Iso-Seq assembly and functional annotation of full-length transcriptome of turbot (Scophthalmus maximus) during bacterial infection.

Turbot (Scophthalmus maximus) is a flatfish, which is not only important in mariculture worldwide with the unique characteristic of body asymmetry, but also as an economically important species in aquaculture. Herein, we performed the first full-length transcriptome sequencing of turbot during the bacterial infection. A total of 307.1 Gb raw reads were obtained and processed with Iso-Seq, generating 187,509 high-quality redundant transcripts with an average length of 3005 base pairs. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis identified 81.5% complete BUSCOs and only 1.7% fragmented BUSCOs, suggesting a transcript structural completeness and functional diversity of this transcriptome. Moreover, the redundant transcripts were collapsed and compared to ENSEMBL reference with Cupcake and SQANTI3. Among 60,476 collapsed transcripts, we identified 12,059 annotated and 1684 novel genes. 42,956 (71.1%) transcripts provided new evidence for splice junctions identification. Furthermore, the untranslated region (UTR) identification was also benefited from the transcriptome. The open read frames prediction was conducted with PASApipeline. 42,118 transcripts were assigned with known function by aligning against Swiss-Prot or functional domain prediction. Taken together, the full-length transcriptome built in this study could provide important resources for immunologic research on turbot.