Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex

Background: Long non-coding RNAs (IncRNAs) have been defined as mRNA-like transcripts longer than 200 nucleotides that lack significant protein-coding potential, and many of them constitute scaffolds for ribonucleoprotein complexes with critical roles in epigenetic regulation. Various IncRNAs have been implicated in the modulation of chromatin structure, transcriptional and post-transcriptional gene regulation, and regulation of genomic stability in mammals, Caenorhabditis elegans, and Drosophila melanogaster. The purpose of this study is to identify the IncRNA landscape in the malaria vector An. gambiae and assess the evolutionary conservation of IncRNAs and their secondary structures across the Anopheles genus. Results: Using deep RNA sequencing of multiple Anopheles gambiae life stages, we have identified 2,949 IncRNAs and more than 300 previously unannotated putative protein-coding genes. The IncRNAs exhibit differential expression profiles across life stages and adult genders. We find that across the genus Anopheles, IncRNAs display much lower sequence conservation than protein-coding genes. Additionally, we find that IncRNA secondary structure is highly conserved within the Gambiae complex, but diverges rapidly across the rest of the genus Anopheles. Conclusions: This study offers one of the first IncRNA secondary structure analyses in vector insects. Our description of IncRNAs in An. gambiae offers the most comprehensive genome-wide insights to date into IncRNAs in this vector mosquito, and defines a set of potential targets for the development of vector-based interventions that may further curb the human malaria burden in disease-endemic countries.