The early embryonic transcriptome of a Hawaiian Drosophila picture-wing fly shows evidence of altered gene expression and novel gene evolution

A massive adaptive radiation on the Hawaiian archipelago has produced approximately one quarter of the fly species in the family Drosophilidae. The Hawaiian Drosophila clade has long been recognized as a model system for the study of both the ecology of island endemics and the evolution of developmental mechanisms, but relatively few genomic and transcriptomic datasets are available for this group. We present here a differential expression analysis of the transcriptional profiles of two highly conserved embryonic stages in the Hawaiian picture-wing fly Drosophila grimshawi. When we compared our results to previously published datasets across the family Drosophilidae, we identified cases of both gains and losses of gene representation in D. grimshawi, including an apparent delay in Hox gene activation. We also found high expression of unannotated genes. Most transcripts of unannotated genes with open reading frames do not have homologs in non-Hawaiian Drosophila species, although the vast majority have sequence matches in other genomes of the Hawaiian picture-wing flies. Some of these genes may have arisen from non-coding sequence in the ancestor of Hawaiian flies or during the evolution of the clade. Our results suggests that both the modified use of ancestral genes and the evolution of new ones may occur in rapid radiations.

Re-annotation of eight Drosophila genomes

The sequenced genomes of the Drosophila phylogeny are a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system. These have also facilitated evolutionary studies on the selected and random differences that distinguish the thousands of extant species of Drosophila. However, full utility has been hampered by uneven genome annotation. We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on D. melanogaster that best matched the extensively curated annotation. We then applied this to the other species to add more than 10000 transcript models per species. We also developed new orthologs to facilitate cross-species comparisons. We validated the new annotation of the distantly related Drosophila grimshawi with an extensive collection of newly sequenced cDNAs. This re-annotation will facilitate understanding both the core commonalities and the species differences in this important group of model organisms, and suggests a strategy for annotating the many forthcoming genomes covering the tree of life.

Reannotation of eight Drosophila genomes

The sequenced genomes in the Drosophila phylogeny is a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system. These have also facilitated studying the selected and random differences that distinguish the thousands of extant species of Drosophila. However, full utility has been hampered by uneven genome annotation. We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on Drosophila melanogaster to develop a pipeline that best matched the extensively curated annotation. We then applied this to the other species to add tens of thousands of new gene models per species. We also developed new orthologs to facilitate cross-species comparisons. We validated the new annotation of the distantly related Drosophila grimshawi with an extensive collection of newly sequenced cDNAs. This reannoation will facilitate understanding both the core commonalities and the species differences in this important group of model organisms.

Male–male pheromone signalling in a lekking Drosophila

Interest in sex pheromones has mainly been focused on mate finding, while relatively little attention has been given to the role of sex pheromones in mate choice and almost none to competition over mates. Here, we study male response to male pheromones in the lekking Drosophila grimshawi , where males deposit long-lasting pheromone streaks that attract males and females to the leks and influence mate assessment. We used two stocks of flies and both stocks adjusted their pheromone depositing behaviour in response to experimental manipulation, strongly indicating male ability to distinguish between competitors from qualitative differences in pheromone streaks alone. This is the first example of an insect distinguishing between individual odour signatures. Pheromone signalling influenced competition over mates, as males adjusted their investment in pheromone deposition in response to foreign pheromone streaks. Both sexes adapt their behaviour according to information from olfactory cues in D. grimshawi , but the relative benefits from male–female, as compared to male–male signalling, remain unknown. It seems likely that the pheromone signalling system originally evolved for attracting females to leks. The transition to a signalling system for conveying information about individuals may well, however, at least in part have been driven by benefits from male–male signalling.