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

AI Article Synopsis

  • Hilsa fish, an important species for Bangladesh's fish production, lacks comprehensive transcriptome data.
  • This study presents a catalog of Hilsa's transcriptome using RNA-Seq from various tissues (brain, gill, kidney, liver, muscle) and aquatic habitats (freshwater, brackish, seawater).
  • The research identified 462,085 transcript isoforms and annotated them using the UniPortKB reference, aiding future studies in gene expression and candidate gene identification.

Article 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.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10106452PMC
http://dx.doi.org/10.1038/s41597-023-02132-zDOI Listing

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