Thousands of long noncoding RNAs (lncRNAs) have been annotated in eukaryotic genomes, but comparative transcriptomic approaches are necessary to understand their biological impact and evolution. To facilitate such comparative studies in Drosophila, researchers at the University of Maryland identified and characterized lncRNAs in a second Drosophilid – the evolutionary model D. pseudoobscura. Using RNA-Seq and computational filtering of protein-coding potential, they identified 1,589 intergenic lncRNA loci in D. pseudoobscura. The researchers surveyed multiple sex-specific developmental stages and found, like in D. melanogaster, increasingly prolific lncRNA expression through male development and an overrepresentation of lncRNAs in the testes. Other trends seen in D. melanogaster, like reduced pupal expression, were not observed. Nonrandom distributions of female-biased and non-testis-specific male-biased lncRNAs between the X chromosome and autosomes are consistent with selection-based models of gene trafficking to optimize genomic location of sex-biased genes. The numerous testis-specific lncRNAs, however, are randomly distributed between the X and autosomes, and we cannot reject the hypothesis that many of these are likely to be spurious transcripts. Finally, using annotated lncRNAs in both species, the researchers identified 134 putative lncRNA homologs between D. pseudoobscura and D. melanogaster and find that many have conserved developmental expression dynamics, making them ideal candidates for future functional analyses.
Computational identification of D. pseudoobscura lncRNAs from RNA-Seq data
(A) RNA from 12 different samples of D. pseudoobscura were sequenced, filtered for quality, mapped to the D. pseudoobscura genome, and assembled into a single comprehensive transcriptome. Unannotated, intergenic loci were screened for protein-coding ability using three complementary approaches, with the numbers of protein-coding loci identified via each approach detailed in (B). In total, 1,589 putative lncRNA loci were identified.