Comparative transcriptomics of long intergenic noncoding RNAs in Drosophila

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Without the constraints of the amino acid code, long intergenic noncoding RNAs (lincRNAs) can be expected to evolve along different trajectories than protein-coding genes. Most studies of lincRNA evolution analyze evolution only at the sequence level without ascertaining whether the lincRNA is expressed. Over 2,000 lincRNAs (and counting) have already been identified in the classic model system Drosophila melanogaster. Here, using RNA-Seq and computational identification of protein-coding ability, we identify 1,768 lincRNA transcripts at 1,586 unique loci in a second species of Drosophila - D. pseudoobscura. These lincRNAs are expressed in every surveyed developmental stage (1st instar larva, 3rd instar larva, pupa, and adult) in both sexes, with a large number increasing in expression as male development proceeds. This male bias can largely be explained by overrepresentation of lincRNAs in the testes. Unequal distributions of sex-biased lincRNAs on the X chromosome and autosomes are consistent with selection-based models of gene trafficking on or off the X chromosome, implying function for some of these lincRNAs. Finally, reciprocal blast searches between annotated lincRNAs in the D. pseudoobscura and D. melanogaster transcriptomes identify 80 conserved lincRNAs. Interestingly, direct coordinate conversions between the two genomes reveal another 54 D. pseudoobscura lincRNAs that are expressed in the same position as a D. melanogaster lincRNA but have low enough sequence conservation to preclude alignment via blast. Whether these positionally equivalent lincRNAs are true homologs with similar functions in both genomes is unclear, but we look at other transcript features, such as transcript orientation, gene structure, and developmental expression profiles to explore this possibility. We find 22 high-confidence lincRNA homologs with conservation of multiple transcript-level features, and we designate these as high-confidence homologs that warrant further biological investigation. This work represents the first comparative transcriptomic analyses of lincRNAs in Drosophila.