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

Abstract

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.

Genome-wide identification of myeloblastosis gene family and its response to cadmium stress in Ipomoea aquatica

“…While, we did not detect any 5R-type MYB gene in I. aquatica . The MYB gene containing only one MYB repeat or two separated MYB repeats are defined as MYB -related gene or 1R-type MYB ( Jiang et al, 2004 ; Islam et al, 2021 ). 1R-type IaMYB constituted the second largest subfamily of MYB TF superfamily in I. aquatica .…”

Integrated omics analysis identified genes and their splice variants involved in fruit development and metabolites production in Capsicum species

“…Also, CaMYBs such CaMYB31, CaMYB48 were found to be involved in regulation/accumulation of capsaicinoids in C. annuum (Arce-Rodríguez et al, 2021; B. Sun et al, 2020), while CaMYB homologs in C. chinense such as CcDIV1, CcMYB4, CcMYB52, CcMYB86, and CcMYB108 were found to be co-expressed with capsaicinoids biosynthesis pathway genes (Islam et al, 2021). Additionally, other MYBs such as CaMYB3R-1, CaMYB3R-5 were reported to involve cell cycle process, CaGLK in chloroplast development and plant defense, while CaDIV1 in regulation of Capsanthin/capsorubin synthase (Ccs) gene (Arce-Rodríguez et al, 2021).…”

“…Fruit tissues from three different developmental stages i.e. early green (EG; 5-10 Day Post Anthesis; DPA), mature green (MG; 20-25 DPA) and breaker (Br; 30-45 DPA) stage were collected separately in liquid nitrogen and stored at -80 ˚C until RNA and DNA extraction, as previously described by (Islam et al, 2021). The total RNA from each tissue sample was extracted using the MN Nucleospin RNA Plant kit (Takara, USA) following manufacturers' standard method as described previously by (Dubey et al, 2019).…”

“…5A). Around 31.16% (24) genes including 4-coumarate--CoA ligase-like 6 (4CL-like 6; LOC107869755), 4CL-2-like (LOC107877487), agmatine coumaroyltransferase-2-like (ACT-2-like; LOC107875625), caffeoyl-CoA O-methyltransferase 6 (CCoAOMT6; LOC107840262), CcoAOMT-like (LOC107860279), cinnamoyl-CoA reductase 1-like (CCR1; LOC107861980, LOC107861981), caffeic acid 3-Omethyltransferase (COMT; LOC107862989, LOC107862991), COMT-like (LOC107875336), probable cinnamyl alcohol dehydrogenase 6 (CAD6; LOC107858423), peroxidase gene (POD; LOC107840010, LOC107851630, LOC107859813), beta-glucosidase 40 (BGL40; LOC107876837), BGL42 (LOC107851487), BGL11-like (LOC107854417), and BGL18-like (LOC107859563) etc. were alternatively spliced (Fig.…”

Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid

“…Total RNA from each sample was extracted using NucleoSpin RNA plant Kit (Macherey-Nagel, Germany) following standard protocol. The quality and integrity of RNA were checked using an Agilent bioanalyzer and then RNA with RNA integrity number (RIN) > 8 was sequenced as described earlier ( Rawoof et al., 2020 ; Islam et al., 2021 ). Briefly, an equal amount of total RNA (5–10 μg) from each sample was used for library preparation using Illumina TruSeq RNA sample preparation kit (Illumina, San Diego, CA) following manufacturer’s protocols and paired-end sequencing was performed on Illumina HiSeq 4000 to develop 150 bp paired-end reads from three samples (two biological replicate of each sample).…”