Marine Biotechnology Fish Nutrition and Health Division, ICAR- Central Marine Fisheries Research Institute, Kochi, Kerala, 682018, India.
Mandapam Regional Centre of ICAR- Central Marine Fisheries Research Institute, Mandapam Camp, Tamil Nadu, 623520, India.
Sci Data. 2023 Feb 16;10(1):97. doi: 10.1038/s41597-022-01907-0.
Cobia (Rachycentron canadum, Rachycentridae) is one of the prospective species for mariculture. The transcriptome-based study on cobia was hampered by an inadequate reference genome and a lack of full-length cDNAs. We used a long-read based sequencing technology (PacBio Sequel II Iso-Seq3 SMRT) to obtain complete transcriptome sequences from larvae, juveniles, and various tissues of adult cobia, and a single SMRTcell generated 99 gigabytes of data and 51,205,946,694 bases. A total of 8609435, 7441673 and 9140164 subreads were generated from the larval, juvenile, and adult sample pools, with mean sub-read lengths of 2109.9, 1988.2 and 1996.2 bp, respectively. All samples were combined to increase transcript recovery and clustered into 35661 high-quality reads. This is the first report on a full-length transcriptome from R. canadum. Our results illustrate a significant increase in the identified amount of cobia LncRNAs and alternatively spliced transcripts, which will help improve genome annotation. Furthermore, this information will be beneficial for nutrigenomics and functional studies on cobia and other commercially important mariculture species.
军曹鱼（Rachycentron canadum，军曹鱼科）是一种有潜力的海水养殖品种。由于缺乏参考基因组和全长 cDNA，基于转录组的军曹鱼研究受到了阻碍。我们使用长读长测序技术（PacBio Sequel II Iso-Seq3 SMRT），从幼鱼、幼鱼和成鱼的各种组织中获得了完整的转录组序列，单个 SMRT 细胞产生了 99 千兆字节的数据和 51,205,946,694 个碱基。从幼鱼、幼鱼和成鱼样本池中分别产生了 8609435、7441673 和 9140164 个亚读长，平均亚读长分别为 2109.9、1988.2 和 1996.2bp。所有样本合并以增加转录本的回收率，并聚类为 35661 个高质量的转录本。这是第一个关于 R. canadum 全长转录组的报告。我们的结果表明，鉴定出的军曹鱼长非编码 RNA 和可变剪接转录本的数量显著增加，这将有助于改善基因组注释。此外，这些信息将有助于军曹鱼和其他商业上重要的海水养殖物种的营养基因组学和功能研究。
