Draft genome assembly of Tenualosa ilisha, Hilsa shad, provides resource for osmoregulation studies

Abstract

This study provides the first high-quality draft genome assembly (762.5 Mb) of Tenualosa ilisha that is highly contiguous and nearly complete. We observed a total of 2,864 contigs, with 96.4% completeness with N50 of 2.65 Mbp and the largest contig length of 17.4 Mbp, along with a complete mitochondrial genome of 16,745 bases. A total number of 33,042 protein coding genes were predicted, among these, 512 genes were classified under 61 Gene Ontology (GO) terms, associated with various homeostasis processes. Highest number of genes belongs to cellular calcium ion homeostasis, followed by tissue homeostasis. A total of 97 genes were identified, with 16 GO terms related to water homeostasis. Claudins, Aquaporins, Connexins/Gap junctions, Adenylate cyclase, Solute carriers and Voltage gated potassium channel genes were observed to be higher in number in T. ilisha, as compared to that in other teleost species. Seven novel gene variants, in addition to claudin gene (CLDZ), were found in T. ilisha. The present study also identified two putative novel genes, NKAIN3 and L4AM1, for the first time in fish, for which further studies are required for pinpointing their functions in fish. In addition, 1.6 million simple sequence repeats were mined from draft genome assembly. The study provides a valuable genomic resource for the anadromous Hilsa. It will form a basis for future studies, pertaining to its adaptation mechanisms to different salinity levels during migration, which in turn would facilitate in its domestication.

Morpho-Genetic Divergence and Adaptation of Anadromous Hilsa shad (Tenualosa ilisha) Along Their Heterogenic Migratory Habitats

“…The significant regulation of molecular activities by these transmembrane and signaling pathways prove their importance in up-keeping the intracellular homeostasis of Hilsa shad under various salinity and osmotic conditions. Very recently, the association of SLCs, GRIKs, and MYOs has also been observed in C. harengus in maintaining ionic homeostasis (Mohindra et al, 2019). PrRPR was found to be reported to involve in neuromodulation in the brain of the guppy as well as in tilapia (Amano et al, 2007;Watanabe and Kaneko, 2010).…”

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

“…4). An appropriate reference genome of Hilsa with chromosomal information is not available [4][5][6] . Thus, transcriptome was reconstructed from the RNA-Seq data using the Trinity de novo RNA-Seq assembler which outperforms others in terms of overall reads representation of the assembly, completeness, mismatch and mis-assembly, etc 25 .…”

“…Since, Hilsa is of central importance as a primary fisheries species in Bangladesh, more in-depth molecular work is needed to understand their physiology and adaptation mechanism in both marine and fresh aquatic environments. At present, 3 draft genome assemblies of Hilsa are publicly available [4][5][6] . The publicly available de novo transcriptome assemblies for Hilsa are limited to either muscle or liver tissues 7,8 .…”

Unveiling the gut bacteriome diversity and distribution in the national fish hilsa (Tenualosa ilisha) of Bangladesh

“…Recognised as an iconic flagship species of the country, it is commonly identified by various names such as ilish, hilsa herring, or hilsa shad. As a member of the Clupeidae family, it shares a close relationship with herring species [ 1 , 2 ]. Due to its distinct flavor and exceptional taste, the hilsa fish holds significant economic value and experiences high demand worldwide.…”