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.

Systematic Analysis of the 4-Coumarate:Coenzyme A Ligase (4CL) Related Genes and Expression Profiling during Fruit Development in the Chinese Pear

“…Therefore, we postulated that pear 4CL-related genes should occur at a certain degree of specific evolution to adapt to the environment during the process of differentiation from monocotyledonous plants. In the study of the MYB gene family, Cao et al found that the AtMYB genes in subfamily S12 may be a specific gene type to adapt to phytophagous conditions [55,56]. …”

Structural, Evolutionary, and Functional Analysis of the Class III Peroxidase Gene Family in Chinese Pear (Pyrus bretschneideri)

“…We found that 94 PbPRX genes contained different numbers of exons or introns, implying a great diversity in PRX gene family of pear. Many studies have shown that structural diversification of genes plays an important role in the evolution of multi-gene families (Muthamilarasan et al, 2014; Cao et al, 2016a,b,c; Han et al, 2016). In our research, we found that there presented different characteristics of PRXs from different subfamilies, indicating PbPRXs have functionally diversified.…”

Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa)

“…Both events of tandem duplication and large-scale duplication are the main patterns of gene family expansion in plants, such as the MYB gene family in pear (Cao et al, 2016a), CHS gene family in maize (Han et al, 2016), or MYB gene family in Setaria italica (Muthamilarasan et al, 2014). In the present study, a high frequency of GRF genes was distributed in duplicated blocks, implying that large-scale duplications (whole-genome or segmental duplication) contributed to the expansion of the GRF gene family in plants.…”