Genome-Wide Identification of Long Non-coding RNAs in the Gravid Ectoparasite Varroa destructor.

Zheguang Lin,Cong Han,Guohong Chen,Yibing Liu,Heng Chen,Wei Wang,Hao Xu,Xiaoling Su,Xiaomei Chen,Yujiao Li,Yalu Ke,Ting Ji

doi:10.3389/fgene.2020.575680

Abstract

Long non-coding RNAs (lncRNAs) emerge as critical regulators across a wide variety of biological functions in living organisms. However, to date, no systematic characterization of lncRNAs has been investigated in the ectoparasitic mite Varroa destructor, the most severe biotic threat to honey bees worldwide. Here, we performed an initial genome-wide identification of lncRNAs in V. destructor via high-throughput sequencing technology and reported, for the first time, the transcriptomic landscape of lncRNAs in the devastating parasite. By means of a lncRNA identification pipeline, 6,645 novel lncRNA transcripts, encoded by 3,897 gene loci, were identified, including 2,066 sense lncRNAs, 2,772 lincRNAs, and 1,807 lncNATs. Compared with protein-coding mRNAs, V. destructor lncRNAs are shorter in terms of full length, as well as of the ORF length, contain less exons, and express at lower level. GO term and KEGG pathway enrichment analyses of the lncRNA target genes demonstrated that these predicted lncRNAs may be potentially responsible for the regulatory functions of cellular and biological progresses in the reproductive phase of V. destructor. To our knowledge, this is the first catalog of lncRNA profile in the parasitiformes species, providing a valuable resource for genetic and genomic studies. Understanding the characteristics and features of lncRNAs in V. destructor would promote sustainable parasite control.

Highlights

Colony losses of the western honey bee Apis mellifera in the Western world are a serious issue due to the critical role of honey bees in the balance of the ecosystem, sustainable agriculture, and food security (Neumann and Carreck, 2010; Potts et al, 2016; Steinhauer et al, 2018)
We reported the Long non-coding RNAs (lncRNAs) profile of V. destructor by genome-wide RNA-seq in this study, and the genomic and structural features of the lncRNAs showed consistent with their counterparts in other species
Evidence is becoming increasingly clear that the function of lncRNAs is associated with their unique subcellular localization (Chen, 2016), and most of the lncRNAs detected in V. destructor were accumulated in nucleus

Summary

Introduction

Colony losses of the western honey bee Apis mellifera in the Western world are a serious issue due to the critical role of honey bees in the balance of the ecosystem, sustainable agriculture, and food security (Neumann and Carreck, 2010; Potts et al, 2016; Steinhauer et al, 2018). V. destructor feasts on the fat body (Ramsey et al, 2018, 2019) of honey bees, transmits viruses, and affects host immunity (Yang and Cox-Foster, 2005; Rosenkranz et al, 2010; Di Prisco et al, 2016), severely interrupting the social organization and demographic continuity in A. mellifera colonies. Without treatment against this mite, infested A. mellifera colonies usually die within 6 months to 2 years (Kraus and Page, 1995; Le Conte et al, 2010). The emerging functional elements of non-coding RNAs (ncRNAs) have yet to report with this parasitic mite

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