Comparative genomics of duplicate γ-glutamyl transferase genes in teleosts: medaka (Oryzias latipes), stickleback (Gasterosteus aculeatus), green spotted pufferfish (Tetraodon nigroviridis), fugu (Takifugu rubripes), and zebrafish (Danio rerio).
Comparative genomics of duplicate γ-glutamyl transferase genes in teleosts: medaka (Oryzias latipes), stickleback (Gasterosteus aculeatus), green spotted pufferfish (Tetraodon nigroviridis), fugu (Takifugu rubripes), and zebrafish (Danio rerio).
复制标题
硬骨鱼中重复γ-谷氨酰转移酶基因的比较基因组学：青鳉（Oryzias latipes）、棘鱼（Gasterosteus aculeatus）、绿斑河豚（Tetraodon nigroviridis）、河豚（Takifugu rubripes）和斑马鱼（Danio rerio）。
DOI：
10.1002/jez.b.21439
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发表时间：
2012
期刊：
影响因子：
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通讯作者：
Kullman,SethWilliam
中科院分区：
文献类型：
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作者：
Law,SheranHiuWan;Redelings,BenjaminDavid;Kullman,SethWilliam
多硬骨鱼（硬骨鱼）基因组的可用性提供了前所未有的机会，了解基因复制事件的多样性和功能，使用比较基因组学。在这里，我们研究了多个旁系同源基因的γ-谷氨酰转移酶（GGT）在几个远亲硬骨鱼物种，包括青鳉，棘鱼，绿色斑点河豚，河豚和斑马鱼。通过挖掘基因组数据库，我们已经确定了多个GGT直系同源物。鉴定了每个种属的GGT 1（GGT 1 a和B）、GGT 1（GGT 1 a和B）和GGT 3（GGT 3 a和B）的重复（旁系同源）GGT序列。系统发育分析表明，GGT是在大多数后生动物门中保守的古老蛋白质，硬骨鱼类中的旁系同源GGT可能是由一系列3R基因组重复事件引起的。在绿色斑点河豚中发现了第三个GGTL 1基因（GGTL 1c）;然而，该基因不存在于青鳉、棘鱼或河豚中。类似地，GGTL 3的一个或两个旁系同源物似乎在绿色斑点河豚、河豚和斑马鱼中丢失。同线关系在重复的硬骨鱼染色体之间、硬骨鱼之间以及在鳍条鱼（辐鳍鱼）和叶鳍鱼（肉鳍鱼）物种之间高度维持。为了评估亚功能划分，克隆了六个青鳉GGT基因，并评估了发育和组织特异性表达。在这些数据的基础上，我们提出了一个修改的“复制-退化-互补”模型的子功能分区，在基因旁系同源物之间观察到基因表达的定量差异，而不是绝对差异。我们的结果表明，硬骨鱼基因组中保留了多个GGT基因。然而，关于多种GGT在这些物种中的功能作用仍存在问题。Zool.（Mol. Dev. Evol.）318：35-49，2012.© 2011 Wiley Periodicals，Inc.
The availability of multiple teleost (bony fish) genomes is providing unprecedented opportunities to understand the diversity and function of gene duplication events using comparative genomics. Here we examine multiple paralogous genes of γ‐glutamyl transferase (GGT) in several distantly related teleost species including medaka, stickleback, green spotted pufferfish, fugu, and zebrafish. Through mining genome databases, we have identified multiple GGT orthologs. Duplicate (paralogous) GGT sequences for GGT1 (GGT1 a and b), GGTL1 (GGTL1 a and b), and GGTL3 (GGTL3 a and b) were identified for each species. Phylogenetic analysis suggests that GGTs are ancient proteins conserved across most metazoan phyla and those paralogous GGTs in teleosts likely arose from the serial 3R genome duplication events. A third GGTL1 gene (GGTL1c) was found in green spotted pufferfish; however, this gene is not present in medaka, stickleback, or fugu. Similarly, one or both paralogs of GGTL3 appear to have been lost in green spotted pufferfish, fugu, and zebrafish. Syntenic relationships were highly maintained between duplicated teleost chromosomes, among teleosts and across ray‐finned (Actinopterygii) and lobe‐finned (Sarcopterygii) species. To assess subfunction partitioning, six medaka GGT genes were cloned and assessed for developmental and tissue‐specific expression. On the basis of these data, we propose a modification of the “duplication‐degeneration‐complementation” model of subfunction partitioning where quantitative differences rather than absolute differences in gene expression are observed between gene paralogs. Our results demonstrate that multiple GGT genes have been retained within teleost genomes. Questions remain, however, regarding the functional roles of multiple GGTs in these species.J. Exp. Zool. (Mol. Dev. Evol.) 318:35–49, 2012. © 2011 Wiley Periodicals, Inc.