AUTHOR=Islam Khushbu , Rawoof Abdul , Ahmad Ilyas , Dubey Meenakshi , Momo John , Ramchiary Nirala 

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

JOURNAL=Frontiers in Plant Science

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.721265

DOI=10.3389/fpls.2021.721265

ISSN=1664-462X

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