Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh.
Center for Computational and Data Sciences (CCDS), Independent University, Bangladesh (IUB), Dhaka, Bangladesh.
Sci Data. 2023 Apr 17;10(1):214. doi: 10.1038/s41597-023-02132-z.
The silver pride of Bangladesh, migratory shad, Tenualosa ilisha (Hilsa), makes the highest contribution to the total fish production of Bangladesh. Despite its noteworthy contribution, a well-annotated transcriptome data is not available. Here we report a transcriptomic catalog of Hilsa, constructed by assembling RNA-Seq reads from different tissues of the fish including brain, gill, kidney, liver, and muscle. Hilsa fish were collected from different aquatic habitats (fresh, brackish, and sea water) and the sequencing was performed in the next generation sequencing (NGS) platform. De novo assembly of the sequences obtained from 46 cDNA libraries revealed 462,085 transcript isoforms that were subsequently annotated using the Universal Protein Resource Knowledgebase (UniPortKB) as a reference. Starting from the sampling to final annotation, all the steps along with the workflow are reported here. This study will provide a significant resource for ongoing and future research on Hilsa for transcriptome based expression profiling and identification of candidate genes.
孟加拉国的银色瑰宝、洄游性鱼类长吻鮠（Tenualosa ilisha）对孟加拉国的鱼类总产量贡献最大。尽管它的贡献显著，但仍缺乏经过充分注释的转录组数据。在这里，我们报告了一个长吻鮠的转录组目录，该目录是通过对来自鱼体不同组织（脑、鳃、肾、肝和肌肉）的 RNA-Seq 数据进行组装构建的。我们从不同的水生栖息地（淡水、半咸水和海水）中采集了长吻鮠鱼，并在下一代测序（NGS）平台上进行了测序。从 46 个 cDNA 文库中获得的序列的从头组装揭示了 462,085 个转录本异构体，随后使用通用蛋白质资源知识库（UniPortKB）作为参考进行了注释。从采样到最终注释，我们在这里报告了所有步骤以及工作流程。这项研究将为长吻鮠基于转录组的表达谱分析和候选基因鉴定的当前和未来研究提供重要资源。
