Nanopore based direct RNA sequencing across development of C elegans.

We applied nanopore-based direct RNA sequencing to characterize the developmental polyadenylated transcriptome of C. elegans. Taking advantage of long reads spanning the full length of mRNA transcripts we provide support for 20,902 splice isoforms across 14,115 genes, without the need for computational reconstruction of gene models. Of the isoforms identified, 2,188 are novel splice isoforms not present in the Wormbase WS265 annotation. Furthermore, we identified 16,325 three-prime untranslated region (3'UTR) isoforms, 2,304 of which are novel and do not fall within 10 bp of existing 3'UTR datasets and annotations. Combining 3' UTRs and splice isoforms we identified 25,944 full-length isoforms. We used nanopore data to measure the poly(A) tail lengths for each of our reads, and examine properties of these lengths.