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

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.

B-BOX genes: genome-wide identification, evolution and their contribution to pollen growth in pear (Pyrus bretschneideri Rehd.)

“…During the course of plant evolution, gene duplication plays an important role for generating novel genes. Gene duplication in plants has two main duplication patterns, including segmental duplication and tandem duplication [ 26 ], which had been demonstrated to play a key role in the expansion of gene family members in many species, such as the families WOX , MYB , PRX and 4CL in pear [ 12 , 27 – 29 ], the CHS in maize [ 30 ]. To further reveal the potential mechanism of evolution of the BBX gene family, both the segmental and tandem duplication events were analyzed in pear.…”

Genome-Wide Study of YABBY Genes in Upland Cotton and Their Expression Patterns under Different Stresses

“…The likelihood ratio test (LRT) was used to assess which was the more suitable of the two models. For site model analysis, the amino acid sequences from each branch were extracted to construct an NJ tree and the corresponding sequences were converted to a codon alignment as an input file for the CONDEML program, as described previously (Cao et al, 2017 ).…”

Zinc Finger-Homeodomain Transcriptional Factors (ZHDs) in Upland Cotton (Gossypium hirsutum): Genome-Wide Identification and Expression Analysis in Fiber Development

“…To identify the ZHD genes in Gossypium genomes, the genome sequences of the cotton species Gossypium arboreum (BJI, version 1.0), G. raimondii (JGI, version 2.0), and G. hirsutum (NAU, version 1.1) were downloaded from COTTONGEN 1 ( Yu et al, 2014 ), according to previously reported methods ( Cao et al, 2017 ; Su et al, 2017 ; Abdullah et al, 2018b ). Proteins with ZHD domains (PF04770) were retrieved from the Pfam database.…”