Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes
Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes
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DOI：
10.1101/gr.1975204
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发表时间：
2004-04-01
期刊：
影响因子：
7
通讯作者：
Tesler, G
中科院分区：
文献类型：
--
作者：
Bourque, G;Pevzner, PA;Tesler, G
最近对人类和小鼠基因组重排的分析揭示了比以前认为的更多重排的证据，并揭示了哺乳动物进化中以前未知的特征，如断点重复使用和许多微重排。然而，双向分析不能揭示祖先哺乳动物的基因组结构或将重排事件分配给不同的谱系。因此，Nadeau和Sankoff先前提出的“原始同线性”问题仍然没有解决，因为至少需要三个哺乳动物基因组来推导出祖先哺乳动物的核型。我们表明，大鼠基因组的可用性允许一个重建的祖先鼠科啮齿动物基因组的推定的基因组结构。这一重建表明，这一祖先的基因组保留了许多以前假设的胎盘祖先的染色体协会，并揭示了其他超出细胞遗传学，辐射杂交映射和染色体绘画技术的分辨率。三向分析重排导致一个可靠的重建的特定区域的基因组结构的murid祖先，包括X染色体，并首次允许一个分配到人类，小鼠和大鼠谱系的主要重排事件。我们的分析表明，在鼠啮齿类动物的重排率比在人类谱系高得多，并证实了重排热点的存在，在所有三个谱系。
Recent analysis of genome rearrangements in human and mouse genomes revealed evidence for more rearrangements than thought previously and shed light on previously unknown features of mammalian evolution, like breakpoint reuse and numerous microrearrangements. However, two-way analysis cannot reveal the genomic architecture of ancestral mammals or assign rearrangement events to different lineages. Thus, the "original synteny" problem introduced by Nadeau and Sankoff previously, remains unsolved, as at least three mammalian genomes are required to derive the ancestral mammalian karyotype. We show that availability of the rat genome allows one to reconstruct a putative genomic architecture of the ancestral murid rodent genome. This reconstruction suggests that this ancestral genome retained many previously postulated chromosome associations in the placental ancestor and reveals others that were beyond the resolution of cytogenetic, radiation hybrid mapping, and chromosome painting techniques. Three-way analysis of rearrangements leads to a reliable reconstruction of the genomic architecture of specific regions in the murid ancestor, including the X chromosome, and for the first time allows one to assign major rearrangement events to one of human, mouse, and rat lineages. Our analysis implies that the rate of rearrangements is much higher in murid rodents than in the human lineage and confirms the existence of rearrangement hot-spots in all three lineages.