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

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.

Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica)

“…On the other hand, the highly conserved motif number and position among members in each HD-ZIP subfamily in peach also implies that they may have similar functions or a complex pattern of overlapping functions. As previously concluded, proteins within a subfamily that share motifs are likely to share similar functions (Hu and Liu, 2011). In Arabidopsis, the 5 members of HD-ZIP III show a close relationship in vascular development (Baima et al, 2001;McConnell et al, 2001;Ohashi-Ito et al, 2002;Zhong and Ye, 2004;Prigge et al, 2005).…”

“…It is widely accepted that the intron/exon position pattern provides clues to evolutionary relationships (Hu and Liu, 2011). Hu et al (2012) reported that 4 (18%) of 22 Populus HD-ZIP I members had no introns in their coding regions, and this phenomenon did not exist in other Populus HD-ZIP subfamilies.…”

Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica)

“…The availability of the complete genome sequences and the previous identification of ERF/AP2 superfamily genes from some plant species (Nakano et al, 2006;Licausi et al, 2010;Hu and Liu, 2011) enabled the comparison of individual families and groups, basing the classification of these genes on Arabidopsis (Nakano et al, 2006) as a criterion. Overall (Table 1), the AP2/ERF superfamily has a similar number of genes in peach and cucumber, which is less than that in Arabidopsis (147), grapevine (149), and rice (180).…”

“…It has been widely accepted that the intron/exon position pattern provides clues about evolutionary relationships (Hu and Liu, 2011). Sakuma et al (2002) reported that most genes in the ERF family of Arabidopsis possess no introns, with only 4 genes having an intron.…”

“…All genes in the RAV family have Motif 5, with the exception of ppa021899m. Proteins within a subgroup that share these motifs are likely to share similar functions (Hu and Liu, 2011). Although the functions of most of these motifs have not been identified, some may play vital roles in transcriptional regulation.…”