Long-read direct RNA sequencing by 5’-Cap capturing in locusts. Locusta migratoria migratoria

The large genome of the migratory locust (Locusta migratoria) genome accumulates massive amount of accumulated transposable elements (TEs), which show intrinsic transcriptional activities. Hampering the ability to precisely determine full-length RNA transcript sequences are TEs, which produce numerous highly similar fragments that are difficult to resolve using short-read sequencing technology. Here, we developed a 5’-Cap capturing method using Nanopore long-read direct RNA sequencing to characterize full-length transcripts in their native RNA form and to analyze the TE exonization pattern in the locust transcriptome. TE-derived sequences were detected in more than half of all RNA transcripts analyzed, indicating widespread establishment of TE exonization in the locust transcriptome. The results of the transcriptomic spectrum influenced by Piwi expression are consistent with those of previous studies in which transcripts containing TE-derived sequences were the main targets of Piwi-mediated repression. However, taking advantage of sequencing the full-length untranslated region (UTR) by the 5’-Cap capturing method with Nanopore RNA sequencing, our study showed that Piwi expression regulates the length of RNA transcripts containing TE-derived sequences, creating an alternative UTR usage. Overall, our results reveal the transcriptomic characteristics of TE exonization in the organism with large and repetitive genomes.