Full-Length Transcriptome Analysis Reveals New Insights into the Immune System of Black Amur Bream (<i>Megalobrama terminalis</i>) Using PacBio Iso-Seq

The Megalobrama genus is economically significant in China, with M. amblycephala (Wuchang bream) being the most studied species due to its prominence. However, the immune system of M. terminalis (Black Amur bream), another species within the genus, remains underexplored despite its notable resistance to bacterial infections, including those caused by Aeromonas hydrophila. This study aimed to address this gap by conducting a comprehensive transcriptomic analysis of M. terminalis, focusing on immune-related genes. By employing a combination of PacBio Isoform Sequencing (Iso-Seq) and Illumina short-read sequencing, we identified and annotated 12,426 non-redundant isoforms, of which 11,872 were successfully annotated across multiple databases. The study also revealed 853 alternative splicing events, with retained introns being the most common type, and the identification of 672 transcription factors and 426 long non-coding RNAs. Importantly, we observed isoforms of several key immune-related genes, including alpha-2-macroglobulins, complement component 3, mannose-binding lectins, and those involved in the adaptive immune system, such as immunoglobulin heavy chains, and major histocompatibility complex (MHC) classes I and II. These findings offer valuable insights into the immune complexity of M. terminalis and reveal a sophisticated network of immune responses, providing a foundation for future research to enhance disease resistance in aquaculture. The study not only fills a critical knowledge gap but also has significant implications for improving the health and resilience of aquaculture stocks. CorrectHQ.fa - LoRDEC-corrected transcripts. hq_isoforms.fasta.no5merge.collapsed.rep.fa - Non-redundant isoforms. cogent.fake_genome.fasta and cogent.fake_genome.gff - Fake genome FASTA file and its corresponding GFF annotation.