Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes

被引:617
作者
Kent, WJ [1 ]
Baertsch, R
Hinrichs, A
Miller, W
Haussler, D
机构
[1] Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA
[2] Univ Calif Santa Cruz, Howard Hughes Med Inst, Dept Comp Sci, Santa Cruz, CA 95064 USA
[3] Penn State Univ, Dept Comp Sci & Engn, University Pk, PA 16802 USA
关键词
comparative genomics; cross-species alignments; synteny; chromosomal inversion; breakpoints;
D O I
10.1073/pnas.1932072100
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
This study examines genomic duplications, deletions, and rearrangements that have happened at scales ranging from a single base to complete chromosomes by comparing the mouse and human genomes. From whole-genome sequence alignments, 344 large (>100-kb) blocks of conserved synteny are evident, but these are further fragmented by smaller-scale evolutionary events. Excluding transposon insertions, on average in each megabase of genomic alignment we observe two inversions, 17 duplications (five tandem or nearly tandem), seven transpositions, and 200 deletions of 100 bases or more. This includes 160 inversions and 75 duplications or transpositions of length >100 kb. The frequencies of these smaller events are not substantially higher in finished portions in the assembly. Many of the smaller transpositions are processed pseudogenes; we define a "syntenic" subset of the alignments that excludes these and other small-scale transpositions. These alignments provide evidence that approximate to2% of the genes in the human/mouse common ancestor have been deleted or partially deleted in the mouse. There also appears to be slightly less nontransposon-induced genome duplication in the mouse than in the human lineage. Although some of the events we detect are possibly due to misassemblies or missing data in the current genome sequence or to the limitations of our methods, most are likely to represent genuine evolutionary events. To make these observations, we developed new alignment techniques that can handle large gaps in a robust fashion and discriminate between orthologous and paralogous alignments.
引用
收藏
页码:11484 / 11489
页数:6
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