Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection

Abstract

Long non-coding RNAs (lncRNAs) are a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins, and lncRNAs have been proven to play pivotal roles in a wide range of biological processes in animals and plants. However, knowledge of expression patterns and potential roles of honeybee lncRNA response to Nosema ceranae infection is completely unknown. Here, we performed whole transcriptome strand-specific RNA sequencing of normal midguts of Apis mellifera ligustica workers (Am7CK, Am10CK) and N. ceranae-inoculated midguts (Am7T, Am10T), followed by comprehensive analyses using bioinformatic and molecular approaches. A total of 6353 A. m. ligustica lncRNAs were identified, including 4749 conserved lncRNAs and 1604 novel lncRNAs. These lncRNAs had minimal sequence similarities with other known lncRNAs in other species; however, their structural features were similar to counterparts in mammals and plants, including shorter exon and intron length, lower exon number, and lower expression level, compared with protein-coding transcripts. Further, 111 and 146 N. ceranae-responsive lncRNAs were identified from midguts at 7-days post-inoculation (dpi) and 10 dpi compared with control midguts. Twelve differentially expressed lncRNAs (DElncRNAs) were shared by Am7CK vs. Am7T and Am10CK vs. Am10T comparison groups, while the numbers of unique DElncRNAs were 99 and 134, respectively. Functional annotation and pathway analysis showed that the DElncRNAs may regulate the expression of neighboring genes by acting in cis and trans fashion. Moreover, we discovered 27 lncRNAs harboring eight known miRNA precursors and 513 lncRNAs harboring 2257 novel miRNA precursors. Additionally, hundreds of DElncRNAs and their target miRNAs were found to form complex competitive endogenous RNA (ceRNA) networks, suggesting that these DElncRNAs may act as miRNA sponges. Furthermore, DElncRNA-miRNA-mRNA networks were constructed and investigated, the results demonstrated that a portion of the DElncRNAs were likely to participate in regulating the host material and energy metabolism as well as cellular and humoral immune host responses to N. ceranae invasion. Our findings revealed here offer not only a rich genetic resource for further investigation of the functional roles of lncRNAs involved in the A. m. ligustica response to N. ceranae infection, but also a novel insight into understanding the host-pathogen interaction during honeybee microsporidiosis.

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

“…Besides, the shorter length of the putative lncRNAs and the ORFs compared to mRNA also shared similar features with other well-studied species (Trapnell et al, 2010;Zhang et al, 2014;Wang et al, 2016;Wu et al, 2016;Zhan et al, 2016;Guo et al, 2018a,b;Liu et al, 2019). Although lncRNAs always performed lower expression level than the protein-coding genes (this study; Guo et al, 2018a,b;Chen et al, 2019;Liu et al, 2019), their role in the functional activities of organisms has been widely proved to be of significance (Furuno et al, 2006;Mercer et al, 2009;Zhang et al, 2014;Wu et al, 2016;Chen et al, 2019;Liu et al, 2019).…”

“…The present a few studies have demonstrated that these functional elements of lncRNAs participate in the regulation of the physiological processes of honey bees, such as labor division, ovary development, neural networks, pesticide metabolism, and pathogen resistance (Kiya et al, 2008;Humann et al, 2013;Jayakodi et al, 2015;Chen et al, 2017Chen et al, , 2019Liu et al, 2019;Fent et al, 2020). Guo et al (2018a,b) screened the lncRNAs in two honey bee fungi, Ascospheara apis and Nosema ceranae, providing the first two lncRNA profiles in honey bee pathogenic agents.…”

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

“…However, most studies of insect transcriptome analysis have focused on protein-coding genes, and non-coding RNAs were less informative [ 7 ]. According to the genomic location [ 8 ], lncRNAs are classified into four subcategories: long intergenic non-coding RNA (lincRNA), sense lncRNA, anti-sense lncRNA, and intronic lncRNA [ 9 ]. In eukaryotes, lncRNAs are transcribed at several sites of the genome by RNA polymerase II and RNA polymerase III [ 10 ].…”

The PacBio Full-Length Transcriptome of the Tea Aphid as a Reference Resource

“…The lncRNAs identification was widely reported in eukaryote mammals ( Kaushik et al, 2013 ; Zhan et al, 2016 ), plants ( Lv et al, 2016 ), and microorganisms ( Wang Z. et al, 2019 ). In insects, lncRNAs have been investigated in many species ( Zhu et al, 2016 ), e.g., Drosophila Melanogaster ( Wen et al, 2016 ), Apis mellifera ligustica ( Chen D. et al, 2019 ), and Nilaparvata lugens ( Chen M. Y. et al, 2019 ). In this study, only the lncRNAs with a poly “A” tailed were sequenced, so the number of the lncRNAs was less than that in other insects.…”