Hox cluster characterization of Banna caecilian (Ichthyophis bannanicus) provides hints for slow evolution of its genome.
Hox cluster characterization of Banna caecilian (Ichthyophis bannanicus) provides hints for slow evolution of its genome.
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版纳蚓螈（Ichthyophis bannanicus）的 Hox 簇特征为其基因组缓慢进化提供了线索
DOI：
10.1186/s12864-015-1684-0
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发表时间：
2015-06-18
期刊：
影响因子：
4.4
通讯作者：
Liang D
中科院分区：
文献类型：
--
作者：
Wu R;Liu Q;Meng S;Zhang P;Liang D
无足目动物，有着离散的生活方式，是两栖动物中最少被探索的一组。虽然具有独特的特征，但其生物学的许多方面都没有得到充分的研究。获得该基因组序列将为进一步研究该动物的生物学基础提供新的视角。在两栖动物比较基因组学研究中，盲肠动物基因组序列也具有重要的实用价值。然而，目前，只有稀疏的基因组序列的无尾目。Hox基因是一个古老的转录因子家族，在后生动物体型的形成中起着重要作用。了解它们的结构和基因组组织可以提供对动物基因组的见解，这对于没有测序基因组的动物是有价值的。采用长距离PCR和基因组步移相结合的方法，测定了班纳鱼蜥Hox基因簇的序列。我们获得了4个Hox基因簇中的大部分，并鉴定了39个Hox基因，5个microRNA基因和1个假基因（HoxD 12）。还有七个基因间的空白我们无法填补。从所获得的序列中，包含较少的重复序列和更多的保守的非编码元件（CNEs）比青蛙的对应物。我们发现，腔棘鱼和无脊椎动物的CNEs共享量远高于蛙和腔棘鱼。序列进化的相对速率表明，在这项研究中使用的其他四足动物物种，并与缓慢进化的腔棘鱼的Hox基因，盲肠Hox基因进化显着更慢。系统发育树分析显示，4个Hox类群的分支长度较短，特别是在无足目HoxA、HoxB和HoxD类群中。这些特征的盲肠Hox集群建议一个缓慢进化的基因组，这是支持进一步分析的一个大的orthopathic蛋白数据集。我们的分析极大地扩展了从以前的PCR调查有关的盲肠Hox集群的知识。从获得的Hox序列和orthophosphate蛋白数据集，盲肠Hox基因座和它的基因组出现相对缓慢的演变。作为两栖动物和陆栖脊椎动物的基础谱系，无足目基因组的这一特征在两栖动物和早期四足动物的基因组生物学和进化研究中具有重要价值。本文的在线版本（doi：10.1186/s12864-015-1684-0）包含补充材料，可供授权用户使用。
Caecilians, with a discrete lifestyle, are the least explored group of amphibians. Though with distinct traits, many aspects of their biology are poorly investigated. Obtaining the caecilian genomic sequences will offer new perspectives and aid the fundamental studies in caecilian biology. The caecilian genomic sequences are also important and practical in the comparative genomics of amphibians. Currently, however, only sparse genomic sequences of caecilians are available. Hox genes, an old family of transcription factors playing central roles in the establishment of metazoan body plan. Understanding their structure and genomic organization may provide insights into the animal’s genome, which is valuable for animals without a sequenced genome. We sequenced and characterized the Hox clusters of Banna caecilian (Ichthyophis bannanicus) with a strategy combining long range PCR and genome walking. We obtained the majority of the four caecilian Hox clusters and identified 39 Hox genes, 5 microRNA genes and 1 pseudogene (ψHoxD12). There remained seven intergenic gaps we were unable to fill. From the obtained sequences, the caecilian Hox clusters contained less repetitive sequences and more conserved noncoding elements (CNEs) than the frog counterparts. We found that caecilian and coelacanth shared many more CNEs than frog and coelacanth did. Relative rate of sequence evolution showed that caecilian Hox genes evolved significantly more slowly than the other tetrapod species used in this study and were comparable to the slowly evolving coelacanth Hox genes. Phylogenetic tree of the four Hox clusters also revealed shorter branch length especially for the caecilian HoxA, HoxB and HoxD clusters. These features of the caecilian Hox clusters suggested a slowly evolving genome, which was supported by further analysis of a large orthologous protein dataset. Our analyses greatly extended the knowledge about the caecilian Hox clusters from previous PCR surveys. From the obtained Hox sequences and the orthologous protein dataset, the caecilian Hox loci and its genome appear evolving comparatively slowly. As the basal lineage of amphibians and land vertebrate, this characteristic of the caecilian genome is valuable in the study concerning the genome biology and evolution of amphibians and early tetrapods. The online version of this article (doi:10.1186/s12864-015-1684-0) contains supplementary material, which is available to authorized users.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
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