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

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.

Identification of long noncoding RNAs reveals the effects of dinotefuran on the brain in Apis mellifera (Hymenopptera: Apidae)

“…Studies on lncRNA expression in honey bees have been increasing in recent years, focused mainly on caste determination [ 19 , 31 ], the behavioral transition from nurse to forager [ 25 ], oviposition [ 32 , 33 ], and the response to pathogen infestation [ 20 , 21 , 34 ]. In the current study, RNA-seq was performed to identify the lncRNA and mRNA profiles of honey bees exposed to 0.01 mg/L dinotefuran for 1, 5, and 10 d to assess the potential regulators of honey bee growth and immune responses related to neonicotinoid insecticides.…”

Genome-Wide Characterization and Identification of Long Non-Coding RNAs during the Molting Process of a Spider Mite, Panonychus citri

“…lncRNA expression in the biological processes of development have been examined in insects [7,9]. In the mites, lncRNA has been identified in many physiological processes of mites such as V. destructor [33], T. cinnabarinus [34], and Dermatophagoides farina [36]. However, there is no previous report on the lncRNA involved in mite development and molting.…”

“…Although lncRNAs have been characterized in insects, there are few studies on the identification and functional annotation of lncRNAs in mites. In Varroa destructor, 6645 novel lncRNA transcripts were identified by RNA-seq, and function enrichment analysis predicted that these lncRNAs could regulate the reproductive phase of V. destructor [33]. In Tetranychus cinnabarinus, 4454 lncRNAs were identified in a cyflumetofen-resistant strain, and lincRNA_Tc13743.2 could decrease the inhibitory function of miR-133-5p that affected the expression of TcGSTm02 to regulate cyflumetofen resistance [34].…”

Difference between uncapping and removal behaviors in Apis cerana from the perspective of long non-coding RNAs

“…Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs with lengths exceeding 200 nt and contain two or more exons, although these do not encode proteins [31]. Despite lacking protein-coding abilities, lncRNAs are, nevertheless, extensively involved in a diverse range of physiological, metabolic, immune, and disease processes in eukaryotes [32][33][34]. Moreover, it has been established that the division of labor [35], caste differentiation [36], immune defense [37], reproduction [38], and other processes in honeybees are regulated by lncRNAs.…”