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

TitleRevised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.
Publication TypeJournal Article
Year of Publication2014
AuthorsRogers, RL, Shao, L, Sanjak, JS, Andolfatto, P, Thornton, KR
JournalG3 (Bethesda)
Volume4
Issue12
Pagination2345-51
Date Published2014 Oct 01
ISSN2160-1836
KeywordsAnimals, Drosophila melanogaster, Female, Gene Expression Regulation, Gene Fusion, Genetic Linkage, Genome, Male, Molecular Sequence Annotation, Ovary, Sequence Analysis, RNA, Sex Characteristics, Species Specificity, Testis
Abstract

<p>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. </p>

DOI10.1534/g3.114.013532
Alternate JournalG3 (Bethesda)
PubMed ID25273863
PubMed Central IDPMC4267930
Grant ListF32-GM099377 / GM / NIGMS NIH HHS / United States
R01-GM083228 / GM / NIGMS NIH HHS / United States
F32 GM099377 / GM / NIGMS NIH HHS / United States
R01 GM085183 / GM / NIGMS NIH HHS / United States
P30 CA062203 / CA / NCI NIH HHS / United States
R01 GM083228 / GM / NIGMS NIH HHS / United States
R01-GM085183 / GM / NIGMS NIH HHS / United States
P30CA062203 / CA / NCI NIH HHS / United States