Affordable Access

Analysis of segmental duplications and genome assembly in the mouse.

Authors
  • Bailey, Jeffrey A
  • Church, Deanna M
  • Ventura, Mario
  • Rocchi, Mariano
  • Eichler, Evan E
Type
Published Article
Journal
Genome Research
Publisher
Cold Spring Harbor Laboratory
Publication Date
May 01, 2004
Volume
14
Issue
5
Pages
789–801
Identifiers
PMID: 15123579
Source
Medline
License
Unknown

Abstract

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 approximately 57% of all highly identical segmental duplications (>or=90%) 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.

Report this publication

Statistics

Seen <100 times