Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis

Abstract

BackgroundThe MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB repeats. MYB transcription factors are involved in plant development, secondary metabolism, hormone signal transduction, disease resistance and abiotic stress tolerance. A comparative analysis of MYB family genes in rice and Arabidopsis will help reveal the evolution and function of MYB genes in plants.ResultsA genome-wide analysis identified at least 155 and 197 MYB genes in rice and Arabidopsis, respectively. Gene structure analysis revealed that MYB family genes possess relatively more number of introns in the middle as compared with C- and N-terminal regions of the predicted genes. Intronless MYB-genes are highly conserved both in rice and Arabidopsis. MYB genes encoding R2R3 repeat MYB proteins retained conserved gene structure with three exons and two introns, whereas genes encoding R1R2R3 repeat containing proteins consist of six exons and five introns. The splicing pattern is similar among R1R2R3 MYB genes in Arabidopsis. In contrast, variation in splicing pattern was observed among R1R2R3 MYB members of rice. Consensus motif analysis of 1kb upstream region (5′ to translation initiation codon) of MYB gene ORFs led to the identification of conserved and over-represented cis-motifs in both rice and Arabidopsis. Real-time quantitative RT-PCR analysis showed that several members of MYBs are up-regulated by various abiotic stresses both in rice and Arabidopsis.ConclusionA comprehensive genome-wide analysis of chromosomal distribution, tandem repeats and phylogenetic relationship of MYB family genes in rice and Arabidopsis suggested their evolution via duplication. Genome-wide comparative analysis of MYB genes and their expression analysis identified several MYBs with potential role in development and stress response of plants.

Function of MYB domain transcription factors in abiotic stress and epigenetic control of stress response in plant genome

“…Arabidopsis thaliana transcriptomic data analyses have revealed increased expression of about 51%; of MYB genes in response to drought while 41%; gene were found to be down-regulated. 5,16,53 In Arabidopsis, various MYB transcription factor genes like AtMYB2, AtMYB74 and AtMYB102 showed enhanced expression under drought stress. 2 Previous studies have revealed involvement of several MYB genes in drought stress and ABA signaling network, governing various plant specific responses under abiotic stress.…”

Genome-wide analysis of the MYB gene family in physic nut ( Jatropha curcas L.)

“…The exon-intron structures of R2R3 repeats were conserved in rice, grape, and Arabidopsis R2R3 MYB genes, and the intron-containing genes were classified into 4-6 models (Jiang et al, 2004;Matus et al, 2008;Katiyar et al, 2012). After analysis of the overall exon-intron arrangements, we observed that MYB genes from physic nut could be grouped into nine models (include an intronless group) based on the coding sequences for the structures of the two types of MYB repeats (R2 and R3; Fig.…”

“…According to previous studies, MYB superfamily genes can be divided into MYB family (R2R3-, 3R-, and 4R-MYB) and MYB-related (R-R-type, CCA1-like, and 1R-MYB) families (Martin and Paz-Ares, 1997;Jiang et al, 2004;Chen et al, 2006;Dubos et al, 2010;Katiyar et al, 2012). The 4R-MYB group is the smallest and contains four R1/R2-like repeats; little is known of their functions in plants (Dubos et al, 2010).…”

Molecular Characterization of a MYB Protein from Oryza sativa for its Role in Abiotic Stress Tolerance

“…JcMYB1 transcript level was reported to be up-regulated by PEG, NaCl and cold stresses as well as by hormones 16 . Katiyar et al 17 observed the upregulation of various MYB genes in rice under drought, salt and cold stresses. It has been accounted that MYB transcription factors can recognize a specific binding motif, WAACCA and YAACKG 18 .…”