ArticleGenome research2004
Recent segmental duplications in the working draft assembly of the brown Norway rat.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Genome organization and botanical diversity.The Plant cell · 2024Review
- Translational outcomes in a full gene deletion of ubiquitin protein ligase E3A rat model of Angelman syndrome.Translational psychiatry · 2020Article
- Developmental social communication deficits in the Shank3 rat model of phelan-mcdermid syndrome and autism spectrum disorder.Autism research : official journal of the International Society for Autism Research · 2018Article
- Analysis of Copy Number Variation in the Abp Gene Regions of Two House Mouse Subspecies Suggests Divergence during the Gene Family Expansions.Genome biology and evolution · 2017Article
- Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals.BMC genomics · 2017Article
- Bovine NK-lysin: Copy number variation and functional diversification.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Sequence, structural and expression divergence of duplicate genes in the bovine genome.PloS one · 2014Article
- Resolving genomic disorder-associated breakpoints within segmental DNA duplications using massively parallel sequencing.Nature protocols · 2014Article
- Segmental duplications in the silkworm genome.BMC genomics · 2013Article
- The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family.BMC evolutionary biology · 2013Article
- Evolutionary dynamism of the primate LRRC37 gene family.Genome research · 2013Article
- Mechanisms of Gene Duplication and Translocation and Progress towards Understanding Their Relative Contributions to Animal Genome Evolution.International journal of evolutionary biology · 2012Article
- Analysis of recent segmental duplications in the bovine genome.BMC genomics · 2009Article
- Mechanisms of change in gene copy number.Nature reviews. Genetics · 2009Review
- Repair-mediated duplication by capture of proximal chromosomal DNA has shaped vertebrate genome evolution.PLoS genetics · 2009Article
- The genomic architecture of segmental duplications and associated copy number variants in dogs.Genome research · 2009Article
- The evolution of human segmental duplications and the core duplicon hypothesis.Cold Spring Harbor symposia on quantitative biology · 2009Review
- Comparative genomics and molecular dynamics of DNA repeats in eukaryotes.Microbiology and molecular biology reviews : MMBR · 2008Review
- Comparative sequence analyses reveal sites of ancestral chromosomal fusions in the Indian muntjac genome.Genome biology · 2008Article
- Evolutionary toggling of the MAPT 17q21.31 inversion region.Nature genetics · 2008Article
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Authors and funding
3 authors.
Funding
Abstract
We assessed the content, structure, and distribution of segmental duplications (> or =90% sequence identity, > or =5 kb length) within the published version of the Rattus norvegicus genome assembly (v.3.1). The overall fraction of duplicated sequence within the rat assembly (2.92%) is greater than that of the mouse (1%-1.2%) but significantly less than that of human ( approximately 5%). Duplications were nonuniformly distributed, occurring predominantly as tandem and tightly clustered intrachromosomal duplications. Regions containing extensive interchromosomal duplications were observed, particularly within subtelomeric and pericentromeric regions. We identified 41 discrete genomic regions greater than 1 Mb in size, termed "duplication blocks." These appear to have been the target of extensive duplication over millions of years of evolution. Gene content within duplicated regions ( approximately 1%) was lower than expected based on the genome representation. Interestingly, sequence contigs lacking chromosome assignment ("the unplaced chromosome") showed a marked enrichment for segmental duplication (45% of 75.2 Mb), indicating that segmental duplications have been problematic for sequence and assembly of the rat genome. Further targeted efforts are required to resolve the organization and complexity of these regions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.