Evaluation of various RNA-seq approaches for identification of outrons in the flatworm Opisthorchis felineus

As a result of spliced leader trans-splicing (SLTS), the original 5'-end (outron) of the transcripts is replaced by a short spliced leader sequence, donated from a specialized SL RNA. SLTS is involved in the RNA processing of more than half of O. felineus genes, making it hard to determine the structure of outrons and bona fide transcription start sites of the corresponding genes and operons, being based solely on mRNA-seq data. In the study, associated with the current dataset, we evaluated four experimental approaches for identifying outrons in O. felineus using low-depth massive parallel sequencing. Two of them were developed by us for targeted sequencing of already processed outrons. The first (SLi-RT) is based on a sequence-specific reverse transcription from the SL intron toward the 5'-end of the Y-branched outron. The second (SLi-BC) utilizes outron hybridization with an immobilized single-stranded DNA probe complementary to the SL intron. Additionally, two approaches to the sequencing of rRNA-depleted total RNA, the commercially available Zymo-Seq RiboFree kit (ZymoSeq) and digestion by Terminator^TM 5´-Phosphate-Dependent Exonuclease (TermExo), were used to assess the identification of a wider range of transcripts compared to mRNA-seq. The dataset contains the raw paired-end data in FASTQ format for the corresponding RNA-seq libraries sequenced at a low depth on Illumina MiSeq platform.