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11 11, 2019;9 (1): 16511.

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

Vindhya Mohindra, Tanushree Dangi, Ratnesh K Tripathi, Rajesh Kumar, Rajeev K Singh, J K Jena, T Mohapatra
Author Information
  1. Vindhya Mohindra: ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002, India. vindhyamohindra@gmail.com. ORCID
  2. Tanushree Dangi: ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002, India.
  3. Ratnesh K Tripathi: ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002, India.
  4. Rajesh Kumar: ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002, India.
  5. Rajeev K Singh: ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002, India.
  6. J K Jena: Indian Council of Agricultural Research (ICAR), Krishi Anusandhan Bhawan - II, New Delhi, 110 012, India.
  7. T Mohapatra: Indian Council of Agricultural Research (ICAR), Krishi Anusandhan Bhawan - II, New Delhi, 110 012, India.
PMID: 31712633 DOI: 10.1038/s41598-019-52603-w

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 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.

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MeSH Term

Adaptation, Biological
Animals
Computational Biology
Conserved Sequence
Fishes
Gene Expression Profiling
Genome
Genome, Mitochondrial
Genomics
Homeostasis
Molecular Sequence Annotation
Multigene Family
Osmoregulation
Repetitive Sequences, Nucleic Acid
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 1

Word Cloud

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