Genome-Wide Identification and Analysis of the MYB Transcription Factor Gene Family in Chili Pepper (Capsicum spp.).

Octavio Martínez,Magda L. Arce-Rodríguez,Neftalí Ochoa-Alejo

doi:10.3390/ijms22052229

Abstract

The MYB transcription factor family is very large and functionally diverse in plants, however, only a few members of this family have been reported and characterized in chili pepper (Capsicum spp.). In the present study, we performed genome-wide analyses of the MYB family in Capsicum annuum, including phylogenetic relationships, conserved domain, gene structure organization, motif protein arrangement, chromosome distribution, chemical properties predictions, RNA-seq expression, and RT-qPCR expression assays. A total of 235 non-redundant MYB proteins were identified from C. annuum, including R2R3-MYB, 3R-MYB, atypical MYB, and MYB-related subclasses. The sequence analysis of CaMYBs compared with other plant MYB proteins revealed gene conservation, but also potential specialized genes. Tissue-specific expression profiles showed that CaMYB genes were differentially expressed, suggesting that they are functionally divergent. Furthermore, the integration of our data allowed us to propose strong CaMYBs candidates to be regulating phenylpropanoid, lignin, capsaicinoid, carotenoid, and vitamin C biosynthesis, providing new insights into the role of MYB transcription factors in secondary metabolism. This study adds valuable knowledge about the functions of CaMYB genes in various processes in the Capsicum genus.

Highlights

Transcription factors (TFs) are sequence specific DNA binding proteins that recognize specific cis-elements in the promoters of target genes to activate or repress their expression in response to endogenous or exogenous stimuli and in order to control biochemical and physiological processes
The identification of MYB family genes in C. annuum genome was carried out with a Blastp search using as query the Pfam domains: PF00249 and PF13921
We identified 345 proteins with at least one MYB domain, which were localized in 235 loci, representing almost 11% of TFs in Capsicum

Summary

Introduction

Transcription factors (TFs) are sequence specific DNA binding proteins that recognize specific cis-elements in the promoters of target genes to activate or repress their expression in response to endogenous or exogenous stimuli and in order to control biochemical and physiological processes. TFs can be divided into many multigene families according to their DNA-binding domains [1]. MYB proteins are widely distributed in plants and they have been implicated in the regulation of many biological processes, such as primary and secondary metabolism, plant growth and development, circadian clock control, cell cycling development, response to biotic and abiotic stresses, and plant defense [3]. The first plant MYB gene identified was COLORED1 (C1) from Zea mays, involved in the regulation of anthocyanin biosynthesis in the aleurone and scutellum tissues of the kernel [4]

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Discussion

Conclusion