Genome-wide identification and classification of MYB superfamily genes in peach.

Chunhua Zhang,Mingliang Yu,Ruchao Feng,Ruijuan Ma,Lei Guo,Jianlan Xu,Juan Song,Juan Yan,Yuepeng Han

doi:10.1371/journal.pone.0199192

Chunhua Zhang, Mingliang Yu + Show 7 more

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https://doi.org/10.1371/journal.pone.0199192

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Abstract

The MYB transcription factor superfamily is one of the largest superfamilies modulating various biological processes in plants. Over the past few decades, many MYB superfamily genes have been identified and characterized in some plant species. However, genes belonging to the MYB superfamily in peach (Prunus persica) have not been comprehensively identified and characterized although the genome sequences of peach were released several years ago. In total, this study yielded a set of 256 MYB superfamily genes that was divided into five subfamilies: the R2R3-MYB (2R-MYB), R1R2R3-MYB (3R-MYB), MYB-related (1R-MYB), 4R-MYB, and Atypical-MYB subfamilies. These subfamilies contained 128, 4, 109, 1, and 14 members, respectively. The 128 R2R3-MYB subfamily genes in peach were further clustered into 35 groups, and the 109 MYB-related subfamily genes were further clustered into 6 groups: the CCA1-like, CPC-like, TBP-like, I-box-binding-like, R-R-type, and Peach-specific groups. The motif compositions and exon/intron structures within each group within the R2R3-MYB or MYB-related subfamily in peach were highly conserved. The logo sequences of the R2 and R3 repeats of R2R3-MYB subfamily members were highly conserved with those in these repeats of several other plant species. Except for 48 novel peach-specific MYB genes, the remaining 208 out of 256 MYB genes in peach were conserved with the corresponding 198 MYB genes in A. thaliana. Additionally, the 256 MYB genes unevenly distributed on chromosomes 1 to 8 of the peach genome. Eighty-one orthologous pairs of peach/A. thaliana MYB genes were identified among 256 MYB genes in peach and 198 MYB genes in A. thaliana in this study. In addition, 146 pairs of paralogous MYB genes were identified on the eight chromosomes of peach. The expression levels of some of the 51 MYB genes selected for qRT-PCR analysis decreased or increased with red-fleshed fruit development, while the expression patterns of some genes followed no clear rules over the five developmental stages of fruits. This study laid the foundation for further functional analysis of MYB superfamily genes in peach and enriched the knowledge of MYB superfamily genes in plant species.

Highlights

Transcription factors (TFs) control gene expression, and they play key roles in the regulation of cell activities [1,2]
Combined with the number of MYB genes identified in other plant species in previous studies, this finding in peach is consistent with the MYB superfamily being one of the largest TF superfamilies in plants [5,24]
This study yielded a set of 256 MYB superfamily genes containing 128 R2R3-MYB subfamily genes (2R-MYB), 4 R1R2R3-MYB subfamily genes (3R-MYB), 109 MYB-related subfamily genes (1R-MYB), one 4R-MYB subfamily gene, and 14 Atypical-MYB subfamily genes

Summary

Introduction

Transcription factors (TFs) control gene expression, and they play key roles in the regulation of cell activities [1,2]. Among the various TF families in the genome, the MYB family is one of the largest and functionally diverse families [5] It is usually called the MYB superfamily. MYB superfamily proteins are characterized by having a highly conserved MYB domain at the N-terminus that is usually composed of 1–4 adjacent imperfect tandem repeats (R1-R4) [6]. As an increasing number of genome sequences have been released, a variety of MYB superfamily proteins have been identified and analyzed in a wide range of plant species such as sesame [6], Arabidopsis thaliana (A. thaliana) [7], Brassica napus (B. napus) [8], kiwi [9], Brachypodium distachyon (B. distachyon) [10], foxtail millet [11], and pear [12]. The results from these studies have proved that they are involved in regulating a wide range of intricate networks, growth, development, and stress resistancethroughout the plant life cycle, including the anthocyanin biosynthetic pathway [13,14], the coloration of fruit skin [14], flavonoid/phenylpropanoid metabolism [15], secondary wall biosynthesis [16], sugar signaling [17], and responses to drought and waterlogging stress [6]

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