Long non-coding RNA response of 6-day-old Apis cerana cerana larvae to Ascosphaera apis infection

Abstract:

[Objective] This study aims to investigate the differential expression pattern of long non-coding RNAs (lncRNAs) and their regulatory function involved in Apis cerana cerana 6-day-old larval gut response to Ascosphaera apis infection. [Methods] Un-infected and Ascosphaera apis-infected 6-day-old larval guts of Apis cerana cerana (AcCK and AcT) were sequenced using strand-specific cDNA library-based RNA-seq technology. Structural characteristics and expression pattern of lncRNAs were analyzed using related bioinformatic softwares. DElncRNAs were screened followed by investigation of their cis-acting role and competitive endogenous RNA (ceRNA) network. RT-qPCR was conducted to verify the sequencing data and expression pattern of DElncRNAs. [Results] Here, 642 known lncRNAs and 487 novel lncRNAs were identified. Compared with mRNAs, these Apis cerana cerana lncRNAs were shorter in exon and intron length, fewer in exon number and lower in expression level. Additionally, 43 antisense lncRNAs were discovered to have complementary relationship with 40 sense-strand mRNAs. In AcCK vs. AcT comparison group, 367 up-regulated lncRNAs and 268 down-regulated ones were identified. In total, 194 DElncRNAs were found to potentially regulate 461 upstream and downstream genes, which were annotated to 38 functional terms such as cellular process, metabolic process and catalytic activity, as well as 191 pathways including amino acid metabolism, endocytosis and MAPK signaling pathways. Moreover, 180 DElncRNAs can target 50 DEmiRNAs, further regulating 6365 mRNAs; additionally, complex regulatory networks existed among them. [Conclusion] These results demonstrated that partial antisense lncRNAs may participate in host response to Ascosphaera apis infection; some DElncRNAs may regulate upstream and downstream genes relative to material metabolism and immune-associated pathways, thus mediating host Ascosphaera apis-response; a portion of DElncRNAs including TCONS_00010661 and TCONS_00003104 were likely to regulate Jak-STAT signaling pathway and oxidative phosphorylation and corresponding enriched genes via ceRNA networks, further participating in the response of host to Ascosphaera apis invasion.