MYB Transcription Factors in Chinese Pear (Pyrus bretschneideri Rehd.): Genome-Wide Identification, Classification, and Expression Profiling during Fruit Development

Abstract

The MYB family is one of the largest families of transcription factors in plants. Although, some MYBs were reported to play roles in secondary metabolism, no comprehensive study of the MYB family in Chinese pear (Pyrus bretschneideri Rehd.) has been reported. In the present study, we performed genome-wide analysis of MYB genes in Chinese pear, designated as PbMYBs, including analyses of their phylogenic relationships, structures, chromosomal locations, promoter regions, GO annotations, and collinearity. A total of 129 PbMYB genes were identified in the pear genome and were divided into 31 subgroups based on phylogenetic analysis. These PbMYBs were unevenly distributed among 16 chromosomes (total of 17 chromosomes). The occurrence of gene duplication events indicated that whole-genome duplication and segmental duplication likely played key roles in expansion of the PbMYB gene family. Ka/Ks analysis suggested that the duplicated PbMYBs mainly experienced purifying selection with restrictive functional divergence after the duplication events. Interspecies microsynteny analysis revealed maximum orthology between pear and peach, followed by plum and strawberry. Subsequently, the expression patterns of 20 PbMYB genes that may be involved in lignin biosynthesis according to their phylogenetic relationships were examined throughout fruit development. Among the 20 genes examined, PbMYB25 and PbMYB52 exhibited expression patterns consistent with the typical variations in the lignin content previously reported. Moreover, sub-cellular localization analysis revealed that two proteins PbMYB25 and PbMYB52 were localized to the nucleus. All together, PbMYB25 and PbMYB52 were inferred to be candidate genes involved in the regulation of lignin biosynthesis during the development of pear fruit. This study provides useful information for further functional analysis of the MYB gene family in pear.

Keywords: MYB transcription factor; expression; gene family; lignin synthesis; pear.

FIGURE 1

Phylogenetic analysis and exon–intron structures of pear MYB proteins. Complete alignments of all PbMYB proteins were used to construct a phylogenetic tree. The bootstrap values are indicated on the nodes of the branches. The green boxes, gray lines, and blue lines in the exon–intron structure diagram represent exons, introns, and UTRs, respectively. The scale on the bottom is provided as a reference.

FIGURE 2

Phylogenetic relationships of MYB proteins between pear and Arabidopsis. Complete alignments of 238 MYB proteins between pear and Arabidopsis were performed to construct a phylogenetic tree. The bootstrap values are indicated on the nodes of the branches.

FIGURE 3

The sequence logos of the R2 (A) and R3 (B) MYB repeats. These logos were based on multiple alignment analysis of 105 typical PbR2R3-MYBs. The bit score indicates the information content for each position in the sequence. The asterisks indicate the typical conserved Trp residues in the MYB domain.

FIGURE 4

Localization and synteny of the MYB genes in the pear genome. The MYB genes in pear (PbMYB) were mapped to different chromosomes. The chromosome number is indicated on the outside. The numbers along the chromosome boxes represent sequence lengths in megabases. Gene pairs with a syntenic relationship are joined by a line.

FIGURE 5

Microsynteny of MYB regions among pear, peach and yang mei. The chromosomes of pear, peach and yang mei, represented by the different-colored boxes, are labeled Pb, Pp, and Pm, respectively. The numbers along the chromosome boxes indicate sequence lengths in megabases. The black lines represent syntenic relationships between the MYB regions.

FIGURE 6

Expression patterns of PbMYB genes during eight developmental stages of pear fruit at 15, 39, 47, 55, 63, 79, 102, and 145 days after flowering (DAF). The expression profile data were obtained using qRT-PCR, and the relative expression levels were log₂ transformed. *Significant difference compared with the expression level at 15 DAF (p < 0.05).

FIGURE 7

Subcellular localization of PbMYB25 and PbMYB52.