title: Genome-wide comparison of AP2/ERF superfamily genes between Gossypium arboreum and G. raimondii.
abstract: The APETALA2/ethylene response factor (AP2/ERF) transcription factor superfamily is known to regulate diverse processes of plant development and stress responses. We conducted a genome-wide analysis of the AP2/ERF gene in Gossypium arboreum and G. raimondii. Using RPSBLAST and HMMsearch, a total of 271 and 269 AP2/ERF genes were identified in the G. arboreum and G. raimondii genomes, respectively. A phylogenetic analysis classified diploid Gossypium spp AP2/ERF genes into 4 families and 16 subfamilies. Orthologous genes predominated the terminal branch of the phylogenetic tree. Physical mapping showed at least 30% of AP2/ERF genes clustered together. A high level of intra- and inter-species collinearity involving AP2/ERF genes was observed, indicating common (before species divergence) or parallel (after species divergence) segmental duplications, along with tandem duplications, resulting in the species-specific expansion of AP2/ERF genes in diploid Gossypium species. Motif analyses of the AP2/ERF proteins revealed that motif arrangements were highly diverse among subfamilies, but shared by orthologous gene pairs. An examination of nucleotide divergence of AP2/ERF coding regions identified small and non-significant sequence differences among orthologs. Expression profiling of AP2/ERF orthologous gene pairs showed similar abundance levels of orthologous copies between G. arboreum and G. raimondii. Thus, cotton species possess abundant and diverse AP2/ERF genes, resulting from tandem and segmental duplications. Protein and nucleotide sequence and mRNA expression analyses revealed symmetrical evolution, indicating that most AP2/ ERF genes may not have undergone significant biochemical and morphological divergence between sister species. Our study provides detailed insights into the evolutionary characteristics and functional importance of AP2/ERF genes, and could aid in the genetic improvement of agriculturally significant crops in this genus.
authors.affiliation: College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.|College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Z P
authors.initials: ZP
authors.lastname: Lei
authors.affiliation: College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China daohuahe@nwafu.edu.cn.
authors.forename: D H
authors.initials: DH
authors.lastname: He
authors.affiliation: College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: H Y
authors.initials: HY
authors.lastname: Xing
authors.affiliation: College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: B S
authors.initials: BS
authors.lastname: Tang
authors.affiliation: College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: B X
authors.initials: BX
authors.lastname: Lu
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant; D003368:Gossypium / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors