Plouhinec J-L, Granier C, Le Mentec C, Lawson K A, Sabéran-Djoneidi D, Aghion J, Shi D L, Collignon J, Mazan S
Développement et Evolution des Vertébrés, UMR 8080, Université Paris-Sud, 91405 ORSAY, France.
Gene Expr Patterns. 2004 Nov;5(1):11-22. doi: 10.1016/j.modgep.2004.06.010.
Despite the great morphological diversity of early embryos, the underlying mechanisms of gastrulation are known to be broadly conserved in vertebrates. However, a number of genes characterized as fulfilling an essential function in this process in several model organisms display no clear ortholog in mammalian genomes. We have devised an in silico phylogenomic approach, based on exhaustive similarity searches in vertebrate genomes and subsequent bayesian phylogenetic analyses, to identify such missing genes, presumed to be highly divergent. This approach has been used to identify mammalian orthologs of Not, an homeodomain containing gene previously characterized in Xenopus, chick and zebrafish as playing a critical role in the formation of the notochord. This attempt led to the identification of a highly divergent mammalian Not-related gene in the mouse, human and rat. The results from phylogenetic reconstructions, synteny analyses, expression pattern analyses in wild-type and mutant mouse embryos, and overexpression experiments in Xenopus embryos converge to confirm these genes as representatives of the Not family in mammals. The identification of the mammalian Not gene delivers an important component for the understanding of the genetics underlying notochord formation in mammals and its evolution among vertebrates. The phylogenomic method used to retrieve this gene thus provides a tool, which can complement or validate genome annotations in situations when they are weakly supported.
尽管早期胚胎在形态上具有很大的多样性，但已知原肠胚形成的潜在机制在脊椎动物中广泛保守。然而，一些在几种模式生物中被认为在这一过程中发挥重要功能的基因，在哺乳动物基因组中却没有明显的直系同源基因。我们设计了一种基于脊椎动物基因组中详尽相似性搜索及后续贝叶斯系统发育分析的计算机系统发育基因组学方法，以识别这些缺失的基因，推测它们具有高度的分化。这种方法已被用于鉴定Not基因的哺乳动物直系同源基因，Not是一个含有同源结构域的基因，先前在非洲爪蟾、鸡和斑马鱼中被鉴定为在脊索形成中起关键作用。这一尝试导致在小鼠、人类和大鼠中鉴定出一个高度分化的与Not相关的基因。系统发育重建、共线性分析、野生型和突变型小鼠胚胎中的表达模式分析以及非洲爪蟾胚胎中的过表达实验结果都一致证实这些基因是哺乳动物中Not家族的代表。哺乳动物Not基因的鉴定为理解哺乳动物脊索形成的遗传学基础及其在脊椎动物中的进化提供了一个重要组成部分。用于检索该基因的系统发育基因组学方法因此提供了一种工具，可在基因组注释支持不足的情况下对其进行补充或验证。
