Comprehensive reconstruction and characterization of long non-coding RNAs in Opisthorchis viverrini

Abstract

Background: Opisthorchis viverrini is a parasitic flatworm that causes opisthorchiasis and is a major risk factor for cholangiocarcinoma (CCA) in Southeast Asia. Previous studies explored parasite biology, using the available reference genome annotation, specifically the mRNA expression. The information on genomic features of Long Non-Coding RNA (lncRNA), which can affect parasite biological function, is largely unannotated and remains unknown.

Objectives: We aimed to reconstruct and classify lncRNA derived from O. viverrini in vivo from a definitive host to understand its features and provide a new alternative option for lncRNA as an intervention target against opisthorchiasis.

Methods: Our study used rRNA-depleted data obtained by the Illumina NextSeq 550Dx platform to reassemble and classify lncRNA using available public bioinformatic tools.

Results: Our findings revealed a total of 38,282 transcripts assembled from uniquely mapped reads. A total of 20,607 transcripts were predicted as long non-coding transcripts of various lengths. In those transcripts, 11,077 antisense and 9,530 sense lncRNAs were accounted for based on transcription direction. Based on genomic location, we classified lncRNAs into four types: long intronic ncRNAs, long exonic ncRNAs, upstream longintergenic ncRNAs, and downstream long-intergenic ncRNAs.

Conclusion: Using an rRNA-depleted library, we provided a comprehensive profile of O. viverrini lncRNA and reconstructed 20,607 novel lncRNAs that may interact with protein-coding genes. This information will contribute to opisthorchiasis intervention by providing insight into the biological mechanisms of lncRNAs, serving as stage-specific biomarkers for therapeutic strategies in opisthorchiasis, laying the foundation for research on lncRNA mechanisms, and further improving the reference genome annotation.