Genes & Genomics

, Volume 41, Issue 1, pp 1–15 | Cite as

Muscle transcriptome resource for growth, lipid metabolism and immune system in Hilsa shad, Tenualosa ilisha

  • B. K. Divya
  • Vindhya MohindraEmail author
  • Rajeev K. Singh
  • Prabhaker Yadav
  • Prachi Masih
  • J. K. Jena
Research Article


The information on the genes involved in muscle growth, lipid metabolism and immune systems would help to understand the mechanisms during the spawning migration in Hilsa shad, which in turn would be useful in its future domestication process. The primary objective of this study was to generate the transcriptome profile of its muscle through RNA seq. The total RNA was isolated and library was prepared from muscle tissue of Tenualosa ilisha, which was collected from Padma River at Farakka, India. The prepared library was then sequenced by Illumina HiSeq platform, HiSeq 2000, using paired-end strategy. A total of 8.68 GB of pair-end reads of muscle transcriptome was generated, and 43,384,267 pair-end reads were assembled into 3,04,233 contigs, of which 23.99% of assembled contigs has length ≥ 150 bp. The total GO terms were categorised into cellular component, molecular function and biological process through PANTHER database. Fifty-three genes related to muscle growth were identified and genes in different pathways were: 75 in PI3/AKT, 46 in mTOR, 76 in MAPK signalling, 24 in Janus kinase–signal transducer and activator of transcription, 45 in AMPK and 27 in cGMP pathways. This study also mined the genes involved in lipid metabolism, in which glycerophospholipid metabolism contained highest number of genes (32) and four were found to be involved in fatty acid biosynthesis. There were 58 immune related genes found, in which 31 were under innate and 27 under adaptive immunity. The present study included a large genomic resource of T. ilisha muscle generated through RNAseq, which revealed the essential dataset for our understanding of regulatory processes, specifically during the seasonal spawning migration. As Hilsa is a slow growing fish, the genes identified for muscle growth provided the basic information to study myogenesis. In addition, genes identified for lipid metabolism and immune system would provide resources for lipid synthesis and understanding of Hilsa defense mechanisms, respectively.


Functional contigs PI3/AKT Fatty acid Immunity Innate Adaptive 



This work was undertaken under ICAR-National Agricultural Science Fund (NASF) sponsored consortium project code: CN No. 6932 (Reg.No. WQ-3023) and financial support by ICAR-NASF is duly acknowledged. The authors thankfully acknowledge the research facilities extended by Director, ICAR-NBFGR for this work.

Supplementary material

13258_2018_732_MOESM1_ESM.docx (1005 kb)
Supplementary material 1 (DOCX 1005 KB)
13258_2018_732_MOESM2_ESM.docx (44 kb)
Supplementary material 2 (DOCX 44 KB)


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Copyright information

© The Genetics Society of Korea and Springer Nature B.V. 2018

Authors and Affiliations

  • B. K. Divya
    • 1
  • Vindhya Mohindra
    • 1
    Email author
  • Rajeev K. Singh
    • 1
  • Prabhaker Yadav
    • 1
  • Prachi Masih
    • 1
  • J. K. Jena
    • 1
    • 2
  1. 1.ICAR- National Bureau of Fish Genetic Resources (NBFGR)LucknowIndia
  2. 2.Division of Fisheries ScienceIndian Council of Agricultural Research (ICAR)New DelhiIndia

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