Abstract
The Sox gene family is found in a broad range of animal taxa and encodes important gene regulatory proteins involved in a variety of developmental processes. We have obtained clones representing the HMG boxes of twelve Sox genes from grass carp (Ctenopharyngodon idella), one of the four major domestic carps in China. The cloned Sox genes belong to group B1, B2 and C. Our analyses show that whereas the human genome contains a single copy of Sox4, Sox11 and Sox14, each of these genes has two co-orthologs in grass carp, and the duplication of Sox4 and Sox11 occurred before the divergence of grass carp and zebrafish, which support the "fish-specific whole-genome duplication" theory. An estimation for the origin of grass carp based on the molecular clock using Sox1, Sox3 and Sox11 genes as markers indicates that grass carp (subfamily Leuciscinae) and zebrafish (subfamily Danioninae) diverged approximately 60 million years ago. The potential uses of Sox genes as markers in revealing the evolutionary history of grass carp are discussed.
Highlights
The Sox (SRY-related genes containing an HMG box; HMG, high mobility group) gene family was first identified in 1990 as a group of genes related to the mammalian testis determining factor Sry based on conservation of the single HMG box, which encodes a 79-amino acid DNA-binding HMG domain [10]
The SoxX primers (ATGAAYGCNTTYATGGTNTGG and GGNCGRTAYTTRTARTCNGG) correspond to the motifs MNAFMVW and PDYKYRP, which are found in the HMG boxes of almost all Sox proteins that belong to groups B and C
Since our combined analyses led to unambiguous gene assignment, we refer to the grass carp Sox genes by their nomenclature proposed in this paper
Summary
The Sox (SRY-related genes containing an HMG box; HMG, high mobility group) gene family was first identified in 1990 as a group of genes related to the mammalian testis determining factor Sry based on conservation of the single HMG box, which encodes a 79-amino acid DNA-binding HMG domain [10]. For all Sox proteins, the HMG domains, outside of which Sox sequences are highly variable, are highly conserved in primary structure, and all appear to be capable of binding to the same target DNA sequence [39]. A total of 20 Sox genes has been identified in the mouse and human by whole-genome sequence analyses [35], and primary sequence comparison and other structural indicators such as intron-exon organization indicate that these genes fall into eight clear groups, A–H [2]
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