Genome-Wide Identification, Evolution and Functional Divergence of MYB Transcription Factors in Chinese White Pear (Pyrus bretschneideri)

Abstract

The MYB superfamily is large and functionally diverse in plants. To date, MYB family genes have not yet been identified in Chinese white pear (Pyrus bretschneideri), and their functions remain unclear. In this study, we identified 231 genes as candidate MYB genes and divided them into four subfamilies. The R2R3-MYB (PbrMYB) family shared an R2R3 domain with 104 amino acid residues, including five conserved tryptophan residues. The Pbr MYB family was divided into 37 functional subgroups including 33 subgroups which contained both MYB genes of Rosaceae plants and AtMYB genes, and four subgroups which included only Rosaceae MYB genes or AtMYB genes. PbrMYB genes with similar functions clustered into the same subgroup, indicating functional conservation. We also found that whole-genome duplication (WGD) and dispersed duplications played critical roles in the expansion of the MYB family. The 87 Pbr MYB duplicated gene pairs dated back to the two WGD events. Purifying selection was the primary force driving Pbr MYB gene evolution. The 15 gene pairs presented 1-7 codon sites under positive selection. A total of 147 expressed genes were identified from RNA-sequencing data of fruit, and six Pbr MYB members in subgroup C1 were identified as important candidate genes in the regulation of lignin synthesis by quantitative real-time PCR analysis. Further correlation analysis revealed that six PbrMYBs were significantly correlated with five structural gene families (F5H, HCT, CCR, POD and C3'H) in the lignin pathway. The phylogenetic, evolution and expression analyses of the MYB gene family in Chinese white pear establish a solid foundation for future comprehensive functional analysis of Pbr MYB genes.

Genome-Wide Identification, Classification, and Expression Profiling Reveals R2R3-MYB Transcription Factors Related to Monoterpenoid Biosynthesis in Osmanthus fragrans

“…The number of OfMYBs in some subgroups (Of1, Of6, Of9, Of10, Of23, Of26, Of31, Of33) was far greater than that of AtMYBs, which suggested that MYBs were subjected to duplications after the divergence of sweet osmanthus and Arabidopsis. This has been observed in pear and soybean [6,7]. The subgroup Of17 did not contain any AtMYB members, which indicated that these MYB family members in sweet osmanthus may have specialized roles.…”

“…As increasing numbers of plants have undergone genome sequencing, many 2R-MYB TFs have been characterized. For example, 126 members of the 2R-MYB gene family were reported in Arabidopsis thaliana [3], 244 in soybean [6], 185 in pear [7], 122 in tomato [8], and 114 in moso bamboo [9]. A conserved N-terminus and variable domain in the C-terminus ensure that MYB genes play comprehensive regulatory roles in plant growth and development [5,10].…”

Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in sea buckthorn (Hippophae rhamnoides L.)

“…By reason of Arabidopsis was a model species in plants, and all the gene of MYB had almostly studied. In particular, all 27 evolutionary branches of R2R3-AtMYBs had annotations [22,36]. Therefore, in order to predict the function of the HrMYBs, a co-constructed ML phylogenetic tree by R2R3-MYB proteins of Arabidopsis and Hippophae rhamnoides were utilized in our study (Fig.…”

Phylogenetic and expression analysis of protein disulfide isomerase unravels good reference genes for gene expression studies in pear and peach fruits

“…Duplication events have been widely studied in Rosaceae species by the analysis of various gene families including F-box genes (Wang et al 2013), heat shock factors (Qiao et al 2015), MYB and WRKY transcription factors (Huang et al 2015;Li et al 2016), lipoxygenases (Li et al 2014), sugar transporters (Li et al 2015), and cation proton antiporters (Zhou et al 2016). In this study, based on the chromosome location of each PDI gene, the synteny of chromosome segments containing PDI gene(s) was analyzed among three different phenotypical species: drupe (peach), pome apple, and berry (strawberry).…”