Dataset Information

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

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.

SUBMITTER: Chowdhury MAA

PROVIDER: S-EPMC10106452 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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

Chowdhury Md Arko Ayon MAA Islam Md Rakibul MR Amin Al A Mou Sadia Noor SN Ullah Kazi Newaz KN Baten Abdul A Shoyaib Mohammad M Ali Amin Ahsan AA Chowdhury Farhana Tasnim FT Rahi Md Lifat ML Khan Haseena H Amin M Ashraful MA Islam Mohammad Riazul MR

Scientific data 20230417 1

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 w ...[more]

PMID: 37062771

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Project description:Small-scale fisheries (SSFs) have been playing a crucial role in meeting the basic needs of millions of people around the world. Despite this, the sustainability of global fisheries is a growing concern, and the factors enabling or constraining the sustainable management of small-scale fisheries remain poorly understood. Hilsa shad (Tenualosa ilisha) is the single most valuable species harvested in Bangladesh waters, serves nutrition, income, and employment to the large population. This study analyzed the state and challenges of hilsa fishery in the Gangetic River systems (Padma and Meghna Rivers) by using two frameworks, namely the social-ecological systems (SES) and drivers-pressure-state-impact-responses (DPSIR) frameworks. Primary data for this analysis were collected by in-depth interviews (n = 130) and focus group discussions (n = 8) with various stakeholders in the hilsa fisheries. The perspectives explored here have been both critical and constructive, including the identification of problems and suggestions for improving the management of this particular social-ecological system. Hilsa fisheries, however, have come under severe threat since 2003 because of population growth, overfishing, pollution, climate change, the disruption of migration routes due to siltation, etc. All these have caused reduced catches and less stable incomes for fishers. This, in turn, has led to poverty, malnutrition, social tensions, stakeholder conflicts, and debt cycles amongst more impoverished fishing communities. These problems have been compounded by improved fishing technology amongst larger-scale ventures, the use of illegal fishing gears, and the non-compliance of government fishery management programs. Recommendations include the promotion of community-supported fisheries, the enhancement of stakeholder's social resilience, the introduction of co-management approach, an increase in incentives and formal financial supports, and possible community-managed sustainable ecotourism including hilsa fishing-based tourism.

Dataset Information

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

Publications

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

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