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

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.

Genome-wide characterization of the R2R3-MYB transcription factors in pepper (Capsicum spp.) unveils the role of CaMYB101 as repressor in anthocyanin biosynthesis

“…Nevertheless, there is no comprehensive comparison of R2R3-MYBs across different pepper genomes and most of their functions are unclear. As one of the most cultivated species among the Capsicum genus, 108 and 116 C. annuum R2R3-MYBs have been genome-widely analyzed based on the Zunla 1.0 genome sequence by Wang et al (2020) and Arce-Rodríguez et al (2021), respectively. The reason for the disparity in different number of R2R3-MYBs could be that other known R2R3-MYB plant proteins were also used for identification in Arce-Rodríguez et al (2021) work.…”

“…As one of the most cultivated species among the Capsicum genus, 108 and 116 C. annuum R2R3-MYBs have been genome-widely analyzed based on the Zunla 1.0 genome sequence by Wang et al (2020) and Arce-Rodríguez et al (2021), respectively. The reason for the disparity in different number of R2R3-MYBs could be that other known R2R3-MYB plant proteins were also used for identification in Arce-Rodríguez et al (2021) work. The 108 CaR2R3-MYBs that Wang et al (2020) identified in C. annuum were used for further analysis in this study, together with 106 CbR2R3-MYBs and 110 CcR2R3-MYBs we identified in C. baccatum and C. chinense , respectively.…”

“…However, no MYB repressors for flavonoid biosynthesis have been identified in pepper yet. Genome-wide identification of the R2R3-MYB gene family has been studied in C. annuum (Wang et al, 2020; Arce-Rodríguez et al, 2021). The recently released pepper genomes make the study of the R2R3-MYB gene family in C. baccatum and C. chinense possible.…”

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

“…The duplicate sequences were removed manually, and the remaining sequences were cross-checked for the presence of the MYB domain using the Conserved Domains Database (CDD) of the National Centre for Biotechnology Information (NCBI) (Lu et al, 2020) and the Simple Modular Architecture Research Tool (SMART); http://smart.embl-heidelberg.de/) database. The resultant C. chinense and C. baccatum MYB encoding genes were given acronyms according to their amino acid sequence homology with C. annuum MYB genes (Arce-Rodríguez et al, 2021). Physicochemical features, such as molecular weight, theoretical isoelectric point (pI), instability index, aliphatic index, and grand average of hydrophobicity (GRAVY) of the MYB protein sequences were estimated using ProtParam (https://web.…”

“…Myeloblastosis genes have been identified only in C. annuum (Wang et al, 2020c;Arce-Rodríguez et al, 2021), and no comprehensive study has been reported in other Capsicum species, such as C. chinense, C. baccatum, and C. frutescens. In this study, we identified MYB genes in the C. chinense, C. baccatum, and C. annuum genomes, and the analysis of their expression was performed using transcriptome data and validated by quantitative real-time (qRT) PCR in the early green (EG), mature green (MG), and breaker (Br) fruit developmental stages of highly pungent C. chinense and lowly pungent C. annuum.…”