The S. purpuratus genome: a comparative perspective.
The S. purpuratus genome: a comparative perspective.
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S. purpuratus 基因组：比较视角。
DOI：
10.1016/j.ydbio.2006.09.033
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发表时间：
2006
影响因子：
2.7
通讯作者：
Cameron,RAndrew
中科院分区：
文献类型：
--
作者：
Materna,StefanC;Berney,Kevin;Cameron,RAndrew
从海胆基因组中得到的预测基因模型与从其他已完成的基因组中得到的基因目录进行了比较。这些模型根据它们与保守蛋白结构域的最佳匹配度进行分类。通过BLAST比对和聚类算法，确定潜在的同源基因并将海胆基因模型分配到同源基因组。第一次，海胆基因工具箱的概述出现了，并通过扩展，更精确地了解了表征动物超级进化的基因目录中的共同特征：后生动物，双边动物，脊索动物和非脊索动物后口动物，外生动物和光栖动物原口动物。在海胆基因模型中40个最普遍的结构域中，大约有三分之一在其他基因组中并不丰富，因此构成了至少是海胆特有的扩展，如果不是所有棘皮动物。许多以前局限于脊椎动物的同源基因群都有海胆的代表，从而扩大了后口动物的补充。相反，海胆中没有代表证实了一些脊索动物的特定发明。海胆基因组中特定的基因补充很大程度上是由于在普通后生动物基因“工具箱”中已经发现的现有家族的微小扩张和收缩。然而，几次惊人的扩张揭示了海胆是如何生活和发育的。
The predicted gene models derived from the sea urchin genome were compared to the gene catalogs derived from other completed genomes. The models were categorized by their best match to conserved protein domains. Identification of potential orthologs and assignment of sea urchin gene models to groups of homologous genes was accomplished by BLAST alignment and through the use of a clustering algorithm. For the first time, an overview of the sea urchin genetic toolkit emerges and by extension a more precise view of the features shared among the gene catalogs that characterize the super-clades of animals: metazoans, bilaterians, chordate and non-chordate deuterostomes, ecdysozoan and lophotrochozoan protostomes. About one third of the 40 most prevalent domains in the sea urchin gene models are not as abundant in the other genomes and thus constitute expansions that are specific at least to sea urchins if not to all echinoderms. A number of homologous groups of genes previously restricted to vertebrates have sea urchin representatives thus expanding the deuterostome complement. Obversely, the absence of representatives in the sea urchin confirms a number of chordate specific inventions. The specific complement of genes in the sea urchin genome results largely from minor expansions and contractions of existing families already found in the common metazoan “toolkit” of genes. However, several striking expansions shed light on how the sea urchin lives and develops.