Authors

Discussion

Parasitic infections account for a large burden of disease in animals, plants, and humans. The gastrointestinal parasitic nematode genus Strongyloides has a unique and complex life cycle that alternates between genetically identical parasitic and free-living generations, making them a great model to study parasitism. Identification and characterization of life cycle specific gene expression is important for understanding the fundamental principles of parasitic mechanisms, its evolution, and the control/treatment of the parasite infections. Previous research has shown that parasitic and free-living adults both express a unique set of mRNA and sRNAs, respectively, implying an underlining mechanism of post-transcriptional gene regulation. Most of our knowledge about mRNA transcripts in parasites is incomplete as it relies on short read sequencing which often results in missing information about alternative splicing, 5’UTRs, 3’UTRs and polyA tails. These play an important role in gene regulation and currently need to be predicted computationally. In this study, using nanopore sequencing, we have identified full-length transcripts for the gastrointestinal parasite Strongyloides ratti; a species that has one of the best assembled genomes among nematodes (Hunt et al., 2016). We have obtained 50 million reads across 4 life cycle stages with a minimum of 76% of reads representing full-length transcripts. The sequenced life cycle stagesof S. ratti include genetically identical parasitic and free-living adults, both with at least 2 million full-length transcripts per replicate. 10,000 novel isoforms were identified across the 4 life cycle stages. In at least 80% and almost 50% of full-length mRNA we have established a 3’UTR* or a 5’UTR, respectively. To better understand the mechanisms of gene regulation in parasitism, we investigate how alternatively spliced transcripts, UTRs and polyA tails vary between life cycle stages. This new data will help us recognise the role of isoforms and UTR variation in parasitism and show how long read sequencing can improve our current genome annotations.