ArticleGenome research2013
A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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112 citing papers in PubMed.
- Comparative single-nucleus transcriptomics reveals asymmetric evolution of the Drosophila male and female germlines.PLoS biology · 2026Article
- An RNAi-based platform for spatiotemporal control of histone gene expression during animal development.Epigenetics & chromatin · 2026Article
- Gene age shapes functional and evolutionary properties of theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Adaptive gene expression parallelism in the male reproductive tract of two Drosophila species.Genetics · 2025Article
- Dichotomous transcriptome divergence at the cell-type level between thebioRxiv : the preprint server for biology · 2025Article
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- Two major-effect loci influence interspecific mating in females of the sibling species, Drosophila simulans and D. sechellia.G3 (Bethesda, Md.) · 2025Article
- Gene model for the ortholog ofmicroPublication biology · 2025Article
- Chromosome-scale genome of the polyphagous pest Anastrepha ludens (Diptera: Tephritidae) provides insights on sex chromosome evolution in Anastrepha.G3 (Bethesda, Md.) · 2024Article
- Comparative analysis of Wolbachia maternal transmission and localization in host ovaries.Communications biology · 2024Article
- Comparative analysis ofbioRxiv : the preprint server for biology · 2024Article
- IntroUNET: Identifying introgressed alleles via semantic segmentation.PLoS genetics · 2024Article
- IntroUNET: identifying introgressed alleles via semantic segmentation.bioRxiv : the preprint server for biology · 2024Article
- High levels of intra-strain structural variation in Drosophila simulans X pericentric heterochromatin.Genetics · 2023Article
- Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract.Journal of evolutionary biology · 2023Article
- Chromosome-Aware Phylogenomics of Assassin Bugs (Hemiptera: Reduvioidea) Elucidates Ancient Gene Conflict.Molecular biology and evolution · 2023Article
- The Transmission Patterns of the EndosymbiontGenes · 2023Article
- Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans.PLoS biology · 2023Article
- Distinct Wolbachia localization patterns in oocytes of diverse host species reveal multiple strategies of maternal transmission.Genetics · 2023Article
- Trans-regulatory changes underpin the evolution of the Drosophila immune response.PLoS genetics · 2022Article
52 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
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.
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