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 <em>O. felineus</em> 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 <em>O. felineus</em> using low-depth massive parallel sequencing. Two of them were developed by us for targeted sequencing of already processed outrons. The first (<strong>SLi-RT</strong>) is based on a sequence-specific reverse transcription from the SL intron toward the 5'-end of the Y-branched outron. The second (<strong>SLi-BC</strong>) 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 (<strong>ZymoSeq</strong>) and digestion by Terminator^TM 5´-Phosphate-Dependent Exonuclease (<strong>TermExo</strong>), 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.