Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vesca.

Yunpeng Cao,Yahui Han,Dandan Meng,Dahui Li,Guohui Li,Qing Jin,Yongping Cai,Muhammad Abdullah,Yi Lin

doi:10.3389/fgene.2017.00078

Abstract

WUSCHEL-related homeobox (WOX) family is one of the largest group of transcription factors (TFs) specifically found in plant kingdom. WOX TFs play an important role in plant development processes and evolutionary novelties. Although the roles of WOXs in Arabidopsis and rice have been well-studied, however, little are known about the relationships among the main clades in the molecular evolution of these genes in Rosaceae. Here, we carried out a genome-wide analysis and identified 14, 10, 10, and 9 of WOX genes from four Rosaceae species (Fragaria vesca, Prunus persica, Prunus mume, and Pyrus bretschneideri, respectively). According to evolutionary analysis, as well as amino acid sequences of their homodomains, these genes were divided into three clades with nine subgroups. Furthermore, due to the conserved structural patterns among these WOX genes, it was proposed that there should exist some highly conserved regions of microsynteny in the four Rosaceae species. Moreover, most of WOX gene pairs were presented with the conserved orientation among syntenic genome regions. In addition, according to substitution models analysis using PMAL software, no significant positive selection was detected, but type I functional divergence was identified among certain amino acids in WOX protein. These results revealed that the relaxed purifying selection might be the main driving force during the evolution of WOX genes in the tested Rosaceae species. Our result will be useful for further precise research on evolution of the WOX genes in family Rosaceae.

Highlights

The WUSCHEL-related homeobox (WOX) gene family encodes a group of plant-specific transcription factors (TFs), which belongs to the homeodomain (HD) TF superfamily (Deveaux et al, 2008; Zhang et al, 2015)
AtWUS and AtWOX5 within modern/WUS clade, can redundantly maintain the apical stem cells under undifferentiated status (Sarkar et al, 2007); AtWOX4 can influent the process of secondary growth by modulating the activity of vascular cambium (Hirakawa et al, 2010); AtWOX1/3 can coordinate the development of paraxial and distal ends during the leaf development; the primordial initiation and development within meristem were terminated by overexpression of AtWOX6
In both P. persica and P. mume, three WOX genes distributed were found on one chromosome, with others scattered across different chromosomes (Figure 1)

Summary

Introduction

The WUSCHEL-related homeobox (WOX) gene family encodes a group of plant-specific transcription factors (TFs), which belongs to the homeodomain (HD) TF superfamily (Deveaux et al, 2008; Zhang et al, 2015). AtWOX13 can promote the formation of embryonic placenta during fruit development (Romera-Branchat et al, 2013); AtWOX14 and AtWOX4 can redundantly regulate the differentiation of vascular meristem (Etchells et al, 2013). These studies suggest that the WOX gene family is widely involved in the regulation of plant meristem. The members of WOX gene family appear to be functionally diverse This gene family in some model plants, such as Arabidopsis and rice, has been studied on a phylogenetic scale, a comprehensive molecular evolutionary study remains elusive in Rosaceae species.

Methods

Results

Conclusion