Dsim
A second generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.
We create a new assembly of the D. 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 than those previously reported. Specifically, we find that D. 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 suggests that partly recessive beneficial mutations may comprise a substantial fraction of non-coding DNA divergence observed between species. Our results have more general implications for the interpretation of evolutionary analyses of genomes of different quality.