China Botanical GardenThe Chinese Academy of SciencesGuangzhou 510650China Guangdong Provincial Key Laboratory of Applied Botany South China Botanical GardenThe Chinese Academy of SciencesGuangzhou 510650China National Institute of Biological Resources Incheon 22689South Korea School of Ecology and Nature Conservation Beijing Forestry UniversityBeijing 100083China Department of plant and Microbial biology North Carolina State UniversityRaleigh 27965NCUSA State Key Laboratory of Genetic Engineering and Collaborative Innovation center of Genetics and Development Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200433China Department of biology Huck Institutes of the Life SciencesPennsylvania State University510D Mueller LaboratoryUniversity ParkPennsylvania 16802USA College of life Sciences Liaocheng UniversityLiaocheng 252059China

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting *** this study,785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato,an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy *** nuclear phylogeny recovered the monophyly of Malus s.l.(including Docynia);however,the genus was supported to be biphyletic in the plastid *** ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear *** conflict analysis demonstrated that ILS,hybridization,and allopolyploidy could explain the widespread nuclear gene tree *** deep hybridization event(Malus doumeri)and one recent event(Malus coronaria)were detected in Malus ***,our historical biogeographic analysis integrating living and fossil data supported a widespread East Asianwestern North American origin of Malus *** the Eocene,followed by several extinction and dispersal events in the Northern *** also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

关键词： deep genome skimming genomic discordance historical biogeography massive extinction reticulate evolution single-copy nuclear genes

Uncovering the dynamic evolution of nucleotidebinding site-leucine-rich repeat(NBS-LRR) genes in Brassicaceae

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Journal of Integrative plant biology 2016年第2期58卷 165-177页

作者： Yan-Mei Zhang Zhu-Qing Shao Qiang Wang Yue-Yu Hang Jia-Yu Xue Bin Wang Jian-Qun Chen State Key Laboratory of Pharmaceutical Biotechnology Center of Plant Genetics and Molecular EvolutionSchool of Life SciencesNanjing University Institute of Botany Jiangsu Province and Chinese Academy of Sciences

plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat （NBS-LRR） genes; however, the long-term evolutionary history of these resistance genes has not been fully understood, This study focuses on five Brassicaceae genomes and the Carica papaya genome to explore changes in NBS-LRR genes that have taken place in this Rosid II lineage during the past 72 million years. Various numbers of NBS-LRR genes were identified from Arabidopsis lyrata （198）, A. thaliana （165）, Brassica rapa （204）, Capsella rubella （127）, Thellungiella salsuginea （88）, and C. papaya （51）. In each genome, the identified NBS-LRR genes were found to be unevenly distributed among chromosomes and most of them were clustered together. Phylogenetic analysis revealed that, before and after Brassicaceae speciation events, both toll/interleukin-1 receptor-NBS-LRR （TNL） genes and non-toll/interleukin-1 receptor-NBS-LRR （nTNL） genes exhibited a pattern of first expansion and then contraction, suggesting that both subclasses of NBS-LRR genes were responding to pathogen pressures synchronically. Further, by examining the gain/loss of TNL and nTNL genes at different evolutionary nodes, this study revealed that both events often occurred more drastically in TNL genes. Finally, the phylogeny of nTNL genes suggested that this NBS-LRR subclass is composed of two separate ancient gene types： RPW8-NBS-LRR and Coiled-coiI-N BS-LRR.

关键词： Dynamic evolution nucleotide-binding site-leucine-rich repeat gene phylogenetic relationship plant disease resistance

A Genome-Wide Transcription Analysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids

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Molecular plant 2008年第5期1卷 720-731页

作者： Hui-Yong Zhang Hang He Liang-Bi Chen Lei Li Man-Zhong Liang Xiang-Feng Wang Xi-Gang Liu Guang-Ming He Run-Sheng Chen Li-Geng Ma Xing Wang Deng National Institute of Biological Sciences Zhongguancun Life Science Park Beijing 102206 China Institute of Biophysics Chinese Academy of Sciences. 15 Oatun Road Beiiing 100101 China Department of Botany College of Life Sciences Hunan Normal University Changsha 410081 China Peking-Yale Joint Research center of plant Molecular Genetics and Agrobiotechnology College of Life Sciences Peking University Beijing 100871 China Department of Molecular Cellular and Developmental Biology Yale University New Haven Connecticut 06520 USA

Heterosis, or hybrid vigor, refers to the phenomenon in which hybrid progeny of two inbred varieties exhibits enhanced growth or agronomic performance. Although a century-long history of research has generated several hypotheses regarding the genetic basis of heterosis, the molecular mechanisms underlying heterosis and heterotic gene expression remain elusive. Here, we report a genome-wide gene expression analysis of two heterotic crosses in rice, taking advantage of its fully sequenced genomes. Approximately 7-9% of the genes were differentially expressed in the seedling shoots from two sets of heterotic crosses, including many transcription factor genes, and exhibited multiple modes of gene action. Comparison of the putative promoter regions of the ortholog genes between inbred parents revealed extensive sequence variation, particularly small insertions/deletions （INDELs）, many of which result in the formation/disruption of putative cis-regulatory elements. Together, these results suggest that a combinatorial interplay between expression of transcription factors and polymorphic promoter cis-regulatory elements in the hybrids is one plausible molecular mechanism underlying heterotic gene action and thus heterosis in rice.

关键词： Genome-Wide INDEL

Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms

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Molecular plant 2018年第3期11卷 414-428页

作者： Ren Ren Haifeng Wang Chunce Guo Ning Zhang Liping Zeng Yamao Chen Hong Ma Ji Qi State Key Laboratory of Genetic Engineering and Collaborative Innovation center for Genetics and Development Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Science Institute of Plant Biology Center for Evolutionary Biology School of Life Sciences Fudan University Shanghai China State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops Fujian Agriculture and Forestry University Fuzhou Fujian 350002 China Department of Botany National Museum of Natural History MRC 166 Smithsonian Institution Washington DC USA Institutes of Biomedical Sciences Fudan University Shanghai China These authors contributed equally to this article.

Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication （WGD） doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, and thus are considered as a major driving force in species diversification. We per- formed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene dupli- cation events by surveying tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approx- imately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes.

关键词： whole genome duplication duplicate gene polyploidization angiosperm phylogenomics

Dissecting Maize Productivity:Ideotypes Associated with Grain Yield under Drought Stress and Well-watered Conditions

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Journal of Integrative plant biology 2012年第12期54卷 1007-1020页

作者： Jill E.Cairns Ciro Sanchez Mateo Vargas Raziel Ordoez Jose Luis Araus Global Maize Program International Maize and Wheat Improvement Center(CIMMYT)Mexico D.F.Mexico Bioinformatics and Statistics Unit International Maize and Wheat Improvement Center(CIMMYT)Mexico D.F.Mexico Unit of plant Physiology Department of Plant BiologyUniversity of BarcelonaBarcelonaSpain

To increase maize （Zea mays L.） yields in drought-prone environments and offset predicted maize yield losses under future climates, the development of improved breeding pipelines using a multi-disciplinary approach is essential. Elucidating key growth processes will provide opportunities to improve drought breeding progress through the identification of key phenotypic traits, ideotypes, and donors. In this study, we tested a large set of tropical and subtropical maize inbreds and single cross hybrids under reproductive stage drought stress and well-watered conditions. Patterns of biomass production, senescence, and plant water status were measured throughout the crop cycle. Under drought stress, early biomass production prior to anthesis was important for inbred yield, while delayed senescence was important for hybrid yield. Under well-watered conditions, the ability to maintain a high biomass throughout the growing cycle was crucial for inbred yield, while a stay-green pattern was important for hybrid yield. While new quantitative phenotyping tools such as spectral reflectance （Normalized Difference Vegetation Index, NDVI） allowed for the characterization of growth and senescence patterns as well as yield, qualitative measurements of canopy senescence were also found to be associated with grain yield.

关键词： Climate change drought stress ideotypes maize senescence spectral reflectance.