Document Detail


A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.
MedLine Citation:
PMID:  22936249     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
We create a new assembly of the Drosophila simulans genome using 142 million paired short-read sequences and previously published data for strain w(501). Our assembly represents a higher-quality genomic sequence with greater coverage, fewer misassemblies, and, by several indexes, fewer sequence errors. Evolutionary analysis of this genome reference sequence reveals interesting patterns of lineage-specific divergence that are different from those previously reported. Specifically, we find that Drosophila melanogaster evolves faster than D. simulans at all annotated classes of sites, including putatively neutrally evolving sites found in minimal introns. While this may be partly explained by a higher mutation rate in D. melanogaster, we also find significant heterogeneity in rates of evolution across classes of sites, consistent with historical differences in the effective population size for the two species. Also contrary to previous findings, we find that the X chromosome is evolving significantly faster than autosomes for nonsynonymous and most noncoding DNA sites and significantly slower for synonymous sites. The absence of a X/A difference for putatively neutral sites and the robustness of the pattern to Gene Ontology and sex-biased expression suggest that partly recessive beneficial mutations may comprise a substantial fraction of noncoding DNA divergence observed between species. Our results have more general implications for the interpretation of evolutionary analyses of genomes of different quality.
Authors:
Tina T Hu; Michael B Eisen; Kevin R Thornton; Peter Andolfatto
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2012-08-30
Journal Detail:
Title:  Genome research     Volume:  23     ISSN:  1549-5469     ISO Abbreviation:  Genome Res.     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-01-03     Completed Date:  2013-06-11     Revised Date:  2013-07-12    
Medline Journal Info:
Nlm Unique ID:  9518021     Medline TA:  Genome Res     Country:  United States    
Other Details:
Languages:  eng     Pagination:  89-98     Citation Subset:  IM    
Affiliation:
Department of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA. tthu@princeton.edu
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MeSH Terms
Descriptor/Qualifier:
Animals
Chromosomes, Insect / genetics
Contig Mapping
Drosophila / genetics*
Evolution, Molecular*
Genome, Insect*
Introns
Mutation Rate
Phylogeny
Population / genetics
X Chromosome / genetics
Grant Support
ID/Acronym/Agency:
R01 GM083228/GM/NIGMS NIH HHS; R01 GM085183/GM/NIGMS NIH HHS; R01-GM083228/GM/NIGMS NIH HHS; R01-GM085183/GM/NIGMS NIH HHS
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