Deciphering Salinity-Induced Transcriptomic Variations inOsmoregulatory Tissues Gills and Kidney of Hilsa Shad (Tenualosa ilisha)

Afsana Akter Rupa; Md Arko Ayon Chowdhury; Md Lifat  Rahi; Amin Ahsan Ali; Haseena Khan; Md Ashraful  Amin; Mohammad Riazul  Islam

doi:10.3329/brc.v11i2.82635

Authors

Afsana Akter Rupa Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
Md Arko Ayon Chowdhury Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
Md Lifat Rahi Fisheries and Marine Resource Technology (FMRT) Discipline, Khulna University, Khulna, Bangladesh
Amin Ahsan Ali Central for Computational & Data Sciences, Independent University, Bangladesh (IUB)
Haseena Khan Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
Md Ashraful Amin Central for Computational & Data Sciences, Independent University, Bangladesh (IUB)
Mohammad Riazul Islam Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh

DOI:

https://doi.org/10.3329/brc.v11i2.82635

Keywords:

Hilsa, Anadromous fish, RNA-seq, Transcriptome, Osmoregulation, Differential Gene Ex-pression

Abstract

The hilsa shad (Tenualosa ilisha), the national fish of Bangladesh, is an anadromous species that migrates across environments with varying salinities, placing selective pressure on gene expression to support osmoregulation. This study examined gene expression in the gill and kidney tissues of hilsa, assessing salinity acclimation across freshwater (<0.5 ppt), brackish water (12.0 ppt), and seawater (26.0 ppt). Illumina NovaSeq 6000 sequencing generated over 1.67 billion high-quality reads, which were assembled into a de novo reference transcriptome of 218,867 unigenes with an average contig length of 620 bases. Sequence alignment was performed against NCBI-nr, Swiss-Prot, GO, KEGG, and COG databases, with 6,070 unigenes annotated in all databases. Using freshwater samples as a control, 502 and 257 DEGs were identified in the gills of brackish and seawater hilsa, respectively, while 632 and 89 DEGs were observed in the kidney. GO analysis highlighted osmoregulatory functions such as ion transport, transmembrane transporter activity, and metal ion binding. KEGG pathway analysis revealed involvement in pathways essential to osmoregulation, including MAPK and cAMP signaling, lipid metabolism, and adherens junctions. Differentially expressed genes related to osmoregulation included solute carrier proteins (NKCC, NHE3), channel-mediated proteins (AQP), and tight junction proteins (Claudin, Cadherin). These findings enhance understanding of T. ilisha's osmophysiology and the genetic basis of its adaptive mechanisms.

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