Takatori Naohito, Butts Thomas, Candiani Simona, Pestarino Mario, Ferrier David E K, Saiga Hidetoshi, Holland Peter W H
Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo, Japan.
Dev Genes Evol. 2008 Dec;218(11-12):579-90. doi: 10.1007/s00427-008-0245-9. Epub 2008 Sep 17.
The homeobox genes comprise a large and diverse gene superfamily, many of which encode transcription factors with pivotal roles in the embryonic development of animals. We searched the assembled draft genome sequence of an amphioxus, Branchiostoma floridae, for genes possessing homeobox sequences. Phylogenetic analysis was used to divide these into gene families and classes. The 133 amphioxus homeobox genes comprise 60 ANTP class genes, 29 PRD genes (excluding Pon and Pax1/9), nine TALE genes, seven POU genes, seven LIM genes, five ZF genes, four CUT genes, four HNF genes, three SINE genes, one CERS gene, one PROS gene, and three unclassified genes. Ten of the 11 homeobox gene classes are less diverse in amphioxus than humans, as a result of gene duplication on the vertebrate lineage. Amphioxus possesses at least one member for all of the 96 homeobox gene families inferred to be present in the common ancestor of chordates, including representatives of the Msxlx, Bari, Abox, Nk7, Ro, and Repo gene families that have been lost from tunicates and vertebrates. We find duplication of several homeobox genes in the cephalochordate lineage (Mnx, Evx, Emx, Vent, Nk1, Nedx, Uncx, Lhx2/9, Hmbox, Pou3, and Irx) and several divergent genes that probably originated by extensive sequence divergence (Hx, Ankx, Lcx, Acut, Atale, Azfh, Ahbx, Muxa, Muxb, Aprd1-6, and Ahnf). The analysis reveals not only the repertoire of amphioxus homeobox genes but also gives insight into the evolution of chordate homeobox genes.
同源异型框基因构成了一个庞大且多样的基因超家族，其中许多基因编码在动物胚胎发育中起关键作用的转录因子。我们在佛罗里达文昌鱼（Branchiostoma floridae）的组装基因组草图序列中搜索具有同源异型框序列的基因。系统发育分析用于将这些基因分为基因家族和类别。这133个文昌鱼同源异型框基因包括60个ANTP类基因、29个PRD基因（不包括Pon和Pax1/9）、9个TALE基因、7个POU基因、7个LIM基因、5个ZF基因、4个CUT基因、4个HNF基因、3个SINE基因、1个CERS基因、1个PROS基因以及3个未分类基因。由于脊椎动物谱系上的基因复制，文昌鱼中11个同源异型框基因类别中的10个比人类中的多样性更低。文昌鱼拥有推断存在于脊索动物共同祖先中的96个同源异型框基因家族中的所有家族的至少一个成员，包括被囊动物和脊椎动物中已丢失的Msxlx、Bari、Abox、Nk7、Ro和Repo基因家族的代表。我们发现在头索动物谱系中有几个同源异型框基因发生了复制（Mnx、Evx、Emx、Vent、Nk1、Nedx、Uncx、Lhx2/9、Hmbox、Pou3和Irx）以及几个可能因广泛的序列分歧而起源的分化基因（Hx、Ankx、Lcx、Acut、Atale、Azfh、Ahbx、Muxa、Muxb、Aprd1 - 6和Ahnf）。该分析不仅揭示了文昌鱼同源异型框基因的组成，还深入了解了脊索动物同源异型框基因的进化。
