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

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 N of 2.65 Mbp and the largest contig length of 17.4 Mbp, along with a complete mitochondri...

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Bibliographic Details
Published in:Scientific reports 2019-11, Vol.9 (1), p.16511-14, Article 16511
Main Authors: Mohindra, Vindhya, Dangi, Tanushree, Tripathi, Ratnesh K, Kumar, Rajesh, Singh, Rajeev K, Jena, J K, Mohapatra, T
Format: Article
Language:English
Subjects:
Adaptation, Biological - genetics
Adenylate cyclase
Animals
Aquaporins
Calcium homeostasis
Computational Biology - methods
Connexins
Conserved Sequence
Domestication
Fishes - physiology
Gap junctions
Gene Expression Profiling
Genes
Genome
Genome, Mitochondrial
Genomes
Genomics - methods
Homeostasis
Mitochondria
Molecular Sequence Annotation
Multigene Family
Nucleotide sequence
Osmoregulation
Potassium channels (voltage-gated)
Repetitive Sequences, Nucleic Acid
Simple sequence repeats
Studies
Tenualosa ilisha
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Summary: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 N 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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-019-52603-w