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Identification of Evolutionary Hotspots in the Rodent Genomes

Yap, Von Bing and Pachter, Lior (2004) Identification of Evolutionary Hotspots in the Rodent Genomes. Genome Research, 14 (4). pp. 574-579. ISSN 1088-9051. PMCID PMC383301. doi:10.1101/gr.1967904. https://resolver.caltech.edu/CaltechAUTHORS:20170308-144803591

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Abstract

We describe a whole-genome comparative analysis of the human, mouse, and rat genomes to describe the average substitution patterns of four genomic regions: ancient repeats, rodent-specific DNA, exons, and conserved (coding and noncoding) regions, and to identify rodent evolutionary hotspots. In all types of regions, except the rodent-specific DNA, the rat branch is slightly longer than the mouse branch. Moreover, the mouse–rat distance is longer in the rodent-specific DNA than in the ancient repeats. Analysis of individual conserved regions with different substitution models yielded the conclusion that the Jukes–Cantor model is inadequate, and the Hasegawa–Kishino–Yano model is almost as good as the REV model. Using human as an outgroup, we identified 5055 evolutionary hotspots, which are highly conserved subalignment blocks (each consisting of at least 100 aligned sites and a small fraction of gaps) with a large and statistically significant difference in the branch lengths of the rodent species. The cutoffs used to identify the hotspots are partially based on estimates of the average rates of substitution. The fractions of hotspots overlapping with the rodent RefSeq genes, RefSeq exons, and ESTs are all higher than expected. Still, more than half of the hotspots lie in noncoding regions of the mouse genome. We believe that the hotspots represent biologically interesting regions in the rodent genomes.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1101/gr.1967904DOIArticle
http://genome.cshlp.org/content/14/4/574.abstractPublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC383301/PubMed CentralArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2004 Cold Spring Harbor Laboratory Press. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, http://creativecommons.org/licenses/by-nc/4.0/). Accepted December 27, 2003. Received September 11, 2003. We thank Nicolas Bray and Colin Dewey for generating the whole-genome alignments; and Greg Cooper, Ross Hardison, David Haussler, Webb Miller, and Arend Sidow for extensive discussions. Special appreciation goes to Krishna Roskin for reconciling the findings of the different groups. We also thank the referees for many helpful comments and suggestions. L.P. and V.B.Y. were partially funded by a grant from the NIH (R01-HG02362-01). The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be herebymarked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.
Funders:
Funding AgencyGrant Number
NIHR01-HG02362-01
Issue or Number:4
PubMed Central ID:PMC383301
DOI:10.1101/gr.1967904
Record Number:CaltechAUTHORS:20170308-144803591
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170308-144803591
Official Citation:Identification of Evolutionary Hotspots in the Rodent Genomes Von Bing Yap and Lior Pachter Genome Res. April 2004 14: 574-579; doi:10.1101/gr.1967904
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74925
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:09 Mar 2017 15:34
Last Modified:15 Nov 2021 16:29

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