The amphioxus genome illuminates vertebrate origins and cephalochordate biology
The amphioxus genome illuminates vertebrate origins and cephalochordate biology
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DOI：
10.1101/gr.073676.107
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发表时间：
2008-07-01
期刊：
影响因子：
7
通讯作者：
Holland, Peter W. H.
中科院分区：
文献类型：
--
作者：
Holland, Linda Z.;Albalat, Ricard;Holland, Peter W. H.
鲸脊索动物、尾索动物和脊椎动物是从5.2亿年前的共同祖先进化而来的。为了提高我们对脊索动物进化和脊椎动物起源的理解，我们深入研究了头索动物Branchiostoma floridae（通常称为文昌鱼或文昌鱼）的测序基因组中的特定基因、基因家族和保守的非编码元件。特别注意的是同源框基因，视蛋白基因，参与神经嵴发育的基因，核受体基因，编码内分泌和免疫系统的基因，和保守的顺式调节增强子。文昌鱼基因组包含一组基本的脊索动物基因，参与发育和细胞信号传导，包括第十五个Hox基因。这组基因包括许多在脊椎动物中被增选的基因，在神经嵴发育和适应性免疫中发挥新作用。然而，文昌鱼只有一个基因，而脊椎动物通常有两个、三个或四个来自两个全基因组复制事件的旁系同源物。此外，文昌鱼和脊椎动物之间有几个转录增强子是保守的，系统发育距离很远。相比之下，尿索动物的基因组已经丢失了许多基因，包括同源异型盒家族的多样性和参与类固醇激素功能的基因。文昌鱼的基因组也表现出衍生的特征，包括复制的视蛋白和基因，被认为在先天免疫和内分泌系统中起作用。我们的研究结果表明，文昌鱼的基因组是了解非脊索动物后口动物，无脊椎动物脊索动物和脊椎动物的生物学和进化的基础。
Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates-a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.