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Analysis of segmental duplications and genome assembly in the mouse

Bailey, Jeffrey A ; Church, Deanna M ; Ventura, Mario ; Rocchi, Mariano ; Eichler, Evan E

Genome research, 2004-05, Vol.14 (5), p.789-801 [Periódico revisado por pares]

United States: Cold Spring Harbor Laboratory Press

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Título:
Analysis of segmental duplications and genome assembly in the mouse
Autor: Bailey, Jeffrey A ; Church, Deanna M ; Ventura, Mario ; Rocchi, Mariano ; Eichler, Evan E
Assuntos: Animals ; Base Composition - genetics ; Bone Marrow Cells - chemistry ; Bone Marrow Cells - metabolism ; Cell Nucleus - genetics ; Chromosome Mapping - methods ; Chromosome Mapping - standards ; Chromosome Mapping - statistics & numerical data ; Computational Biology - methods ; Databases, Genetic ; DNA - genetics ; Gene Duplication ; Genes ; Genome ; Genome, Human ; Humans ; In Situ Hybridization, Fluorescence - methods ; Mice ; Mice, Inbred C57BL ; Sequence Alignment - methods ; Sequence Analysis, DNA - methods
É parte de: Genome research, 2004-05, Vol.14 (5), p.789-801
Notas: Corresponding author. E-MAIL eee@cwru.edu ; FAX (216) 368-3432.
Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2238404.
Descrição: 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.
Editor: United States: Cold Spring Harbor Laboratory Press
Idioma: Inglês

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Analysis of segmental duplications and genome assembly in the mouse

Bailey, Jeffrey A ; Church, Deanna M ; Ventura, Mario ; Rocchi, Mariano ; Eichler, Evan E

United States: Cold Spring Harbor Laboratory Press

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