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<p>Abstract</p> <p>Background</p> <p>The <it>MYB</it> 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. <it>MYB</it> transcription factors are involved in plant development, secondary metabolism, hormone signal transduction, disease resistance and abiotic stress tolerance. A comparative analysis of <it>MYB</it> family genes in rice and Arabidopsis will help reveal the evolution and function of <it>MYB</it> genes in plants.</p> <p>Results</p> <p>A genome-wide analysis identified at least 155 and 197 <it>MYB</it> genes in rice and Arabidopsis, respectively. Gene structure analysis revealed that <it>MYB</it> family genes possess relatively more number of introns in the middle as compared with C- and N-terminal regions of the predicted genes. Intronless <it>MYB</it>-genes are highly conserved both in rice and Arabidopsis. <it>MYB</it> 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 <it>MYB</it> genes in Arabidopsis. In contrast, variation in splicing pattern was observed among R1R2R3 <it>MYB</it> members of rice. Consensus motif analysis of 1kb upstream region (5′ to translation initiation codon) of <it>MYB</it> gene ORFs led to the identification of conserved and over-represented <it>cis</it>-motifs in both rice and Arabidopsis. Real-time quantitative RT-PCR analysis showed that several members of <it>MYBs</it> are up-regulated by various abiotic stresses both in rice and Arabidopsis.</p> <p>Conclusion</p> <p>A comprehensive genome-wide analysis of chromosomal distribution, tandem repeats and phylogenetic relationship of <it>MYB</it> family genes in rice and Arabidopsis suggested their evolution <it>via</it> duplication. Genome-wide comparative analysis of <it>MYB</it> genes and their expression analysis identified several <it>MYBs</it> with potential role in development and stress response of plants.</p>