Prediction of Contiguous Regions in the Amniote Ancestral Genome

We investigate the problem of inferring contiguous ancestral regions (CARs) of the genome of the last common ancestor of all extant amniotes, based on the currently sequenced and assembled amniote genomes as ingroups and three teleost fish genomes as outgroups. We combine a methodological framework using conserved syntenies computed from whole genome alignments of amniote species together with double conserved syntenies (DCS) using gene families from amniote and fish genomes, to take into account the whole genome duplication that occurred in the teleost lineage. From these comparisons, ancestral genome segments are computed using techniques inspired by physical mapping. Due to the difficulty caused by the whole genome duplication and the large evolutionary distance to the closest assembled outgroup, very few methods have been Published with a, reconstruction of the amniote ancestral genome. This one is the first which is founded on a simple and formal methodological framework, whose good stability is shown and whose CARs cover large regions of the human and chicken genomes.

我们研究基于当前已测序和组装的羊膜动物基因组作为内群以及三个硬骨鱼基因组作为外群，推断所有现存羊膜动物最后共同祖先基因组的连续祖先区域（CARs）的问题。我们将一个利用从羊膜动物物种全基因组比对计算出的保守同线性以及利用来自羊膜动物和鱼类基因组的基因家族的双保守同线性（DCS）的方法框架相结合，以考虑在硬骨鱼谱系中发生的全基因组复制。通过这些比较，利用受物理图谱启发的技术计算祖先基因组片段。由于全基因组复制以及与最近的已组装外群的较大进化距离所造成的困难，很少有关于羊膜动物祖先基因组重建的方法被发表。这是第一个基于一个简单且正式的方法框架的研究，其良好的稳定性得以展示，并且其CARs覆盖人类和鸡的基因组的大片区域。