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G3 (Bethesda). 2014 Oct 1;4(12):2345-51. doi: 10.1534/g3.114.013532.

Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

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Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California 92697
Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California 92697.
Ecology and Evolutionary Biology and the Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544.


Here, we provide revised gene models for D. ananassae, D. yakuba, and D. simulans, which include untranslated regions and empirically verified intron-exon boundaries, as well as ortholog groups identified using a fuzzy reciprocal-best-hit blast comparison. Using these revised annotations, we perform differential expression testing using the cufflinks suite to provide a broad overview of differential expression between reproductive tissues and the carcass. We identify thousands of genes that are differentially expressed across tissues in D. yakuba and D. simulans, with roughly 60% agreement in expression patterns of orthologs in D. yakuba and D. simulans. We identify several cases of putative polycistronic transcripts, pointing to a combination of transcriptional read-through in the genome as well as putative gene fusion and fission events across taxa. We furthermore identify hundreds of lineage specific genes in each species with no blast hits among transcripts of any other Drosophila species, which are candidates for neofunctionalized proteins and a potential source of genetic novelty.


D. ananassae; D. simulans; D. yakuba; gene annotation; gene fusion; polycistronic genes; sex-specific gene expression

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