Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers

Lifang Hu,Shiqiang Liu

doi:10.1590/s1415-47572011005000054

Abstract

Members of the ERF transcription-factor family participate in a number of biological processes, viz., responses to hormones, adaptation to biotic and abiotic stress, metabolism regulation, beneficial symbiotic interactions, cell differentiation and developmental processes. So far, no tissue-expression profile of any cucumber ERF protein has been reported in detail. Recent completion of the cucumber full-genome sequence has come to facilitate, not only genome-wide analysis of ERF family members in cucumbers themselves, but also a comparative analysis with those in Arabidopsis and rice. In this study, 103 hypothetical ERF family genes in the cucumber genome were identified, phylogenetic analysis indicating their classification into 10 groups, designated I to X. Motif analysis further indicated that most of the conserved motifs outside the AP2/ERF domain, are selectively distributed among the specific clades in the phylogenetic tree. From chromosomal localization and genome distribution analysis, it appears that tandem-duplication may have contributed to CsERF gene expansion. Intron/exon structure analysis indicated that a few CsERFs still conserved the former intron-position patterns existent in the common ancestor of monocots and eudicots. Expression analysis revealed the widespread distribution of the cucumber ERF gene family within plant tissues, thereby implying the probability of their performing various roles therein. Furthermore, members of some groups presented mutually similar expression patterns that might be related to their phylogenetic groups.

Highlights

The AP2/ERF superfamily, one of the largest groups of transcription factors in plants, is characterized by the presence of the AP2/ERF-type DNA-binding domain consisting of from 60 to 70 highly conserved amino acids (Wessler, 2005)
The ERF family is usually classified into two major subfamilies, CBF/DREB, and ERF, the latter based on the amino acid sequence of the DNA-binding domain
In order to identify the CsERF genes in cucumber genomes, the AP2/ERF domain of a cucumber ethylene response factor sequence (GenBank number AY792593) was used as BLAST query sequence. 131 genes were identified as possibly encoding proteins containing the AP2/ERF domain (Table 1)

Summary

Introduction

The AP2/ERF superfamily, one of the largest groups of transcription factors in plants, is characterized by the presence of the AP2/ERF-type DNA-binding domain consisting of from 60 to 70 highly conserved amino acids (Wessler, 2005). The analysis result showed that the 103 CsERF members were divided into 10 groups, designated I to X, in accordance with the Arabidopsis ERF gene family classification (Nakano et al, 2006).

Results

Conclusion