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Genome-wide Expansion and Expression Divergence of the Basic Leucine Zipper Transcription Factors in Higher Plants with an Emphasis on Sorghum

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Journal of Integrative Plant Biology 2011年第3期53卷 212-231页

作者： Jizhou Wang Junxia Zhou Baolan Zhang Jeevanandam Vanitha Srinivasan Ramachandran Shu-Ye Jiang Institute of Botany and Temasek Life Sciences Laboratory Joint Research & Development Laboratory Institute of Botany the Chinese Academy of Sciences Beijing 100093 China temasek life sciences laboratory 1 Research Link the National University of Singapore Singapore 117604 Singapore

Plant bZIP transcription factors play crucial roles in multiple biological processes. However, little is known about the sorghum bZIP gene family although the sorghum genome has been completely sequenced. In this study, we have carried out a genome-wide identification and characterization of this gene family in sorghum. Our data show that the genome encodes at least 92 bZIP transcription factors. These bZIP genes have been expanded mainly by segmental duplication. Such an expansion mechanism has also been observed in rice, arabidopsis and many other plant organisms, suggesting a common expansion mode of this gene family in plants. Further investigation shows that most of the bZIP members have been present in the most recent common ancestor of sorghum and rice and the major expansion would occur before the sorghum-rice split era. Although these bZlP genes have been duplicated with a long history, they exhibited limited functional divergence as shown by nonsynonymous substitutions （Ka）lsynonymous substitutions （Ks） analyses. Their retention was mainly due to the high percentages of expression divergence. Our data also showed that this gene family might play a role in multiple developmental stages and tissues and might be regarded as important regulators of various abiotic stresses and sugar signaling.

关键词： LEUCINE zippers TRANSCRIPTION factors SORGHUM GENETICS PLANT genomes PLANT gene expression DIVERGENCE (Biology) CARRIER proteins

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The OsFTIP6-OsHB22-OsMYBR57 module regulates drought response in rice

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Molecular Plant 2022年第7期15卷 1227-1242页

作者： Lijia Yang Ying Chen Liang Xu Jiaxuan Wang Haoyue Qi Jiazhuo Guo Liang Zhang Jun Shen Huanyu Wang Fan Zhang Lijun Xie Wenjun Zhu Peitao Lü Qian Qian Hao Yu Shiyong Song State Key laboratory of Rice Biology Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China State Key laboratory of Rice Biology China National Rice Research InstituteHangzhou 311400China College of Horticulture FAFU-UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhou 350002China Department of Biological sciences and temasek life sciences laboratory National University of SingaporeSingapore 117543Singapore

Plants have evolved a sophisticated set of mechanisms to adapt to drought stress.Transcription factors play crucial roles in plant responses to various environmental stimuli by modulating the expression of numerous stress-responsive genes.However,how the crosstalk between different transcription factor families orchestrates initiation of the key transcriptional network and the role of posttranscriptional modification of transcription factors,especially in cellular localization/trafficking in response to stress in rice,remain still largely unknown.In this study,we isolated an Osmybr57 mutant that displays a drought-sensitive phenotype through a genetic screen for drought stress sensitivity.We found that OsMYBR57,an MYB-related protein,directly regulates the expression of several key drought-related OsbZ/Ps in response to drought treatment.Further studies revealed that OsMYBR57 interacts with a homeodomain transcription factor,OsHB22,which also plays a positive role in drought signaling.We further demonstrate that OsFTIP6 interacts with OsHB22 and promotes the nucleocytoplasmic translocation of OsHB22 into the nucleus,where OsHB22 cooperates with OsMYBR57 to regulate the expression of drought-responsive genes.Our findings have revealed a mechanistic framework underlying the OsFTIP6-0sHB22-0sMYBR57 module-mediated regulation of drought response in rice.The OsFTIP6-mediated OsHB22 nucleocytoplasmic shuttling and OsMYBR57-0sHB22 regulation of OsbZIP transcription ensure precise control of expression of OsLEA3 and Rab21,and thereby regulate the response to water deficiency in rice.

关键词： OsMYBR57 OsHB22 OsFTIP6 drought response nucleocytoplasmic trafficking rice

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Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1

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Molecular Plant 2016年第4期9卷 541-557页

作者： Lin Ma Tian Tian Rongcheng Lin Xing-Wang Deng Haiyang Wang Gang Li State Key laboratory of Crop Biology College of Life Sciences Shandong Agricultural University Tai'an 271018 China Key laboratory of Photobiology Institute of Botany Chinese Academy of Science Beijing 100093 China National laboratory of Protein and Plant Gene research Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology Peking-Tsinghua Centerfor Life Sciences College of Life Sciences Peking University Beijing 100871 China Biotechnology research institute Chinese Academy of Agricultural Sciences Beijing 100081 China

myo-lnositol-l-phosphate synthase （MIPS） catalyzes the limiting step of inositol biosynthesis and has crucial roles in plant growth and development. In response to stress, the transcription of MIPS1 is induced and the biosynthesis of inositol or inositol derivatives is promoted by unknown mechanisms. Here, we found that the light signaling protein FAR-RED ELONGATED HYPOCOTYL3 （FHY3） and its homolog FAR- RED IMPAIRED RESPONSE1 （FAR1） regulate light-induced inositol biosynthesis and oxidative stress re- sponses by activating the transcription of MIPS1. Disruption of FHY3 and FAR1 caused light-induced cell death after dark-light transition, precocious leaf senescence, and increased sensitivity to oxidative stress. Reduction of salicylic acid （SA） accumulation by overexpression of SALICYLIC ACID 3-HYDROXYLASE largely suppressed the cell death phenotype of fhy3 far1 mutant plants, suggesting that FHY3- and FARl-mediated cell death is dependent on SA. Furthermore, comparative analysis of chromatin immuno- precipitation sequencing and microarray results revealed that FHY3 and FAR1 directly target both MIPS1 and MIPS2. The fhy3 far1 mutant plants showed severely decreased MIPS1/2 transcript levels and reduced inositol levels. Conversely, constitutive expression of MIPSl partially rescued the inositol contents, caused reduced transcript levels of SA-biosynthesis genes, and prevented oxidative stress in fhy3 far1. Taken together, our results indicate that the light signaling proteins FHY3 and FAR1 directly bind the promoter of MIPS1 to activate its expression and thereby promote inositol biosynthesis to prevent light-induced oxidative stress and SA-dependent cell death.

关键词： Light signal FHY3 FAR1 myo-inositol MIPS SA oxidative stress cell death

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Temporal and spatial comparisons of angiosperm diversity between eastern Asia and North America

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National Science Review 2022年第6期9卷 38-42页

作者： Haihua Hu Jianfei Ye Bing Liu Lingfeng Mao Stephen A.Smith Russell L.Barrett Pamela S.Soltis Douglas E.Soltis Zhiduan Chen Limin Lu State Key laboratory of Systematic and Evolutionary botany Institute of Botany Chinese Academy of Sciences University of Chinese Academy of sciences Sino-Africa joint research Center Chinese Academy of Sciences Beijing Botanical Garden Institute of BotanyChinese Academy of Sciences Co-Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Nanjing Forestry University Department of Ecology and Evolutionary Biology University of Michigan National Herbarium of New South Wales Royal Botanic Gardens and Domain Trust Florida Museum of Natural History University of Florida Department of Biology University of Florida

Comparative approaches that examine floras with similar environments, but different diversity patterns, provide good opportunities to elucidate how uneven distributions of biodiversity were assembled. Eastern Asia(EA) and North America north of Mexico(NA; see definitions of EA and NA in Fig. S1 A) share similar geographical environments with comparable latitude, land area and climate,

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Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis

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National Science Review 2018年第1期5卷 78-87页

作者： Tao Lin Xia Xu Jue Ruan Shizhong Liu Shigang Wu Xiujuan Shao Xiaobo Wang Lin Gan Bi Qin Yushuang Yang Zhukuan Cheng Suhua Yang Zhonghua Zhang Guosheng Xiong Sanwen Huang Hong Yu Jiayang Li State Key laboratory of Plant Genomics and National Center for Plant Gene research Institute of Genetics and Developmental BiologyChinese Academy of Sciences Genome Analysis laboratory of the Ministry of Agriculture Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences The Key laboratory of Biology and Genetic Resources of Rubber Tree Rubber Research InstituteChinese Academy of Tropical Agricultural Sciences Key laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of Sciences Key laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture Sino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural Sciences University of the Chinese Academy of sciences

The Russian dandelion Taraxacum kok-saghyz Rodin(TKS), a member of the Composite family and a potential alternative source of natural rubber(NR) and inulin, is an ideal model system for studying rubber biosynthesis. Here we present the draft genome of TKS, the first assembled NR-producing weed plant. The draft TKS genome assembly has a length of 1.29 Gb, containing 46 731 predicted protein-coding genes and68.56% repeats, in which the LTR-RT elements predominantly contribute to the genome enlargement. We analyzed the heterozygous regions/genes, suggesting its possible involvement in inbreeding depression.Through comparative studies between rubber-producing and non-rubber-producing plants, we found that enzymes of the mevalonate(MVA) pathway and rubber elongation might be critical for rubber biosynthesis, and several key isoforms have been isolated and shown to be predominantly expressed in the latex, indicating their crucial functions in rubber biosynthesis. Moreover, for two important families in rubber elongation, the CPT/CPTL and REF/SRPP families, diverse evolutionary tracks have been revealed. These results provide valuable resources and new insights into the mechanism of NR biosynthesis,and facilitate the development of alternative NR-producing crops.

关键词： Taraxacum kok-saghyz genomics rubber biosynthesis CPT/CPTL REF/SRPP

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Karyomorphology of three endemic plants(Brassicaceae:Euclidieae and Arabideae)from the Qinghai-Tibet Plateau and its significance

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Plant Diversity 2020年第3期42卷 135-141页

作者： Wenguang Sun Haixia Wang Rui Wu Hang Sun Zhimin Li CAS Key laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China School of life Science Engineering Research Center of Sustainable Development and Utilization of Biomass EnergyYunnan Normal UniversityKunming 650500.China University of the Chinese Academy of sciences Beijing 100049China

In the paper,chromosome number and karyotype of three endemic genera from China are reported for the first time.Our results show that Anzhengxia yechengnica has a karyotype formula2 n=2 x=14=6 m+8 sm and belongs to Stebbins-3 A;Shangrilaia nana karyotype formula is2 n=2 x=14=10 m+4 sm(2 sat) and belongs to Stebbins-1 A;Baimashania pulvinata karyotype formula is 2 n=2 x=16=12 m(2 sat)+4 sm and belongs to Stebbins-1 A.Anzhengxia and Shangrilaia are monospecific genera belonging to tribe Euclidieae and both have a basic chromosome x=7.Baimashania,which belongs to tribe Arabideae,has two species which have a basic chromosome x=8.The implications of these cytological data are compared with morphological support and the implications for each tribe are discussed.We also summarize chromosomal number variation and its systematic implications of two tribes from the Qinghai-Tibet Plateau.

关键词： Karyotype Endemic species Anzhengxia Shangrilaia Baimashania Qinghai-Tibet Plateau

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Plant regeneration in the new era: from molecular mechanisms to biotechnology applications

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Science China life sciences 2024年第7期67卷 1338-1367页

作者： Chunli Chen Yuxin Hu Momoko Ikeuchi Yuling Jiao Kalika Prasad Ying Hua Su Jun Xiao Lin Xu Weibing Yang Zhong Zhao Wenkun Zhou Yun Zhou Jian Gao Jia-Wei Wang Sino-German joint research Center on Agricultural Biology Shandong Agricultural University Key laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology(IGDB)CAS CAS-JIC Centre of Excellence for Plant and Microbial Science(CEPAMS) IGDBCAS National Key laboratory of Plant Molecular Genetics CEMPSInstitute of Plant Physiology and Ecology(SIPPE)CAS CEPAMS SIPPECAS Hefei National laboratory for Physical sciences at the Microscale CEMPSSchool of Life SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of China State Key laboratory of Plant Environmental Resilience College of Biological SciencesChina Agricultural University Department of botany and Plant Pathology and Center for Plant Biology Purdue University School of life Science and Technology Shanghai Tech University Key laboratory of Plant Carbon Capture CAS National Key laboratory for Germplasm Innovation & Utilization of Horticultural Crops Hubei Hongshan LaboratoryHuazhong Agricultural University New Cornerstone Science laboratory College of life Science and Technology Huazhong Agricultural University Key laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of Sciences(CAS)China National Botanical Garden Division of Biological sciences Graduate School of Science and TechnologyNara Institute of Science and Technology State Key laboratory of Protein and Plant Gene research School of Life SciencesPeking University Peking-Tsinghua Center for life sciences Center for Quantitative BiologyAcademy for Advanced Interdisciplinary StudiesPeking University Indian institute of Science Education and research Thiruvananthapuram State Key laboratory of Wheat Improvement College of Life SciencesShandong Agricultural University

Plants or tissues can be regenerated through various pathways. Like animal regeneration, cell totipotency and pluripotency are the molecular basis of plant regeneration. Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration. Specifically, plant hormones, cell division, epigenetic remodeling, and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells. Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species, with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity. Conducting multi-omics studies at the single-cell level, tracking plant regeneration processes in real-time, and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration, improve crop regeneration efficiency, and contribute to future crop design.

关键词： apical meristem model species regeneration phytohormone plant cell reprogramming somatic embryogenesis

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Strigolactones interact with other phytohormones to modulate plant root growth and development

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The Crop Journal 2022年第6期10卷 1517-1527页

作者： Huwei Sun Weiqiang Li David J.Burritt Hongtao Tian Heng Zhang Xiaohan Liang Yuchen Miao Mohammad Golam Mostofa Lam-Son Phan Tran laboratory of Rice Biology in Henan Province Collaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhou 450046HenanChina Jilin Da’an Agro-ecosystem National Observation research Station Changchun Jingyuetan Remote Sensing Experiment StationKey Laboratory of Mollisols AgroecologyNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchun 130102JilinChina State Key laboratory of Cotton Biology Henan Joint International Laboratory for Crop Multi-Omics ResearchSchool of Life SciencesHenan UniversityKaifeng 475001HenanChina d Department of botany University of OtagoDunedin 9054New Zealand institute of Genomics for Crop Abiotic Stress Tolerance Department of Plant and Soil ScienceTexas Tech UniversityLubbockTX 79409USA institute of research and development Duy Tan University03 Quang TrungDa Nang 550000Vietnam

Strigolactones(SLs),which are biosynthesized mainly in roots,modulate various aspects of plant growth and development.Here,we review recent research on the role of SLs and their cross-regulation with auxin,cytokinin,and ethylene in the modulation of root growth and development.Under nutrientsufficient conditions,SLs regulate the elongation of primary roots and inhibit adventitious root formation in eudicot plants.SLs promote the elongation of seminal roots and increase the number of adventitious roots in grass plants in the short term,while inhibiting lateral root development in both grass and eudicot plants.The effects of SLs on the elongation of root hairs are variable and depend on plant species,growth conditions,and SL concentration.Nitrogen or phosphate deficiency induces the accumulation of endogenous SLs,modulates root growth and development.Genetic analyses indicate cross-regulation of SLs with auxin,cytokinin,and ethylene in regulation of root growth and development.We discuss the implications of these studies and consider their potential for exploiting the components of SL signaling for the design of crop plants with more efficient soil-resource utilization.

关键词： Cross-regulation development Phytohormones Roots Signaling Strigolactones

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Phytohormone dynamics in developing endosperm influence rice grain shape and quality

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Journal of Integrative Plant Biology 2020年第10期62卷 1625-1637页

作者： Xiao-Fan Zhang Jian-Hua Tong Ai-Ning Bai Chun-Ming Liu Lang-Tao Xiao Hong-Wei Xue School of life Science and Technology Shanghai Tech UniversityShanghai 201210China Hunan Provincial Key laboratory of Phytohormones and Growth development Hunan Agricultural UniversityChangsha 410128China Key laboratory of Plant Molecular Physiology Institute of Botanythe Chinese Academy of SciencesBeijing 100093China institute of Crop sciences Chinese Academy of Agricultural SciencesBeijing 100081China joint Center for Single Cell Biology/School of Agriculture and Biology Shanghai Jiao Tong UniversityShanghai 200240China National Key laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and Ecologythe Chinese Academy of SciencesShanghai 200032China

Hormones are important signaling molecules regulating developmental processes and responses to environmental stimuli in higher plants.Rice endosperm,the portion of the seed surrounding the embryo,is the main determinant of rice grain shape and yield;how-ever,the dynamics and exact functions of phyto-hormones in developing endosperm remain elusive.Through a systemic study including transcriptome analysis,hormone measurement,and transgene-based endosperm-specific expression of phytohormone bio-synthetic enzymes,we demonstrated that dynamic phytohormone levels play crucial roles in the developing rice endosperm,particularly in regard to grain shape and quality.We detected diverse,differential,and dra-matically changing expression patterns of genes related to hormone biosynthesis and signaling during endosperm development,especially at early devel-opmental stages.Liquid chromatography measure-ments confirmed the dynamic accumulation of hor-mones in developing endosperm.Further transgenic analysis performed on plants expressing hormone bio-synthesis genes driven by an endosperm-specific pro-moter revealed differential effects of the hormones,especially auxin and brassinosteroids,in regulating grain shape and quality.Our studies help elucidate the dis-tinct roles of hormones in developing endosperm and provide novel and useful tools for influencing crop seed shape and yield.

关键词： fir grain shape

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青藏高原植被结构变化反映环境变迁

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Science Bulletin 2023年第17期68卷 1928-1937页

作者：王艳芬薛凯胡容海丁柏阳曾弘李瑞津徐斌庞哲宋小宁李聪佳杜剑卿杨秀春张泽林郝彦宾崔骁勇郭柯高清竹张扬建朱军涛孙建李耀明姜丽丽周华坤罗彩云张振华高庆波陈世龙纪宝明徐兴良陈槐李奇赵亮徐世晓刘雅莉胡林勇武建双杨其恩董世魁贺金生赵新全汪诗平朴世龙于贵瑞傅伯杰 College of Resources and Environment University of Chinese Academy of SciencesBeijing 100049China Beijing Yanshan Earth Critical Zone National research Station University of Chinese Academy of SciencesBeijing 101408China State Key laboratory of Tibetan Plateau Earth System Environment and ResourcesInstitute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China State Key laboratory of Plateau Ecology and Agriculture Qinghai UniversityXining 810016China Key laboratory of Adaptation and Evolution of Plateau Biota Northwest Institute of Plateau BiologyChinese Academy of SciencesXining 810001China Binzhou institute of Technology Weiqiao-UCAS Science and Technology ParkBinzhou 256606China College of Mining Engineering North China University of Science and TechnologyTangshan 063210China Key laboratory of Agri-Informatics Ministry of Agriculture and Rural AffairsInstitute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijing 100081China College of life sciences University of Chinese Academy of SciencesBeijing 100049China School of Grassland Science Beijing Forestry UniversityBeijing 100083China State Key laboratory of Vegetation and Environmental Change Institute of BotanyChinese Academy of SciencesBeijing 100093China institute of Environment and Sustainable development in Agriculture Chinese Academy of Agricultural SciencesBeijing 100081China Key laboratory for Agro-Environment&Climate Change Ministry of AgricultureBeijing 100081China Key laboratory of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and Natural Resources ResearchChinese Academy of SciencesBeijing 100101China Key laboratory of Mountain Ecological Restoration and Bioresource Utilization&Ecological Restoration Biodiversity Conservation Key laboratory of Sichuan Province Chengdu Institute of BiologyChinese Academy of SciencesChengdu 610041China Zoige Peatland and Global Change research Station Chinese Academy of SciencesHongyuan 62

草地植被结构对于其生产和生态功能至关重要,但大尺度信息严重匮乏.本研究结合多源遥感数据和深度学习,在区域尺度上厘清了青藏高原高寒草地基于群系的植物群落结构空间格局,并比较了其历史变化.过去40年,高寒草甸在高寒草地中的比例从... 详细信息

草地植被结构对于其生产和生态功能至关重要,但大尺度信息严重匮乏.本研究结合多源遥感数据和深度学习,在区域尺度上厘清了青藏高原高寒草地基于群系的植物群落结构空间格局,并比较了其历史变化.过去40年,高寒草甸在高寒草地中的比例从50%上升到69%,反映了变暖变湿的环境变化.此外,高寒草甸和高寒草原中高山嵩草草甸和紫花针茅草原的优势度分别增强到76%和92%.其中,气候因子驱动了紫花针茅草原近些年的分布;高山嵩草草甸近些年的分布则并非完全由气候驱动,人类活动可能起重要作用.本研究首次探索了区域尺度植被结构特征与历史变化,为认识青藏高原草地变化的驱动力及其空间异质性提供了新视角.

关键词：高寒草地植被结构草地植被多源遥感数据深度学习植物群落结构区域尺度高寒草原

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