期刊
GENOME RESEARCH
卷 14, 期 5, 页码 789-801出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.2238404
关键词
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资金
- NCI NIH HHS [CA094816] Funding Source: Medline
- NHGRI NIH HHS [R01 HG002385, HG002385] Funding Source: Medline
- NIGMS NIH HHS [T32 GM007250, R01 GM058815, GM58815] Funding Source: Medline
- Telethon [C.50] Funding Source: Medline
- Wellcome Trust Funding Source: Medline
Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications. The extent of segmental duplications in other mammalian genomes is unknown and confounded by methodological differences in genome assembly. Here, we present a detailed analysis of recent duplication content within the mouse genome using a whole-genome assembly comparison method and a novel assembly independent method, designed to take advantage of the reduced allelic variation of the C57BL/6J strain. We conservatively estimate that similar to57% of all highly identical segmental duplications ( greater than or equal to90%) were misassembled or collapsed within the working draft WGS assembly. The WGS approach often leaves duplications fragmented and unassigned to a chromosome when compared with the clone-ordered-based approach. Our preliminary analysis suggests that 1.7%-2.0% of the mouse genome is part of recent large segmental duplications (about half of what is observed for the human genome). We have constructed a mouse segmental duplication database to aid in the characterization of these regions and their integration into the final mouse genome assembly. This work suggests significant biological differences in the architecture of recent segmental duplications between human and mouse. In addition, our unique method provides the means for improving whole-genome shotgun sequence assembly of mouse and future mammalian genomes.
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