Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster group

TL;DR

This study revises gene annotations in several Drosophila species, analyzes differential gene expression across tissues, and identifies lineage-specific genes, revealing insights into gene evolution and expression patterns.

Contribution

The paper provides updated gene models with empirical validation and uncovers lineage-specific genes and complex transcriptional events in the Drosophila melanogaster group.

Findings

Thousands of genes are differentially expressed across tissues.

Approximately 60% agreement in ortholog expression patterns.

Identification of lineage-specific genes with no homologs in other species.

Abstract

Here, we provide revised gene models for D. ananassae, D. yakuba, and D. simulans, which include UTRs 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.