Evolnc: A Pipeline for Comparative Genomic and Transcriptomic Analyses of Long Non-Coding RNAs

Transcriptomic analyses from across eukaryotes have led to the conclusion that most of the genome is transcribed at some point in the developmental trajectory of an organism. One class of these transcripts is termed long noncoding RNAs (lncRNAs). Reported lncRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, accounting for ~90% of the genome. Recently, attention has focused on understanding the evolutionary dynamics of lncRNAs, particularly their conservation within genomes. To facilitate lncRNA discovery and comparative analyses at the genomic and transcriptomic level, we present Evolinc.  Evolinc is a custom pipeline that identified long non-coding RNAs from transcriptome assembly files and then searches for homologs in other species. Using sequence similarity, Evolinc reconstructs families of homologous lncRNAs, aligns the constituent sequences, builds gene trees, and uses gene tree / species tree reconciliation to infer evolutionary processes. The novelty of this pipeline is that it allows the user to investigate factors affecting lincRNA diversity within a large number of species. This pipeline is scaleable, working on one to thousands of lncRNAs and can perform comparisons between both large and small genomes. For ease of use we have pre-packaged Evolinc into an instance available in the iPlant's Atmosphere cloud computing service, as well as in iPlant's Discovery Environment. Evolinc is useful not only for inferring mechanisms affecting lncRNA diversity, but also for identifying lncRNAs in non-model systems where genome data is available.