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. 2023 Jul 8;13(14):2246.
doi: 10.3390/ani13142246.

Genome-Wide Identification, Evolutionary and Mutational Analysis of the Buffalo Sox Gene Family

Muhammad Abdullah  1 , Muhammad Saif-Ur Rehman  1 , Muhammad Shah Nawaz-Ul Rehman  2 , Abdullah A AlKahtane  3 , Tahani Mohamed Al-Hazani  4 , Faiz-Ul Hassan  1   5 , Saif Ur Rehman  6
Affiliations

Genome-Wide Identification, Evolutionary and Mutational Analysis of the Buffalo Sox Gene Family

Muhammad Abdullah et al. Animals (Basel). .

Abstract

The Sox gene family constitutes transcription factors with a conserved high mobility group box (HMG) that regulate a variety of developmental processes, including sex differentiation, neural, cartilage, and early embryonic development. In this study, we systematically analyzed and characterized the 20 Sox genes from the whole buffalo genome, using comparative genomic and evolutionary analyses. All the buffalo Sox genes were divided into nine sub-groups, and each gene had a specific number of exons and introns, which contributed to different gene structures. Molecular phylogeny revealed more sequence similarity of buffalo Sox genes with those of cattle. Furthermore, evolutionary analysis revealed that the HMG domain remained conserved in the all members of the Sox gene family. Similarly, all the genes are under strong purifying selection pressure; seven segmental duplications occurred from 9.65 to 21.41 million years ago (MYA), and four potential recombination breakpoints were also predicted. Mutational analysis revealed twenty non-synonymous mutations with potential effects on physiological functions, including embryonic development and cell differentiation in the buffalo. The present study provides insights into the genetic architecture of the Sox gene family in buffalo, highlights the significance of mutations, and provides their potential utility for marker-assisted selection for targeted genetic improvement in buffalo.

Keywords: Sox genes; alterations; buffalo; evolution; functional effect.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree of Sox gene family in buffalo and other related species (including sheep, goat, and cattle) constructed using neighbor joining method with a bootstrap value of 1000.
Figure 2
Figure 2
Gene structures of buffalo Sox gene family.
Figure 3
Figure 3
Buffalo Sox gene family. (A) Phylogenetic relationship, (B) motif orientation, and (C) conserved domain distribution.
Figure 4
Figure 4
Collinearity analysis of Sox genes family in buffalo and cattle.
Figure 5
Figure 5
Site-specific evolutionary forces on the Sox gene family members.
Figure 6
Figure 6
Model-averaged support for breakpoint placement.
Figure 7
Figure 7
Trees for individual fragments. (a) Tree 1, coordinate range 1–880, (b) tree 2, coordinate range 881–1046, (c) tree 3, coordinate range 1047–1308, and (d) tree 4, coordinate range 1309–2478.
See this image and copyright information in PMC

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