A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

Hu, T. T.; Eisen, M. B.; Thornton, K. R.; Andolfatto, P.

doi:10.1101/gr.141689.112

A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

Journal Article · Thu Aug 30 00:00:00 EDT 2012 · Genome Research

DOI:https://doi.org/10.1101/gr.141689.112· OSTI ID:1625619

Hu, T. T. ^[1]; Eisen, M. B. ^[2]; Thornton, K. R. ^[3]; Andolfatto, P. ^[4]

Princeton Univ., NJ (United States). Lewis-Sigler Inst. for Integrative Genomics. Dept. of Ecology and Evolutionary Biology; DOE/OSTI
Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Howard Hughes Medical Inst., Berkeley, CA (United States)
Univ. of California, Irvine, CA (United States). Dept. of Ecology and Evolutionary Biology
Princeton Univ., NJ (United States). Lewis-Sigler Inst. for Integrative Genomics. Dept. of Ecology and Evolutionary Biology

We create a new assembly of the Drosophila simulans genome using 142 million paired short-read sequences and previously published data for strain w501. 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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625619

Journal Information:: Genome Research, Journal Name: Genome Research Journal Issue: 1 Vol. 23; ISSN 1088-9051

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: English

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A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

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