title: Analyses of the NAC transcription factor gene family in Gossypium raimondii Ulbr.: chromosomal location, structure, phylogeny, and expression patterns.
abstract: NAC domain proteins are plant-specific transcription factors known to play diverse roles in various plant developmental processes. In the present study, we performed the first comprehensive study of the NAC gene family in Gossypium raimondii Ulbr., incorporating phylogenetic, chromosomal location, gene structure, conserved motif, and expression profiling analyses. We identified 145 NAC transcription factor (NAC-TF) genes that were phylogenetically clustered into 18 distinct subfamilies. Of these, 127 NAC-TF genes were distributed across the 13 chromosomes, 80 (55%) were preferentially retained duplicates located in both duplicated regions and six were located in triplicated chromosomal regions. The majority of NAC-TF genes showed temporal-, spatial-, and tissue-specific expression patterns based on transcriptomic and qRT-PCR analyses. However, the expression patterns of several duplicate genes were partially redundant, suggesting the occurrence of sub-functionalization during their evolution. Based on their genomic organization, we concluded that genomic duplications contributed significantly to the expansion of the NAC-TF gene family in G. raimondii. Comprehensive analysis of their expression profiles could provide novel insights into the functional divergence among members of the NAC gene family in G. raimondii.
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research, the Chinese Academy of Agricultural Sciences, Anyang, 455004, China.
authors.forename: Haihong
authors.initials: H
authors.lastname: Shang
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Changsong
authors.initials: C
authors.lastname: Zou
authors.forename: Youlu
authors.initials: Y
authors.lastname: Yuan
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D002099:Cacao / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D003198:Computer Simulation; D017124:Conserved Sequence / Q000235:genetics; D020224:Expressed Sequence Tags; D020440:Gene Duplication / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D003368:Gossypium / Q000235:genetics*; D005810:Multigene Family; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D060888:Real-Time Polymerase Chain Reaction; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D014157:Transcription Factors
keywords: Cotton; NAC; expression patterns; phylogeny; structure