Abstract
Long non-coding RNAs (lncRNAs) are critical regulators of gene expression in eukaryotes. Short reads from Illumina sequencing, reverse transcriptase artefacts, and incomplete second-strand degradation in strand-specific cDNA libraries hamper genome-wide identification of lncRNAs, especially in gene-dense genomes such as Plasmodium. Here, we integrated long-read Oxford Nanopore Technology direct RNA sequencing, ribosome profiling, and single-cell transcriptomics to generate a robust and stage-specific characterization of P. falciparum lncRNAs. We generated comprehensive annotations of lncRNAs expressed in both asexual and sexual blood stages and confirmed their non-coding nature using ribosome profiling. Most lncRNAs showed pronounced stage-specific expression and appeared to be particularly abundant in mature gametocytes. Single-cell RNA sequencing revealed differential expression of many lncRNAs in female and male gametocytes, suggesting important roles in gametocytogenesis and transmission. Many lncRNAs are located antisense to protein-coding genes and are co-expressed with their sense mRNA, possibly from putative bidirectional promoters, while others overlap mRNA coding sequences or 3' untranslated regions and showed negatively correlated expression patterns. Overall, our study shows the prevalence of P. falciparum lncRNAs and highlights their possible roles in controlling the regulation of gene expression, particularly during gametocytogenesis.