Genome-Wide Identification, Phylogeny, Evolution and Expression Patterns of AP2/ERF Genes and Cytokinin Response Factors in Brassica rapa ssp. pekinensis

Abstract

The AP2/ERF transcription factor family is one of the largest families involved in growth and development, hormone responses, and biotic or abiotic stress responses in plants. In this study, 281 AP2/ERF transcription factor unigenes were identified in Chinese cabbage. These superfamily members were classified into three families (AP2, ERF, and RAV). The ERF family was subdivided into the DREB subfamily and the ERF subfamily with 13 groups (I– XI) based on sequence similarity. Duplication, evolution and divergence of the AP2/ERF genes in B. rapa and Arabidopsis thaliana were investigated and estimated. Cytokinin response factors (CRFs), as a subclade of the AP2/ERF family, are important transcription factors that define a branch point in the cytokinin two-component signal (TCS) transduction pathway. Up to 21 CRFs with a conserved CRF domain were retrieved and designated as BrCRFs. The amino acid sequences, conserved regions and motifs, phylogenetic relationships, and promoter regions of the 21 BrCRFs were analyzed in detail. The BrCRFs broadly expressed in various tissues and organs. The transcripts of BrCRFs were regulated by factors such as drought, high salinity, and exogenous 6-BA, NAA, and ABA, suggesting their involvement in abiotic stress conditions and regulatory mechanisms of plant hormone homeostasis. These results provide new insight into the divergence, variation, and evolution of AP2/ERF genes at the genome-level in Chinese cabbage.

Genome Triplication Drove the Diversification of Brassica Plants

“…rapa genes belonging to different gene families or having important biological functions have been systematically analyzed. Based on the genome sequencing and comparative genomic study of B. rapa, the evolution of many gene families or categories such as circadian clock genes, 41 resistance genes, 42 stress response genes, [43][44][45] glucosinolate genes, 38 anthocyanin biosynthesis genes, 46 phytohormone-related genes, 47 certain transcript factor families 48 and other genes, [49][50][51][52][53][54] were accurately determined individually and studied in detail. Moreover, some functionally important genes related to self-incompatibility, 55,56 male sterility, 57 flowering regulation, 58-60 leaf heading 61 or color 62 have been identified or cloned, and functional studies have been conducted for some of these genes.…”

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

“…Most notably, Cotton_A_11454 and Cotton_A_17367, as previously mentioned, encode double-AP2/ERF domains, but clustered with subfamilies V and Xb-L in the ERF family, which usually contain genes with single-AP2/ERF domain. Liu et al (2013) also reported this discordance with Bra034249 in B. rapa, but grouped it into the AP2_2 subfamily, which contains exclusively double-AP2/ERF domains. We feel that this finding (Liu et al, 2013) is not totally convincing.…”

“…Liu et al (2013) also reported this discordance with Bra034249 in B. rapa, but grouped it into the AP2_2 subfamily, which contains exclusively double-AP2/ERF domains. We feel that this finding (Liu et al, 2013) is not totally convincing. Alternatively, according to the classification of Sakuma et al (2002), genes in the ERF family identified in the present study were classified into two subfamilies consisting of 163 DREB (subfamily I-IV) and 286 ERF (subfamily V-X) genes.…”

“…This indicates that the diversity of whole sequences is mainly in concert with their functional segments (i.e., the AP2/ERF domain region). On the other hand, for a relatively small number of the genes investigated, further categorization into groups (based on a phylogenetic analysis of full-length protein sequences) is not completely consistent with the relationship of functional segments (based on At = Arabidopsis thaliana (Nakano et al, 2006), Br = Brassica rapa ssp pekinensis (Liu et al 2013), Cs = Citrus sinensis (Xie et al, 2014), Ga = Gossypium arboreum, Gr = Gossypium raimondii, Os = Oryza sativa (Nakano et al, 2006), Pp = Prunus persica (Zhang et al, 2012), Pt = Populus trichocarpa (Zhuang et al, 2008), Tc = Theobroma cacao, Vv = Vitis vinifera (Licausi et al, 2010).…”

“…For instance, numerous arrays of AP2/ERF genes have been identified in the following commercially important species: 147 in A. thaliana (Nakano et al, 2006), 180 in Oryza sativa (Sharoni et al, 2011), 202 in Populus trichocarpa (Zhuang et al, 2008), 126 in Citrus sinensis and C. clementine (Xie et al, 2014), 131 in Prunus persica (Zhang et al, 2012), 281 in Brassica rapa ssp pekinensis (Liu et al, 2013), and 149 in Vitis vinifera (Licausi et al, 2010).…”