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Identification and characterization of rice blast resistance gene Pid4 by a combination of transcriptomic profiling and genome analysis

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Journal of Genetics and genomics 2018年第12期45卷 663-672页

作者： Zhixiong Chen wen Zhao Xiaobo Zhu Chengdong Zou Junjie Yin mawsheng Chern Xiaogang Zhou Heng Ying Xin Jiang Yongzhen Li Haicheng Liao mengping Cheng weitao Li min He Jing wang Jichun wang Bingtian ma Jirui wang Shigui Li Lihuang Zhu Xuewei Chen State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control State Key Laboratory of Hybrid RiceKey Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River BasinRice Research InstituteSichuan Agricultural UniversitySichuan 611130 China Department of Plant Pathology University of CaliforniaDavisCA 95616USA Triticeae Research Institute.Sichuan Agricultural University Sichuan 611130China State Key Laboratory of Plant genomics National Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology，Chinese Academy of SciencesBeijing 100101China

map-based cloning of plant disease resistance (R) genes is time-consuming. Here, we reported the isolation of blast R gene Pid4 using comparative transcriptomic profiling and genome-wide sequence analysis. Pid4 encodes a coiled-coil nucleotide-binding site leucine-rich repeat(CC-NBS-LRR) protein and is constitutively expressed at diverse developmental stages in the rice variety Digu. The Pid4 protein is localized in both the nucleus and cytoplasm. Introduction of Pid4 into susceptible rice cultivars confers race-specific resistance to leaf and neck blast. Amino acid sequence comparison and blast resistance spectrum tests showed that Pid4 is a novel R gene, different from the previously reported R genes located in the same gene cluster. A Pid4 Indel marker was developed to facilitate the identification of Pid4 in different rice varieties. we demonstrated that a plant R gene can be quickly isolated using transcriptomic profiling coupled with genome-wide sequence analysis.

关键词： Blast disease Genome-wide sequence analysis Resistance Rice Transcriptome

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Transcriptome Analysis of Ten-DPA Fiber in an Upland Cotton (<i>Gossypium hirsutum</i>) Line with Improved Fiber Traits from Phytochrome A1 RNAi Plants

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American Journal of Plant Sciences 2017年第10期8卷 2530-2553页

作者： Qing miao Peng Deng Sukumar Saha Johnie N. Jenkins Chuan-Yu Hsu Ibrokhim Y. Abdurakhmonov Zabardast T. Buriev Alan Pepper Din-Pow.m. Department of Biochemistry Molecular Biology Entomology and Plant Pathology Mississippi State University Mississippi State MS USA Department of Pharmacology Weill Cornell Medical College New York NY USA USDA-ARS Crop Science Research Laboratory Mississippi State MS USA Institute for genomics Biocomputing and Biotechnology Mississippi State University Mississippi State MS USA center of genomics and Bioinformatics Academy of Sciences of Uzbekistan Tashkent Uzbekistan Department of Biology Texas A & M University College Station TX USA

Silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium hirsutum L. cv. Coker 312) had generated PHYA1 RNAi lines with improved fiber quality (longer, stronger and finer fiber). To reveal molecular mechanisms that govern fiber development with positive fiber traits, a study of global gene expression profiling of 10-DPA fibers in a PHYA1 RNAi line and its parent Coker 312 was conducted by high-throughput RNA sequencing. A comparative analysis of transcriptomes between the two lines had identified 142 genes that were differentially expressed in the 10-DPA fiber of the RNAi line. Gene Ontology analysis showed that these differentially expressed genes were mainly involved in metabolic pathways, heterocyclic/organic cyclic compound binding and multiple enzyme activities, and cell structures which were reported to play important roles in fiber development. Twenty-eight KEGG pathways were mapped for the 142 genes, and the pathways related to glycolysis/gluconeogenesis and pyruvate metabolism were the most abundant and followed by cytochrome P450-involved pathways, suggesting that fiber improvement could be through the regulation of proteins involved in cytochrome P450 pathways. Genes encoding wRKY transcription factors, sucrose synthase, xyloglucan endotransglucosylase hydrolase, udp-glucuronate: xylan alpha-glucuronosyltransferase, and genes involved in lipid metabolism and ABA/brassinosteroid signal transduction pathways were found differentially expressed in the RNAi line. These genes have direct impacts on cotton fiber quality. The results of this study elucidate molecular signatures and possible mechanisms of fiber improvement in the background of PHYA1 RNAi in cotton and should help for future fine-tuning and programming of cotton fiber development.

关键词： Fiber Development Phytochrome A1 RNA Interference RNA-Seq Transcriptome

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Confirmation of Pearl millet-Napiergrass Hybrids Using EST-Derived Simple Sequence Repeat (SSR) markers

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American Journal of Plant Sciences 2013年第5期4卷 1004-1012页

作者： Charlie D. Dowling Byron L. Burson Jamie L. Foster Lee Tarpley Russell w. Jessup Department of Soil and Crop Sciences Texas A&M University College Station USA Department of Soil and Crop Sciences Texas A&M University College Station USA Texas A&m Agricultural Research and Extension center Texas A&M AgriLife Beaumont USA. Texas A&m Agricultural Research center Texas A&M AgriLife Beeville USA USDA-ARS Crop Germplasm Research Unit Texas A&M University College Station USA

Prospects for deploying perennial grasses that are currently considered leading candidates for dedicated energy crops over large acreages are debatable because of several limitations, including vegetative propagation or small seed size, low biomass production during the first growing season, and incomplete assessments of crop invasiveness risk. Pearl millet-Napiergrass hybrids (“PmN”;Pennisetum glaucum [L.] R. Br. × P. purpureum Schumach.), in contrast, are large-seeded, sterile feedstocks capable of high biomass production during establishment year. Novel methods are warranted for confirmation of PmN hybrids, as traditional morphological observations can be inconclusive and chromosome number determination using cytological methods is laborious and time consuming. Six putative PmN lines were produced in this study, and 10 progeny from each line were evaluated using morphological traits, seed fertility, flow cytometry, and expressed sequence tag-simple sequence repeat (EST-SSR) markers. All putative hybrid lines were sterile and failed to produce seed. The PmN hybrids could not be distinguished from either parent using flow cytometry due to highly similar nuclear genome DNA contents. A number of paternal napiergrass-specific EST-SSRs were identified for each PmN line, and four paternal-specific EST-SSRs conserved across all napiergrass accessions were selected to screen the putative PmN hybrids. These EST-SSRs confirmed that all F1 individuals analyzed were PmN hybrids. The use of paternal-specific markers therefore provides a valuable tool in the development of both “Seeded-yet-Sterile” biofuel PmN feedstocks and additional PmN cultivar-and parental species-specific markers.

关键词： Pennisetum glaucum Pennisetum purpureum Bulked Segregant Analysis marker-Assisted Selection marker-Assisted Breeding EST-SSR Expressed Sequence Tag Simple Sequence Repeat microsatellites Biofuel Biofuels Pearl millet × Napiergrass Pearl millet Napiergrass Interspecific Hybrid PCR Polymerase Chain Reaction comparative genomics

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软件预测和mAST技术筛选mRNA反义核酸靶点的比较

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中国生物化学与分子生物学报 2004年第3期20卷 399-407页

作者：毛建平 Zicai LIANG 毛秉智军事医学科学院放射医学研究所北京100850 center for genomics and Bioinformatics Karolinska InstitutetStockholm 17177瑞典

基因mRNA的结构靶点筛选是反义核酸药物研发的一个难题 .兔 (Oryctolaguscuniculus) β珠蛋白基因mRNA的结构靶位点通过运用mAST技术筛选获得 ,和计算机软件RNAstructure3 71模拟分析的位点进行了比较 ,也和寡核苷酸微阵列杂交技术筛选... 详细信息

基因mRNA的结构靶点筛选是反义核酸药物研发的一个难题 .兔 (Oryctolaguscuniculus) β珠蛋白基因mRNA的结构靶位点通过运用mAST技术筛选获得 ,和计算机软件RNAstructure3 71模拟分析的位点进行了比较 ,也和寡核苷酸微阵列杂交技术筛选获得的靶点结果 (m .Natalie ,1 997)进行了比较 ,显示 :据mAST技术获得的兔 β珠蛋白基因 2个反义核酸结合靶位点 ,和用RNAstructure3 71软件给出的模拟分析的 2个靶位点相同 ,且它们与寡核苷酸微阵列杂交技术的结果完全一致 .运用mAST技术筛选获得绿色荧光蛋白 (GFP)mRNA有 4个结构靶位点 ,体外分析表明这 4个靶位点均有效 ,其中有 3个与RNAstructure3 71软件分析的靶点相同 ,但计算机模拟推荐的结构靶位点较多 ,而且随着基因长度增加确认靶位点的难度增大 ,获得的靶位点还需要实验验证 ,计算机软件模拟分析对实验筛选靶点、设计反义核酸有辅助价值 .mAST方法能筛选各种长度基因mRNA的全部可及位点和准确给定核苷酸的起止位置以供设计反义核酸 ,具有简单快捷的优点 ,将能为反义核酸设计起重要作用 .

关键词： mRNA RNAstructure3.71 mAST β珠蛋白 GFP 可及位点反义核酸

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This work was supported by the European Research Council Advanced Grant(ETAP-742985 to *** J.F.)and by the ministry of Science and Technology(grant 110-2636-B-005-001 to K.-J.L.).

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Plant Communications 2024年第1期5卷 130-147页

作者： Yu Zhang Yuan Fu wenfei Xian Xiuli Li Yong Feng Fengjiao Bu Yan Shi Shiyu Chen Robin van Velzen Kai Battenberg Alison m.Berry marco G.Salgado Hui Liu Tingshuang Yi Pascale Fournier Nicole Alloisio Petar Pujic Hasna Boubakri m.Eric Schranz Pierre-marc Delaux Gane Ka-Shu wong Valerie Hocher Sergio Svistoonoff Hassen Gherbi Ertao wang wouter Kohlen Luis G.wall martin Parniske Katharina Pawlowski Philippe Normand Jeffrey J.Doyle Shifeng Cheng Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China Biosystematics Group Department of Plant SciencesWageningen University6708PB Wageningenthe Netherlands Department of Plant Sciences University of CaliforniaDavisDavisCA 95616USA Department of Ecology Environment and Plant SciencesStockholm University10691 StockholmSweden Germplasm Bank of wild Species Kunming Institute of BotanyChinese Academy of SciencesLanhei RoadKunming 650201China Universite´de Lyon Universite´Lyon 1CNRSUMR5557Ecologie MicrobienneINRAUMR 141843 bd du 11 novembre 191869622 VilleurbanneFrance Laboratoire de Recherche en Sciences Ve´ge´tales(LRSV) Universite´de ToulouseCNRSUPS24 chemin de Borde RougeAuzevilleBP4261731326 Castanet TolosanFrance Department of Biological Sciences University of AlbertaEdmontonAB T6G 2E9Canada French National Research Institute for Sustainable Development(IRD) UMR LSTM(IRD/CIRAD/INRAe/Montpellier University/Supagro)-Campus International BaillarguetTA A-82/J34398 Montpellier Cedex 5France National Key Laboratory of Plant molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologySIBSChinese Academy of SciencesShanghaiChina Laboratory of molecular Biology Department of Plant SciencesWageningen University6708PB Wageningenthe Netherlands Laboratory of Biochemistry Microbiology and Soil Biological InteractionsDepartment of Science and TechnologyNational University of QuilmesCONICETBernalArgentina Faculty of Biology GeneticsLMU MunichGroßhaderner Strasse 2-482152 MartinsriedGermany School of Integrative Plant Science Sections of Plant Biology and Plant Breeding&GeneticsCornell UniversityIthacaNY 14853USA State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China Univer

Plant root-nodule symbiosis(RNS)with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms,the Nitrogen-Fixing Nodulation Clade(NFNC),and is best understood in the legume *** species share many commonalities,explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time ***,comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation—what must be acquired or cannot be lost for a functional symbiosis—and the latitude for Plant Communications Genomic landscape of nodulation variation in the ***,much remains to be learned about nodulation,especially outside of ***,we employed a large-scale phylogenomic analysis across 88 species,complemented by 151 RNA-seq libraries,to elucidate the evolution of *** phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key muta-tions that affect its function across the *** transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants,while also identifying nodule-specific and nitrogen-response *** 70%of symbiosis-related genes are highly conserved in the four representative species,whereas defense-related and host-range restriction genes tend to be lineage *** study also identified over 900000 conserved non-coding elements(CNEs),over 300000 of which are unique to sampled NFNC ***-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions,thus representing a pool of candidate regula-tory elements for genes involved in ***,our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.

关键词： nitrogen-fixing root-nodule symbiosis two competing hypotheses phylogenomics phylotranscrip-tomics conserved non-coding elements convergence deep homology

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Infectious diseases detection by microarray: An overview of clinical relevant infections

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Journal of Biomedical Science and Engineering 2013年第10期6卷 1006-1013页

作者： Sara Elisa Herrera-Rodriguez Darwin Elizondo-Quiroga Ikuri Alvarez-maya Department of medical and Pharmaceutical Biotechnology Center for Research and Assistance in Technology and Design in State of Jalisco (CIATEJ) Guadalajara México

microarray technology is a powerful tool to investigate whole genome expression profiles to study the crosstalk between pathogens and associated hosts that cause illness. microarrays have been used in several comparative genome hybridization studies of pathogens. In addition to detection and identification of pathogens, microarrays are ideal for characterizing genetic differences between bacteria isolates of the same species to the strain level. Furthermore, the use of microarrays has been gaining importance in the detection of viral agents. Here we explore the use of microarrays for simultaneous detection of viruses and modifications made over these techniques. microarray technology has also been incorporated to compensate for time-consuming sequencing. The procedure of fungi identification based on sequences and studies reported the use of microarrays to identify pathogenic yeasts and molds by targeting the internal transcribed spacer regions in fungal rRNA genes. The remarkable advancement in genomics over the last decade has made it possible for microarray technology to evolve towards being the best option for clinical diagnostics because they have several advantages.

关键词： DNA microarray Diagnosis Bacteria Virus Fungi

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comparative study of gut microbiota from captive and confiscatedrescued wild pangolins

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Journal of Genetics and genomics 2021年第9期48卷 825-835页

作者： Chunbing Liu Jingyang Hu Yajiang wu David m.Irwin wu Chen Zhigang Zhang Li Yu State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life SciencesYunnan UniversityKunming 650091China Guangzhou Zoo&Guangzhou wildlife Research center Guangzhou 510070China Department of Laboratory medicine and Pathobiology University of TorontoTorontoOntario M5S 1A8Canada

Pangolins are among the most critically endangered animals due to widespread poaching and worldwide trafficking. Captive breeding is considered to be one way to protect them and increase the sizes of their populations. However, comparative studies of captive and wild pangolins in the context of gut microbiota are rare. Here, the gut microbiome of captive and confiscated-rescued wild pangolins is compared, and the effects of different periods of captivity and captivity with and without antibiotic treatment are *** show that different diets and periods of captivity, as well as the application of antibiotic therapy, can alter gut community composition and abundance in pangolins. Compared to wild pangolins, captive pangolins have an increased capacity for chitin and cellulose/hemicellulose degradation, fatty acid metabolism, and short-chain fatty acid synthesis, but a reduced ability to metabolize exogenous substances. In addition to increasing the ability of the gut microbiota to metabolize nutrients in captivity, captive breeding imposes some risks for survival by resulting in a greater abundance of antibiotic resistance genes and virulence factors in captive pangolins than in wild pangolins. Our study is important for the development of guidelines for pangolin conservation, including health assessment, disease prevention, and rehabilitation of wild pangolin populations.

关键词： Pangolin Gut microbiome Captivity Antibiotic resistance genes Virulence factors

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PGD: Pineapple genomics Database

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Horticulture Research 2018年第1期5卷 276-284页

作者： Huimin Xu Qingyi Yu Yan Shi Xiuting Hua Haibao Tang Long Yang Ray ming Jisen Zhang center for genomics and Biotechnology Haixia Institute of Science and TechnologyFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry University350002FuzhouChina College of Resource and Environment Fujian Agriculture and Forestry University350002FuzhouChina Department of Plant Pathology and microbiology Texas A&M AgriLife ResearchTexas A&M University SystemDallasTX75252USA Agricultural Big-Data Research center and College of Plant Protection Shandong Agricultural University271018TaianChina Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL61801USA

Pineapple occupies an important phylogenetic position as its reference genome is a model for studying the evolution the Bromeliaceae family and the crassulacean acid metabolism(CAm)***,we developed a pineapple genomics database(PGD,http://***/pineapple/html/***)as a central online platform for storing and integrating genomic,transcriptomic,function annotation and genetic marker data for pineapple(Ananas comosus(L.)merr.).The PGD currently hosts significant search tools and available datasets for researchers to study comparative genomics,gene expression,gene co-expression molecular marker,and gene annotation of ***(L).PGD also performed a series of additional pages for a genomic browser that visualizes genomic data interactively,bulk data download,a detailed user manual,and data integration *** was developed with the capacity to integrate future data resources,and will be used as a long-term and open access database to facilitate the study of the biology,distribution,and the evolution of pineapple and the relative plant *** email-based helpdesk is also available to offer support with the website and requests of specific datasets from the research community.

关键词： database browser email

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Sex biased expression of hormone related genes at early stage of sex differentiation in papaya flowers

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Horticulture Research 2021年第1期8卷 2082-2094页

作者： Juan Liu Li-Yu Chen Ping Zhou Zhenyang Liao Hai Lin Qingyi Yu Ray ming FAFU and UIUC Joint center for genomics and Biotechnology Key Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyCollege of Life ScienceFujian Agriculture and Forestry UniversityFuzhou 350002 FujianChina Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Chinese Academy of SciencesWuhan Botanical GardenWuhan 430074China Texas A&m AgriLife Research center at Dallas Texas A&M University SystemDallasTX 75252USA Department of Plant Pathology&microbiology Texas A&M UniversityCollege StationTX 77843USA Department of Plant Biology School of Integrative BiologyUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA

Sex types of papaya are controlled by a pair of nascent sex chromosomes,but molecular genetic mechanisms of sex determination and sex differentiation in papaya are still *** performed comparative analysis of transcriptomic profiles of male and female floral buds at the early development stage before the initiation of reproductive organ primordia at which there is no morphological difference between male and female flowers.A total of 1734 differentially expressed genes(DEGs)were identified,of which 923 showed female-biased expression and 811 showed male-biased *** annotation revealed that genes related to plant hormone biosynthesis and signaling pathways,especially in abscisic acid and auxin pathways,were overrepresented in the *** factor binding motifs,such as mYB2,GAmYB,and AP2/EREBP,were enriched in the promoters of the hormone-related DEGs,and transcription factors with those motifs also exhibited differential expression between sex *** these DEGs,we also identified 11 genes in the non-recombining region of the papaya sex chromosomes and 9 genes involved in stamen and carpel *** results suggested that sex differentiation in papaya may be regulated by multiple layers of regulation and coordination and involved transcriptional,epigenetic,and phytohormone ***,especially ABA and auxin,transcription factors,and genes in the non-recombination region of the sex chromosome could be involved in this *** findings may facilitate the elucidation of signal transduction and gene interaction in sex differentiation of unisexual flowers in papaya.

关键词： expression flowers papaya

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Integrating Genomic and Transcriptomic Data to Reveal Genetic mechanisms Underlying Piao Chicken Rumpless Trait

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genomics, Proteomics & Bioinformatics 2021年第5期19卷 787-799页

作者： Yun-mei wang Saber Khederzadeh Shi-Rong Li Newton Otieno Otecko David m.Irwin mukesh Thakur Xiao-Die Ren ming-Shan wang Dong-Dong wu Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Kunming College of Life Science University of the Chinese Academy of SciencesKunming 650223China center for Neurobiology and Brain Restoration Skolkovo Institute of Science and TechnologyMoscow 143026Russia Department of Laboratory medicine and Pathobiology University of TorontoToronto M5S 1A8Canada Zoological Survey of India Kolkata 700053India

Piao chicken,a rare Chinese native poultry breed,lacks primary tail structures,such as pygostyle,caudal vertebra,uropygial gland,and tail *** far,the molecular mechanisms underlying tail absence in this breed remain *** this study,we comprehensively employed comparative transcriptomic and genomic analyses to unravel potential genetic underpinnings of rumplessness in Piao *** results reveal many biological factors involved in tail development and several genomic regions under strong positive selection in this *** regions contain candidate genes associated with rumplessness,including Irx4,Il18,Hspb2,and *** of quantitative trait loci(QTL)and gene functions implies that rumplessness might be consciously or unconsciously selected along with the high-yield traits in Piao *** hypothesize that strong selection pressures on regulatory elements might lead to changes in gene activity in mesenchymal stem cells of the tail *** ectopic activity could eventually result in tail truncation by impeding differentiation and proliferation of the stem *** study provides fundamental insights into early initiation and genetic basis of the rumpless phenotype in Piao chicken.

关键词： comparative transcriptomics Population genomics Rumplessness Vertebra development Artificial selection

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