Reconstructing the architecture of the ancestral amniote genome
Reconstructing the architecture of the ancestral amniote genome
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DOI：
10.1093/bioinformatics/btr461
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发表时间：
2011-10-01
期刊：
影响因子：
5.8
通讯作者：
Chauve, Cedric
中科院分区：
文献类型：
--
作者：
Ouangraoua, Aida;Tannier, Eric;Chauve, Cedric
动机：鸟类和哺乳动物的祖先生活在大约3亿年前。推测其基因组结构是理解这两个谱系分化进化的关键。然而，由于鸟类和哺乳动物谱系的差异，由于分子进化的积累，在其现存的后代中检测其染色体组织的痕迹是困难的。结果：我们解决了在全基因组复制的背景下检测和组装古代脊椎动物基因组的祖先基因组特征的几个方法学问题，这些特征包括邻接、毗连片段、合体和双合体。对于所有这些问题，我们使用通用但严格的方法，其中一些是新的，我们分析了15个脊椎动物基因组，包括12种羊水动物和3种硬骨鱼，并推断出羊水动物祖先基因组的高分辨率基因组组织，由39个祖先连锁组组成，分辨率为100kb。我们广泛地讨论了该方法的有效性和对数据和参数变化的鲁棒性。我们为每一组引入了支持值，并表明39个组中有36个具有最大支持度。结论：目前不能使用单一的方法学原理来推断羊膜动物祖先基因组的组织，我们证明了将几个原理收集到一个计算古基因组学管道中是可能的。这一策略为古脊椎动物基因组的重建提供了坚实的方法学基础。
Motivation: The ancestor of birds and mammals lived approximately 300 million years ago. Inferring its genome organization is key to understanding the differentiated evolution of these two lineages. However, detecting traces of its chromosomal organization in its extant descendants is difficult due to the accumulation of molecular evolution since birds and mammals lineages diverged.Results: We address several methodological issues for the detection and assembly of ancestral genomic features of ancient vertebrate genomes, which encompass adjacencies, contiguous segments, syntenies and double syntenies in the context of a whole genome duplication. Using generic, but stringent, methods for all these problems, some of them new, we analyze 15 vertebrate genomes, including 12 amniotes and 3 teleost fishes, and infer a high-resolution genome organization of the amniote ancestral genome, composed of 39 ancestral linkage groups at a resolution of 100 kb. We extensively discuss the validity and robustness of the method to variations of data and parameters. We introduce a support value for each of the groups, and show that 36 out of 39 have maximum support.Conclusions: Single methodological principle cannot currently be used to infer the organization of the amniote ancestral genome, and we demonstrate that it is possible to gather several principles into a computational paleogenomics pipeline. This strategy offers a solid methodological base for the reconstruction of ancient vertebrate genomes.