Genome-wide identi cation and expression patterns analysis of the RPD3/HDA1 gene family in cotton

Jingjing Zhang Chinese Academy of Agricultural Sciences Cotton Research Institute Aimin Wu Chinese Academy of Agricultural Sciences Cotton Research Institute Hengling Wei Chinese Academy of Agricultural Sciences Cotton Research Institute Pengbo Hao Chinese Academy of Agricultural Sciences Cotton Research Institute Qi Zhang Chinese Academy of Agricultural Sciences Cotton Research Institute Miaomiao Tian Chinese Academy of Agricultural Sciences Cotton Research Institute Xu Yang Chinese Academy of Agricultural Sciences Cotton Research Institute Shuaishuai Cheng Chinese Academy of Agricultural Sciences Cotton Research Institute Xiaokang Fu Chinese Academy of Agricultural Sciences Cotton Research Institute Liang Ma Chinese Academy of Agricultural Sciences Cotton Research Institute Hantao Wang (  w.wanghantao@163.com ) Chinese Academy of Agricultural Sciences Cotton Research Institute Shuxun Yu (  ysx195311@163.com ) Chinese Academy of Agricultural Sciences Cotton Research Institute https://orcid.org/0000-00029715-3462

[1]  Peer Bork,et al.  SMART: recent updates, new developments and status in 2020 , 2020, Nucleic Acids Res..

[2]  Shuxun Yu,et al.  High‐resolution temporal dynamic transcriptome landscape reveals a GhCAL‐mediated flowering regulatory pathway in cotton (Gossypium hirsutum L.) , 2020, Plant biotechnology journal.

[3]  Shuxun Yu,et al.  Genome-Wide Identification and Characterization of Glycosyltransferase Family 47 in Cotton , 2019, Front. Genet..

[4]  Penghui Zhao,et al.  Comprehensive analyses of ZFP gene family and characterization of expression profiles during plant hormone response in cotton , 2019, BMC Plant Biology.

[5]  Simon C. Potter,et al.  The EMBL-EBI search and sequence analysis tools APIs in 2019 , 2019, Nucleic Acids Res..

[6]  Tianzhen Zhang,et al.  Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton , 2019, Nature Genetics.

[7]  Hongkun Zheng,et al.  Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense , 2018, Nature Genetics.

[8]  Silvio C. E. Tosatto,et al.  The Pfam protein families database in 2019 , 2018, Nucleic Acids Res..

[9]  K. M. Rai,et al.  Role of GhHDA5 in H3K9 deacetylation and fiber initiation in Gossypium hirsutum , 2018, The Plant journal : for cell and molecular biology.

[10]  Wei Fan,et al.  Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits , 2018, Nature Genetics.

[11]  Shouzhou Zhang,et al.  Transcriptomic Analysis of Flower Bud Differentiation in Magnolia sinostellata , 2018, Genes.

[12]  Chengjie Chen,et al.  TBtools, a Toolkit for Biologists integrating various HTS-data handling tools with a user-friendly interface , 2018, bioRxiv.

[13]  Sandui Guo,et al.  CottonFGD: an integrated functional genomics database for cotton , 2017, BMC Plant Biology.

[14]  Y. Hao,et al.  Histone deacetylase HDA6 enhances brassinosteroid signaling by inhibiting the BIN2 kinase , 2016, Proceedings of the National Academy of Sciences.

[15]  K. Hnatuszko-Konka,et al.  Cis-regulatory elements used to control gene expression in plants , 2016, Plant Cell, Tissue and Organ Culture (PCTOC).

[16]  F. Thibaud-Nissen,et al.  Araport11: a complete reannotation of the Arabidopsis thaliana reference genome , 2016, bioRxiv.

[17]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[18]  Xuncheng Liu,et al.  Involvement of rice histone deacetylase HDA705 in seed germination and in response to ABA and abiotic stresses. , 2016, Biochemical and biophysical research communications.

[19]  C. P. Yang,et al.  Characterization and expression analysis of histone deacetylases family RPD3/HDA1 in Populus trichocarpa , 2016, Biologia Plantarum.

[20]  Keqiang Wu,et al.  Regulation of flowering time by the histone deacetylase HDA5 in Arabidopsis. , 2015, The Plant journal : for cell and molecular biology.

[21]  William Stafford Noble,et al.  The MEME Suite , 2015, Nucleic Acids Res..

[22]  Lei Fang,et al.  Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement , 2015, Nature Biotechnology.

[23]  He Zhang,et al.  Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution , 2015, Nature Biotechnology.

[24]  Bo Hu,et al.  GSDS 2.0: an upgraded gene feature visualization server , 2014, Bioinform..

[25]  Yu Xue,et al.  HemI: A Toolkit for Illustrating Heatmaps , 2014, PloS one.

[26]  Zhi Wang,et al.  The roles of histone acetylation in seed performance and plant development. , 2014, Plant physiology and biochemistry : PPB.

[27]  Peer Bork,et al.  SMART: recent updates, new developments and status in 2015 , 2014, Nucleic Acids Res..

[28]  Xuncheng Liu,et al.  Transcriptional repression by histone deacetylases in plants. , 2014, Molecular plant.

[29]  Yingkao Hu,et al.  Soybean (Glycine max) expansin gene superfamily origins: segmental and tandem duplication events followed by divergent selection among subfamilies , 2014, BMC Plant Biology.

[30]  Pasquale Termolino,et al.  Histone Deacetylase AtHDA7 Is Required for Female Gametophyte and Embryo Development in Arabidopsis1[C][W][OPEN] , 2013, Plant Physiology.

[31]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[32]  Daoxiu Zhou,et al.  Arabidopsis histone deacetylase HDA9 regulates flowering time through repression of AGL19. , 2013, Biochemical and biophysical research communications.

[33]  Chuanping Yang,et al.  Histone deacetylases and their functions in plants , 2013, Plant Cell Reports.

[34]  Xujun Ma,et al.  Histone deacetylases and their functions in plants , 2013, Plant Cell Reports.

[35]  D. E. Somers,et al.  Transcriptional corepressor TOPLESS complexes with pseudoresponse regulator proteins and histone deacetylases to regulate circadian transcription , 2012, Proceedings of the National Academy of Sciences.

[36]  Justin T. Page,et al.  Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres , 2012, Nature.

[37]  J. Long,et al.  APETALA2 negatively regulates multiple floral organ identity genes in Arabidopsis by recruiting the co-repressor TOPLESS and the histone deacetylase HDA19 , 2012, Development.

[38]  Jeremy D. DeBarry,et al.  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.

[39]  David M. Goodstein,et al.  Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..

[40]  Robert D. Finn,et al.  HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..

[41]  Andrew J. Bannister,et al.  Regulation of chromatin by histone modifications , 2011, Cell Research.

[42]  Keqiang Wu,et al.  Role of histone deacetylases HDA6 and HDA19 in ABA and abiotic stress response , 2010, Plant signaling & behavior.

[43]  Keqiang Wu,et al.  Involvement of Arabidopsis histone deacetylase HDA6 in ABA and salt stress response , 2010, Journal of experimental botany.

[44]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[45]  Yu Zhao,et al.  Rice histone deacetylase genes display specific expression patterns and developmental functions. , 2009, Biochemical and biophysical research communications.

[46]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[47]  Keqiang Wu,et al.  Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants , 2009, BMC Plant Biology.

[48]  Zhongchi Liu,et al.  Histone deacetylase genes in Arabidopsis development. , 2008, Journal of integrative plant biology.

[49]  Keqiang Wu,et al.  HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. , 2008, Journal of experimental botany.

[50]  Lili Tu,et al.  Suitable internal control genes for qRT-PCR normalization in cotton fiber development and somatic embryogenesis , 2007 .

[51]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[52]  E. Seto,et al.  HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention , 2007, Oncogene.

[53]  Keqiang Wu,et al.  Sequence and expression analysis of histone deacetylases in rice. , 2007, Biochemical and biophysical research communications.

[54]  Z. Chen,et al.  Roles of dynamic and reversible histone acetylation in plant development and polyploidy. , 2007, Biochimica et biophysica acta.

[55]  Wilfred W. Li,et al.  MEME: discovering and analyzing DNA and protein sequence motifs , 2006, Nucleic Acids Res..

[56]  Keqiang Wu,et al.  HISTONE DEACETYLASE19 Is Involved in Jasmonic Acid and Ethylene Signaling of Pathogen Response in Arabidopsis , 2005, The Plant Cell Online.

[57]  Paul R. Ebert,et al.  Antagonistic Interaction between Abscisic Acid and Jasmonate-Ethylene Signaling Pathways Modulates Defense Gene Expression and Disease Resistance in Arabidopsis , 2004, The Plant Cell Online.

[58]  Steven B Cannon,et al.  The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana , 2004, BMC Plant Biology.

[59]  Z. Chen,et al.  Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (AtHD1) expression. , 2003, Genetics.

[60]  L. Hennig,et al.  Chromatin-Remodeling and Memory Factors. New Regulators of Plant Development , 2002, Plant Physiology.

[61]  L. Hurst The Ka/Ks ratio: diagnosing the form of sequence evolution. , 2002, Trends in genetics : TIG.

[62]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[63]  J. Turner,et al.  The Arabidopsis Mutant cev1 Has Constitutively Active Jasmonate and Ethylene Signal Pathways and Enhanced Resistance to Pathogens , 2001, Plant Cell.

[64]  Z. Chen,et al.  Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[65]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[66]  A. Bird,et al.  Histone deacetylases: silencers for hire. , 2000, Trends in biochemical sciences.

[67]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[68]  M. Grunstein Histone acetylation in chromatin structure and transcription , 1997, Nature.

[69]  L. L. Ray,et al.  Morphological Measures of Earliness of Crop Maturity in Cotton 1 , 1966 .

[70]  W. Sung,et al.  Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines , 2005 .

[71]  Kathleen Marchal,et al.  PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences , 2002, Nucleic Acids Res..