A manually curated annotation characterises genomic features of P. falciparum lncRNAs

• DOI: 10.1186/s12864-022-09017-2
• Publication Date: 2022-11-30T06:48:42Z
• Authors: Johanna Hoshizaki; Sophie H. Adjalley; Vandana Thathy; Kim Judge; Matthew Berriman; Adam J. Reid; Marcus C. S. Lee
• Keywords: 0301 basic medicine; /dk/atira/pure/subjectarea/asjc/1300/1311; long-read RNA sequencing.; name=Genetics; Annotation; Plasmodium falciparum; 610; QH426-470; Manual curation; 03 medical and health sciences; lncRNA; long-read RNA sequencing; Genetics; Humans; Malaria, Falciparum; 0303 health sciences; Research; Computational Biology; name=Biotechnology; Genomics; 3. Good health; Noncoding; RNA, Long Noncoding; TP248.13-248.65; /dk/atira/pure/subjectarea/asjc/1300/1305; Biotechnology

Abstract Background Important regulation occurs at the level of transcription in Plasmodium falciparum and growing evidence suggests that these apicomplexan parasites have complex regulatory networks. Recent studies implicate long noncoding RNAs (lncRNAs) as transcriptional regulators in P. falciparum. However, due to limited research and the lack of necessary experimental tools, our understanding of their role in the malaria-causing parasite remains largely unelucidated. In this work, we address one of these limitations, the lack of an updated and improved lncRNA annotation in P. falciparum.

Results We generated long-read RNA sequencing data and integrated information extracted and curated from multiple sources to manually annotate lncRNAs. We identified 1119 novel lncRNAs and validated and refined 1250 existing annotations. Utilising the collated datasets, we generated evidence-based ranking scores for each annotation and characterised the distinct genomic contexts and features of P. falciparum lncRNAs. Certain features indicated subsets with potential biological significance such as 25 lncRNAs containing multiple introns, 335 lncRNAs lacking mutations in piggyBac mutagenic studies and lncRNAs associated with specific biologic processes including two new types of lncRNAs found proximal to var genes.

Conclusions The insights and the annotation presented in this study will serve as valuable tools for researchers seeking to understand the role of lncRNAs in parasite biology through both bioinformatics and experimental approaches.