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Myeloblastosis ( MYB ) genes are important transcriptional regulators of plant growth, development, and secondary metabolic biosynthesis pathways, such as capsaicinoid biosynthesis in  Capsicum . Although  MYB  genes have been identified in  Capsicum annuum , no comprehensive study has been conducted on other  Capsicum  species. We identified a total of 251 and 240  MYB  encoding genes in  Capsicum chinense MYBs  ( CcMYBs ) and  Capsicum baccatum MYBs  ( CbMYBs ). The observation of twenty tandem and 41 segmental duplication events indicated expansion of the  MYB  gene family in the  C. chinense  genome. Five  CcMYB  genes, i.e.,  CcMYB101, CcMYB46, CcMYB6, CcPHR8 , and  CcRVE5 , and two  CaMYBs , i.e.,  CaMYB3  and  CaHHO1 , were found within the previously reported capsaicinoid biosynthesis quantitative trait loci. Based on phylogenetic analysis with tomato  MYB  proteins, the  Capsicum  MYBs were classified into 24 subgroups supported by conserved amino acid motifs and gene structures. Also, a total of 241  CcMYBs  were homologous with 225  C. annuum , 213  C. baccatum , 125 potato, 79 tomato, and 23 Arabidopsis  MYBs . Synteny analysis showed that all 251  CcMYBs  were collinear with  C. annuum, C. baccatum , tomato, potato, and Arabidopsis  MYBs  spanning over 717 conserved syntenic segments. Using transcriptome data from three fruit developmental stages, a total of 54  CcMYBs  and 81  CaMYBs  showed significant differential expression patterns. Furthermore, the expression of 24  CcMYBs  from the transcriptome data was validated by quantitative real-time (qRT) PCR analysis. Eight out of the 24  CcMYBs  validated by the qRT-PCR were highly expressed in fiery hot  C. chinense  than in the lowly pungent  C. annuum . Furthermore, the co-expression analysis revealed several  MYB  genes clustered with genes from the capsaicinoid, anthocyanin, phenylpropanoid, carotenoid, and flavonoids biosynthesis pathways, and related to determining fruit shape and size. The homology modeling of 126 R2R3 CcMYBs showed high similarity with that of the Arabidopsis R2R3  MYB  domain template, suggesting their potential functional similarity at the proteome level. Furthermore, we have identified simple sequence repeat (SSR) motifs in the  CcMYB  genes, which could be used in  Capsicum  breeding programs. The functional roles of the identified  CcMYBs  could be studied further so that they can be manipulated for  Capsicum  trait improvement.

frontiers in plant science

Capsicum chinense MYB Transcription Factor Genes: Identification, Expression Analysis, and Their Conservation and Diversification With Other Solanaceae Genomes