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However, the full extent of transcriptional and posttranscriptional 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 the discovery of full-length transcripts with novel 5\u2032 and 3\u2032 boundaries and uncovered 349 previously unannotated long noncoding 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 highly confident full-length transcript models helped reveal cell type\u2013specific long noncoding RNA (lncRNA) markers in lamellocytes and crystal cells by single-cell analyses, which recapitulated hemocyte differentiation trajectories. Notably, RNAi-based depletion of 2 highly induced lncRNAs impaired lamellocyte formation under wasp infestation, highlighting their functional relevance. Collectively, our findings provide detailed insights into the Drosophila larval immune transcriptomes through the long-read sequencing and highlight the regulatory roles of noncoding RNAs in innate immunity.<\/jats:p>","DOI":"10.1093\/genetics\/iyag208","type":"journal-article","created":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T10:51:39Z","timestamp":1786445499000},"source":"Crossref","is-referenced-by-count":0,"title":["A hybrid transcriptome assembly reveals coding and noncoding landscapes in\n                    <i>Drosophila<\/i>\n                    hemocytes"],"prefix":"10.1093","volume":"234","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5354-6910","authenticated-orcid":false,"given":"Kyung-Tae","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Life Science, College of Natural Sciences, Hanyang University , Seoul 04763 ,","place":["Republic of Korea"]},{"name":"Bio-BigData Center, Hanyang Institute of Bioscience and Biotechnology, Hanyang 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