Reconstructing contiguous regions of an ancestral genome
Reconstructing contiguous regions of an ancestral genome
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DOI：
10.1101/gr.5383506
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发表时间：
2006-12-01
期刊：
影响因子：
7
通讯作者：
Miller, Webb
中科院分区：
文献类型：
--
作者：
Ma, Jian;Zhang, Louxin;Miller, Webb
这篇文章分析了哺乳动物基因组重排在更高的分辨率比已公布的日期。我们确定了3171个区间，覆盖了人类基因组的92%，在这些区间内，我们没有发现从人类、小鼠、大鼠和狗的最近共同祖先到人类、小鼠、大鼠和狗的谱系中大于50个碱基（kb）的重排。将所有同时代物种中相邻的间隔组合产生1338个片段，这些片段可能含有大的插入或缺失，但没有染色体分裂或融合以及长度> 50 kb的倒位或易位。我们描述了一种新的方法来预测祖先的顺序和方向，这些间隔从它们在现代物种中观察到的相邻关系。我们将这种方法的结果与染色体彩绘实验的数据相结合，产生了一个早期哺乳动物基因组的图谱，占现有人类基因组序列数据的96.8%。通过映射小至31 bp的反转，进一步提高了精度。对人类谱系中预测的进化断点的分析证实了某些已发表的观察结果，但与其他人不一致。虽然目前只有少数哺乳动物基因组测序的高精度，我们的理论分析和计算机模拟表明，我们的结果是相当准确的，他们将成为高度准确的在可预见的未来。我们的方法是作为重建人类、狗和大多数其他胎盘哺乳动物最后祖先的基因组序列项目的一部分而开发的。
This article analyzes mammalian genome rearrangements at higher resolution than has been published to date. We identify 3171 intervals, covering similar to 92% of the human genome, within which we find no rearrangements larger than 50 kilobases (kb) in the lineages leading to human, mouse, rat, and dog from their most recent common ancestor. Combining intervals that are adjacent in all contemporary species produces 1338 segments that may contain large insertions or deletions but that are free of chromosome fissions or fusions as well as inversions or translocations > 50 kb in length. We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map of an early mammalian genome that accounts for 96.8% of the available human genome sequence data. The precision is further increased by mapping inversions as small as 31 bp. Analysis of the predicted evolutionary breakpoints in the human lineage confirms certain published observations but disagrees with others. Although only a few mammalian genomes are currently sequenced to high precision, our theoretical analyses and computer simulations indicate that our results are reasonably accurate and that they will become highly accurate in the foreseeable future. Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals.