Evolution of the Tbx6/16 Subfamily Genes in Vertebrates: Insights from Zebrafish
Evolution of the Tbx6/16 Subfamily Genes in Vertebrates: Insights from Zebrafish
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DOI：
10.1093/molbev/mss199
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发表时间：
2012-12-01
影响因子：
10.7
通讯作者：
Kim, Cheol-Hee
中科院分区：
文献类型：
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作者：
Ahn, Daegwon;You, Kwan-Hee;Kim, Cheol-Hee
在任何试图在分子遗传水平上理解生物体的相似性和差异性的比较研究中，关键的第一步是建立不同生物体之间基因的同源性（直系同源和旁系同源）。当基因在序列上经历了快速的分化，或者当涉及的基因是一个基因家族的成员，而该基因家族在不同的分类群中经历了其成分的差异性增加或减少时，基因同源性的确定就变得复杂了。具有重复基因组的生物体，如硬骨鱼，可能特别容易出现这些问题，因为基因的重复拷贝提供的功能冗余会使基因在进化过程中迅速分化或丢失。在这项研究中，我们将证明，在确定鱼类和四足动物基因之间的同源性，如这些问题所产生的许多模糊性，可以通过补充基于序列的同源性与非序列信息，如基因的外显子-内含子结构或基因的基因组邻居的组成。我们将使用斑马鱼的Tbx 6/16亚家族基因（tbx 6、tbx 16、tbx 24和mga基因）作为说明性例子，这些基因因其与四足动物的Tbx 6/16亚家族基因的进化关系的模糊性而众所周知。我们将表明，尽管序列和表达的四足动物Tbx 6基因的相似性，斑马鱼Tbx 6基因实际上是一个新的T-box基因更密切相关的四足动物Tbx 16基因，而斑马鱼Tbx 24基因，迄今被认为是一个新的基因，由于高水平的序列分歧，实际上是一个直系同源的四足动物Tbx 6基因。我们还将表明，在脊椎动物进化之初，Tbx 6/16亚家族的脊椎动物T-box基因最初出现在一个共同的祖先基因的增殖之后，可能在不同的脊椎动物群体中经历了成员基因的差异性丢失，并逐渐汇集了幸存成员中成员基因的功能，这可能会阻止通过序列和功能的比较来揭示成员基因的真实身份。
In any comparative studies striving to understand the similarities and differences of the living organisms at the molecular genetic level, the crucial first step is to establish the homology (orthology and paralogy) of genes between different organisms. Determination of the homology of genes becomes complicated when the genes have undergone a rapid divergence in sequence or when the involved genes are members of a gene family that has experienced a differential gain or loss of its constituents in different taxonomic groups. Organisms with duplicated genomes such as teleost fishes might have been especially prone to these problems because the functional redundancies provided by the duplicate copies of genes would have allowed a rapid divergence or loss of genes during evolution. In this study, we will demonstrate that much of the ambiguities in the determination of the homology between fish and tetrapod genes resulting from the problems like these can be eliminated by complementing the sequence-based phylogenies with nonsequence information, such as the exon-intron structure of a gene or the composition of a gene's genomic neighbors. We will use the Tbx6/16 subfamily genes of zebrafish (tbx6, tbx16, tbx24, and mga genes), which have been well known for the ambiguity of their evolutionary relationships to the Tbx6/16 subfamily genes of tetrapods, as an illustrative example. We will show that, despite the similarity of sequence and expression to the tetrapod Tbx6 genes, zebrafish tbx6 gene is actually a novel T-box gene more closely related to the tetrapod Tbx16 genes, whereas the zebrafish tbx24 gene, hitherto considered to be a novel gene due to the high level of sequence divergence, is actually an ortholog of tetrapod Tbx6 genes. We will also show that, after their initial appearance by the multiplication of a common ancestral gene at the beginning of vertebrate evolution, the Tbx6/16 subfamily of vertebrate T-box genes might have experienced differential losses of member genes in different vertebrate groups and gradual pooling of member gene's functions in surviving members, which might have prevented the revelation of the true identity of member genes by way of the comparison of sequence and function.