Genome-Wide Long Intergenic Noncoding RNAs (lincRNAs) Profiling Reveals a Sub Set of lincRNAs Exhibiting Similar Response to Diverse Viral Diseases in Honey Bees

Long non-coding RNAs (lncRNAs) are classes of RNAs with inability to encode proteins. Recently, lncRNAs have gained special attention owing to their inevitable role in various biological process and diseases. In an attempt to identify long intergenic noncoding RNAs (lincRNAs) and their possible role in honeybee development/involvement in diseases, RNA-seq datasets generated for western honeybee (Apis mellifera) and Asian honeybee (Apis cerana) were used and identified a lincRNAs set of 2,470 with an average length of 1,011 bp from A. cerana and 1,514 with an average length of 790 bp in A. mellifera. The comparative digital gene expression of the seven major tissues showed that, 57% and 18% showed a tissue-specific expression in A. mellifera and A. cerana respectively. On the cutting edge of this study, although several lincRNAs were found to be specifically regulated on viral infection, a unique set of 10 lincRNAs showed similar pattern of differential expression to two different viral infections namely, Sacbrood virus (SBV) which highly affects A. cerana and Deformed-wing virus (DWV) which mainly found in A. mellifera. The real time expression analysis of these 10 lincRNAs after infection with virus in the larval and adult stages of A. cerana and in adult stage of A. mellifera bees using qRT-PCR also shared a similar pattern. This study provides the first comprehensive set of lincRNAs for honeybees and opens up a broad way to discover lincRNAs associated with important biological and hormone signaling pathways and various diseases.