A hybrid transcriptome assembly reveals coding and non-coding landscapes in Drosophila hemocytes

However, the full extent of transcriptional and post-transcriptional regulation underlying these processes remains poorly understood. Here, we employed a hybrid sequencing strategy integrating Oxford Nanopore long-read and Illumina short-read sequencing to provide a more comprehensive transcriptome annotation.

This enabled discovery of full-length transcripts with novel 5′ and 3′ boundaries and uncovered 349 previously unannotated long non-coding RNAs highly induced during late stages of wasp infestation. To ensure high confidence transcript models, we further eliminated potential intra-priming artifacts specific to long-read cDNA data. This high-confident full-length transcript models helped to reveal cell type–specific lncRNA markers in lamellocytes and crystal cells by single-cell analyses, which recapitulated hemocyte differentiation trajectories.