Genome-wide comparison of AP2/ERF superfamily genes between Gossypium arboreum and G. raimondii

Abstract

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.

Regulation of Apetala2/Ethylene Response Factors in Plants

“…AP2/ERFs are mainly plant-specific TFs with 122 and 139 ERF family genes in Arabidopsis and rice respectively, although it has been speculated that they might have been descended from non-plant organisms (Nakano et al, 2006 ). Number of AP2/ERFs present in different plants are: Triticum spp.- 117 (Zhuang et al, 2011 ), Populus spp.- 200 (Zhuang et al, 2008 ), Brassica spp.- 291 (Song et al, 2013 , 2016 ), Vitis spp.- 149 (Ito et al, 2014 ), Citrus spp.- 108 (Licausi et al, 2010 ), Solanum spp.- 155 (Charfeddine et al, 2015 ), Phyllostachys spp.- 116 (Wu et al, 2015 ), Daucus spp.- 267 (Li et al, 2015 ), Eucalyptus spp.- 209 (Cao et al, 2015 ), Salix spp.- 173 (Rao et al, 2015 ), Cassava spp.- 147 (Fan et al, 2016 ), Barley spp.- 121 (Guo et al, 2016 ) Gossypium spp.- 271 (Lei et al, 2016 ) and Bamboo spp.- 142 (Huang Z. et al, 2016 ). His and Asn rich HNH class of homing endonucleases from Tetrahymena thermophile (Eukaryote ciliate), Trichodesmium erythraeum (cyanobacterium), Enterobacteria phage RB49 (virus), and Bacteriophage Felix 01 (Virus) are reported to have an AP2 domain (Magnani et al, 2004 ; Wuitschick et al, 2004 ).…”

Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum

“…Transcription factors play a significant role in plant growth and development, secondary metabolism, organ morphogenesis and resistance against different stresses in cotton [ 58 – 60 ]. Several previous reports computed genome-wide analysis of TF-related genes in different cotton species and compared their physical location on different chromosomes [ 61 – 64 ]. In current study, distribution of TF-related genes showed that homologous chromosomes of G. raimondii (D_D08) and G. arboreum (A_A12) contained almost similar number of TF genes with minimum deviation, and they had good collinear relationship with each other.…”

Transcriptome-Wide Identification, Classification, and Characterization of AP2/ERF Family Genes in the Desert Moss Syntrichia caninervis

“…AP2/ERF classification employs a well-established nomenclature established in Arabidopsis and rice ( Nakano et al, 2006 ) and this nomenclature has been used to classify the AP2/ERF family genes in other plant species ( Mizoi et al, 2012 ; Song et al, 2013 ). Advancements in sequencing technology and the availability of large datasets has aided the identification of AP2/ERF family genes in several plant species using both genomic, transcriptomic or EST data ( Licausi et al, 2010 ; Duan et al, 2013 ; Zhuang and Zhu, 2014 ; Wu et al, 2015 ; Lei et al, 2016 ). In the model moss P. patens AP2/ERFs were demonstrated to be regulated in response to salinity, UV and other stresses indicating that AP2/ERF transcriptional factors also play a central regulatory role during stress response in moss species ( Hiss et al, 2014 ).…”

“…DREB family genes have been documented to respond to drought, desiccation, osmotic stress, salt, low temperature (cold) and elevated temperature (heat) and are candidate genes for improving plant stress tolerance in crop plants ( Lata and Prasad, 2011 ). The genome-wide identification of the AP2/ERF gene family has been accomplished in a number of plant species including Arabidopsis ( Czechowski et al, 2005 ), rice ( Narsai et al, 2010 ), poplar ( Zhuang et al, 2008 ), grape ( Licausi et al, 2010 ), soybean ( Zhang et al, 2008 ), castor bean ( Xu et al, 2013 ), cotton ( Lei et al, 2016 ), lotus ( Sun et al, 2014 ), Chinese cabbage ( Song et al, 2013 ), Medicago truncatula ( Shu et al, 2015 ), and Musa species ( Lakhwani et al, 2016 ). Using transcriptome and EST data, AP2/ERF superfamily genes has been analyzed in Brassica ssp.…”