A genome-wide analysis of the ERF gene family in sorghum

Abstract

ABSTRACT. The ethylene response factor (ERF) family are members of the APETALA2 (AP2)/ERF transcription factor superfamily; they are known to play an important role in plant adaptation to biotic and abiotic stress. ERF genes have been studied in Arabidopsis, rice, grape, and maize; however, there are few reports of ERF genes in sorghum. We identified 105 sorghum ERF (SbERF) genes, which were categorized into 12 groups (A-1 to A-6 and B-1 to B-6) based on their sequence similarity, and this new method of classification for ERF genes was then further characterized. A comprehensive bioinformatic analysis of SbERF genes was performed using a sorghum genomic database, to analyze the phylogeny of SbERF genes, identify other conserved motifs apart from the AP2/ERF domain, map SbERF genes to the 10 sorghum chromosomes, and determine the tissue-specific expression patterns of SbERF genes. Gene clustering indicates that SbERF genes were generated by tandem duplications. Comparison of SbERF genes with maize ERF homologs suggests lateral gene transfer between monocot species. These results can contribute to our understanting of ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 12 (2): 2038-2055 (2013 Analysis of the ERF gene family in sorghum 2039 the evolution of the ERF gene family.

Genome–wide Analysis of Ethylene Responsive Factor in Maize: An in Silico Approach

“…9). We found that Z. mays has 105 ERF genes which are greater than Arabidopsis, sorghum, peach and moso bamboo, while less than Chines cabbage and Carrot ( In chromosomal maps, distribution of ZmERF genes in all the 10 chromosomes was similar to the findings of AP2/ERF in Sorghum (Yan et al, 2013) and Chinese cabbage (Song et al, 2013). Interestingly, ERF gene comprising of same group and present on same chromosome forming cluster, was also observed in Arabidopsis (Sakuma et al It has been found that intron/exon position configuration provides hint in evolutionary relationship (Hu and Liu, 2011).…”

“…AP2 binds to GCAC(A/G)N(A/T)TCCC(A/G)ANG(C/T) (Gong et al, 2008;Wilson and Krizek, 2000). The ERF-associated amphiphilic repression (EAR) motif was also identified in many species of plant like Arabidopsis, Z. mays and sorghum (Yan et al, 2013). The three dimensional analysis of AP2/ERF protein domain shows it consist of 3 anti-parallel beta-sheet and one alpha-helix (Yamasaki et al, 2013) arginine and tryptophan in beta-sheet have basic function in formation of GCC box binding domain and serine/threonine also important residue for DNA binding domain (Shanker et al, 2012).…”

“…2). In order to better understand relative relationship of the same gene family among different species, an evolutionary analysis is performed between Z. mays (105 ERF genes) and Sorghum (53 ERF genes) (Yan et al, 2013), as both species belong to monocot and sorghum represented a model plant. Phylogenetic tree showed all Z. mays and sorghum ERF genes are distributed into 59 sister groups, containing 27 ZmERF-ZmERF, 28 ZmERF-SbERF and 4 SbERF-SbERF (Fig.…”

Transcriptome-based discovery of AP2/ERF transcription factors related to temperature stress in tea plant (Camellia sinensis)

“…AP2/ERF TF families have been identified and characterized in dicotyledonous and monocotyledonous plants (Sakuma et al 2002;Nakano et al 2006;GilHumanes et al 2009;Yan et al 2013;Sun et al 2014). Homologs of the AP2-containing proteins have also been found in gymnosperms, bryophytas, and chlorophytes (Shigyo et al 2006), with even similar sequences in bacteria and viruses (Magnani et al 2004;Balaji et al 2005).…”

Ethylene Signaling in Rice and Arabidopsis: Conserved and Diverged Aspects

“…It has been reported that there are 122, 139, and 105 ERF members in Arabidopsis, rice, and sorghum, respectively (Nakano et al, 2006, Yan et al, 2013. It is likely that only a small group of the ERFs are related to ethylene responses.…”