Integrated transcriptome catalog of Tenualosa ilisha as a resource for gene discovery and expression profiling

Md Arko Ayon Chowdhury; Md Rakibul Islam; Al Amin; Sadia Noor Mou; Kazi Newaz Ullah; Abdul Baten; Mohammad Shoyaib; Amin Ahsan Ali; Farhana Tasnim Chowdhury; Md Lifat Rahi; Haseena Khan; M Ashraful Amin; Mohammad Riazul Islam

doi:10.1038/s41597-023-02132-z

Integrated transcriptome catalog of Tenualosa ilisha as a resource for gene discovery and expression profiling

Sci Data. 2023 Apr 17;10(1):214. doi: 10.1038/s41597-023-02132-z.

Authors

Md Arko Ayon Chowdhury^{1

2}, Md Rakibul Islam^{1

2}, Al Amin^{1

2}, Sadia Noor Mou^{1

2}, Kazi Newaz Ullah^{2

3}, Abdul Baten⁴, Mohammad Shoyaib⁵, Amin Ahsan Ali², Farhana Tasnim Chowdhury¹, Md Lifat Rahi⁶, Haseena Khan¹, M Ashraful Amin⁷, Mohammad Riazul Islam⁸

Affiliations

¹ Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh.
² Center for Computational and Data Sciences (CCDS), Independent University, Bangladesh (IUB), Dhaka, Bangladesh.
³ Department of Zoology, Jagannath University, Dhaka, 1100, Bangladesh.
⁴ Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Royal Prince Alfred Hospital, Camperdown, Australia.
⁵ Institute of Information Technology (IIT), University of Dhaka, Dhaka, 1000, Bangladesh.
⁶ Fisheries and Marine Resource Technology (FMRT) Discipline, Khulna University, Khulna, 9208, Bangladesh.
⁷ Center for Computational and Data Sciences (CCDS), Independent University, Bangladesh (IUB), Dhaka, Bangladesh. aminmdashraful@iub.edu.bd.
⁸ Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh. mriazulislam@du.ac.bd.

Abstract

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.

Publication types

Dataset

MeSH terms

Animals
Fishes* / genetics
Gene Expression Profiling
Genetic Association Studies
Molecular Sequence Annotation
Protein Isoforms / genetics
Transcriptome*

Substances

Protein Isoforms