Genome-Wide Analysis of the R2R3-MYB Gene Family in Fragaria × ananassa and Its Function Identification During Anthocyanins Biosynthesis in Pink-Flowered Strawberry

Abstract

The strawberry (Fragaria × ananassa) is an economically important fruit throughout the world. The large R2R3-MYB gene family participates in a variety of plant functions, including anthocyanin biosynthesis. The present study is the first genome-wide analysis of the MYB gene family in the octoploid strawberry and describes the identification and characterization of the family members using the recently sequenced F. × ananassa genome. Specifically, we aimed to identify the key MYBs involved in petal coloration in the pink-flowered strawberry, which increases its ornamental value. A comprehensive, genome-wide analysis of F. × ananassa R2R3-FaMYBs was performed, investigating gene structures, phylogenic relationships, promoter regions, chromosomal locations, and collinearity. A total of 393 R2R3-FaMYB genes were identified in the F. × ananassa genome and divided into 36 subgroups based on phylogenetic analysis. Most genes with similar functions in the same subgroup exhibited similar exon-intron structures and motif compositions. These R2R3-FaMYBs were unevenly distributed over 28 chromosomes. The expansion of the R2R3-FaMYB gene family in the F. × ananassa genome was found to be caused mainly by segmental duplication. The Ka/Ks analysis indicated that duplicated R2R3-FaMYBs mostly experienced purifying selection and showed limited functional divergence after the duplication events. To elucidate which R2R3-FaMYB genes were associated with anthocyanin biosynthesis in the petals of the pink-flowered strawberry, we compared transcriptional changes in different flower developmental stages using RNA-seq. There were 131 differentially expressed R2R3-FaMYB genes identified in the petals, of which three genes, FaMYB28, FaMYB54, and FaMYB576, appeared likely, based on the phylogenetic analysis, to regulate anthocyanin biosynthesis. The qRT-PCR showed that these three genes were more highly expressed in petals than in other tissues (fruit, leaf, petiole and stolon) and their expressions were higher in red compared to pink and white petals. These results facilitate the clarification on the roles of the R2R3-FaMYB genes in petal coloration in the pink-flowered strawberry. This work provides useful information for further functional analysis on the R2R3-FaMYB gene family in F. × ananassa.

Genome-wide identification of R2R3-MYB gene family and association with anthocyanin biosynthesis in Brassica species

“…The candidate R2R3-MYB members in the six Brassica species were identified by a local BLASTP search with 125 R2R3-MYB genes from Arabidopsis to identify candidates with E-value < 1e-10, then all putative R2R3-MYB genes were identified in the PFAM protein family database ( https://pfam.xfam.org/ ) using the HMMER software version 3.0 [ 15 ] and using the hidden Markov model of the MYB-DNA-binding domain (PF00249) and Myb_DNA-bind_6 domain (PF13921) to search against the six Brassica species genome to identify candidates with E-value < 1e-10 [ 17 ]. All protein sequences were further investigated using different online tools, including the motif search ( https://www.genome.jp/tools/motif/ ), SMART ( http://smart.embl-heidelberg.de/ ), ScanProsite ( https://prosite.expasy.org/scanprosite/ ), NCBI-Conserved Domains Database (CDD) web server ( https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml ), MEME Suite ( https://meme-suite.org/meme/doc/meme-format.html ) [ 28 , 45 ].…”

“…The correlation network diagram was drawn by extracting the non-weight coefficients (weight) of R2R3-MYB and anthocyanin-related genes in the matrix. STRING software ( https://version-11-5.string-db.org/ ) was used to reveal a co-expression plot [ 28 , 45 ].…”

“…For decades, it has been identified and reported in many plants that the R2R3-MYB transcription factor is widely involved in plant development and metabolic regulation [ 13 , 28 , 43 , 45 – 47 ]. Recently, the increasing availability of plant genome sequences have facilitated a better understanding of this large gene family [ 28 , 45 – 47 ]. The first plant R3R3-MYB gene COLORED1 ( C1 ) was isolated from maize ( Zea mays ) which encode a regulatory protein involved in anthocyanin biosynthesis [ 32 ].…”

Genome-wide identification of R2R3-MYB gene family and association with anthocyanin biosynthesis in Brassica species

“…For decades, it has been identi ed and reported in many plants that the R2R3-MYB transcription factor is widely involved in plant development and metabolic regulation (Stracke et al, 2001;Du et al, 2012;Wang et al, 2020;Liu et al, 2021). Recently, the increasing availability of plant genome sequences have facilitated a better understanding of this large gene family Wang et al, 2020;Liu et al, 2021). The rst plant R3R3-MYB gene COLORED1 (C1) was isolated from maize (Zea mays) which encode a regulatory protein involved in anthocyanin biosynthesis (Paz-Ares et al, 1987).…”

“…In the model plant A. thaliana, 125 R2R3-MYB genes were found(Stracke et al, 2001), and then 126 R2R3-MYB genes detected from the whole genome MYB transcription factor identi cation and divided into 26 subfamilies(Dubos et al, 2010), which provides a reference for the identi cation and analysis of R2R3-MYB transcription factors in other plants. In recent years, numerous R2R3-MYB transcription factors have been identi ed and functionally analyzed, such as in Oryza sativa(Chen et al, 2006), Zea mays(Du et al, 2012), B. napus(Hajiebrahimi et al, 2017) and horticultural plants Petunia, Strawberry(Liu et al, 2021) and Capsicum annuum(Wang et al, 2020). Importantly, more and more biological pathways involved in R2R3-MYB have been revealed, such as the transcriptional regulation of anthocyanins(Zhao et al, 2013), ber development(Wang et al, 2020) and root hair development(Slabaugh et al, 2011).…”