| 高進，馬佳璐，劉洋，邵長偉，賈曉東，陳松林.半滑舌鰨（Cynoglossus semilaevis）Sox基因家族生物資訊學分析.漁業科學進展，2016,37（2）：41-48 |
| 半滑舌鰨（Cynoglossus semilaevis）Sox基因家族生物資訊學分析 |
| Bioinformatics Analysis of Sox Gene Family in Cynoglossus semilaevis |
| 投稿時間：2016-01-15 修訂日期：2016-02-21 |
| DOI：10.11758/yykxjz.20160115002 |
| 中文關鍵字： Sox基因 HMG結構域 半滑舌鰨 生物資訊學 |
| 英文關鍵字： Sox genes HMG motif Cynoglossus semilaevis Bioinformatics |
| 基金項目：國家自然科學基金專案（31130057）、山東省自然科學基金（ZR2014CP011）、山東省農業良種工程重大課題和泰山學者攀登計畫專項共同資助 |
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| 摘要點擊次數： 12511 |
| 全文下載次數： 6786 |
| 中文摘要： |
| Sox（SRY-related HMG-box）基因家族是在動物體內發現的一類編碼轉錄因數的基因家族，廣泛參與了動物生長發育、理化反應，特別是性別决定和分化等過程。本研究採用生物資訊學方法，利用Sox基因高度保守的HMG-box區序列作為種子序列，檢索半滑舌鰨（Cynoglossus semilaevis）基因組注釋的蛋白資料庫，共鑒定分離出23個Sox基因。並在全基因組水准對半滑舌鰨Sox基因家族進行了保守結構域序列、進化、基因結構、染色體定位及基因表達模式的系統分析。結果顯示，通過保守結構域分析發現了半滑舌鰨Sox基因家族除CseSox32外，皆存在一段9個胺基酸殘基（RPMNAFMVW）的高度保守基序；結合保守結構域及進化分析，所有半滑舌鰨Sox基因被分為B1、B2、C、D、E、F和K共7個亞族，且不同的亞族在進化上存在種間趨同性和種內特异性；基因結構分析將半滑舌鰨Sox基因分為兩大類，即單外顯子類和多外顯子類；而染色體定位分析則顯示，Sox基因在染色體上散亂分佈，不存在集簇現象；不同類型性腺及幼魚變態前後的Sox基因家族表達譜顯示，半滑舌鰨Sox基因具有不同的組織表達模式，表明其在性別分化、性腺發育及早期幼魚發育過程中可能發揮了重要作用。本研究對於今後半滑舌鰨Sox基因家族深入的功能驗證及分子作用機制研究具有重要的意義，也為日益豐富的水產基因組資源的挖掘利用提供了參攷。 |
| 英文摘要： |
| Sox genes are developmental regulators characterized by the presence of an HMG（high mobility group）DNA-binding domain，and they exist extensively in animal bodies in nature.Members of the Sox gene family have been shown to be conserved during evolution and play crucial roles in a wide variety of developmental processes，including growth and development，hemopoiesis，the development and formation of the nervous system，especially，sex determination and differentiation.Genome resources are growing faster and faster，and it provides a platform for the study gene families by scanning whole genomic sequences.We study Sox genes in Cynoglossus semilaevis by using bioinformatics analysis on the standard of whole genome.A total of 23 Sox genes were identified systematically from C. semilaevis and classified into 7 subfamilies which had not been reported yet.They are subfamily B1，B2，C，D，E，F and K，each of these groups may have distinct and specific functions.Sequence analysis of conserved domain of Sox genes in C. semilaevis shows that，all of members in the family contain 9 amino acid residues（RPMNAFMVW）as a highly conserved motif except CseSox32.On the other hand，the motif in Sox32 is identical in all specie as RPLNAF.Research on the highly conserved HMG box in C. semilaevis causes the discovery of these Sox genes，and phylogenetic analysis supports the classification of subfamily.To date，about 10 and 40 Sox genes have been identified in invertebrates and vertebrates separately.The phylogenetic analysis also suggests that the groups of Sox genes might be extended in the process of evolution.Subfamilies have got convergence between different species，and got otherness inside one of these species.Gene location results show that these 23 Sox genes were distributed randomly on 15 chromosomes，and we do not find gene cluster.The analysis of gene structure divides all of the Sox genes into two categories，evaluation on the basis of the exon numbers of the gene are less or more than two.The expression profiles of C. semilaevis Sox genes show a characteristic of different kinds of gonad and metamorphosis specific，and it indicated Sox genes may play key roles during sex determination，gonad differentiation and early development in C. semilaevis.To sum up the above，we enhance understanding of Sox genes in C. semilaevis with bioinformatics analysis，such as system evolution，gene structure，chromosomal location and gene expression patterns.Our results suggest that bioinformatics analysis may contribute to further functional verification of gene family and be good for genome resources mining and utilization. |
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