Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera.

Murukarthick Jayakodi,Sang-Yoon Shin,Tae-Jin Yang,Chanseok Shin,Sang-Choon Lee,Doori Park,Young-Joon Ahn,Je Won Jung,Hyung Wook Kwon

doi:10.1186/s12864-015-1868-7

Abstract

BackgroundLong non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases.ResultsIn an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an average length of 1011 bp from A. cerana and 1514 lincRNAs with an average length of 790 bp in A. mellifera. Comparative analysis revealed that 5 % of the total lincRNAs derived from both species are unique in each species. Our comparative digital gene expression analysis revealed a high degree of tissue-specific expression among the seven major tissues of honey bee, different from mRNA expression patterns. A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues. Importantly, we identified 11 lincRNAs that are specifically regulated upon viral infection in honey bees, and 10 of them appear to play roles during infection with various viruses.ConclusionsThis study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1868-7) contains supplementary material, which is available to authorized users.

Highlights

Long non-coding RNAs are a class of RNAs that do not encode proteins
Genome-wide identification of Long intergenic non-coding RNA (lincRNA) from two sister honey bee species, A. cerana and A. mellifera To identify a comprehensive set of Asian honey bee lincRNAs, we used Illumina RNA sequencing (RNA-seq) data generated for the A. cerana genome project [41] and newly generated datasets from larvae, and Sacbrood virus (SBV)-infected and non-infected honey bees (Table 1)
The assembled sequences were analyzed to identify putative Long non-coding RNA (lncRNA), and 19,916 transcripts were selected based on nucleotide length ≥200 bp and Open reading frame (ORF) ≤ 100 amino acids (Fig. 1)

Summary

Introduction

Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. LncRNAs have gained special attention for their roles in various biological process and diseases. Advances in RNA sequencing technologies have allowed the rapid exploration of protein-coding and non-coding RNAs in both vertebrate and invertebrate genomes. Only a small portion of sequences code for proteins [1,2,3,4,5]. LncRNAs including Xist play a critical role in X-chromosome dosage compensation [28], genomic imprinting [29], epigenetic regulation [30], cellular pluripotency, and differentiation [31]

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Conclusion