Vol.:(0123456789) 1 3 Genes & Genomics https://doi.org/10.1007/s13258-018-0732-y RESEARCH ARTICLE Muscle transcriptome resource for growth, lipid metabolism and immune system in Hilsa shad, Tenualosa ilisha B. K. Divya 1  · Vindhya Mohindra 1  · Rajeev K. Singh 1  · Prabhaker Yadav 1  · Prachi Masih 1  · J. K. Jena 1,2 Received: 21 December 2017 / Accepted: 22 August 2018 © The Genetics Society of Korea and Springer Nature B.V. 2018 Abstract 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 profle 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 identifed and genes in diferent 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, specifcally during the seasonal spawning migration. As Hilsa is a slow growing fsh, the genes identifed for muscle growth provided the basic information to study myogenesis. In addition, genes identifed for lipid metabolism and immune system would provide resources for lipid synthesis and understanding of Hilsa defense mechanisms, respectively. Keywords Functional contigs · PI3/AKT · Fatty acid · Immunity · Innate · Adaptive Introduction With the advancement of technology, transcriptome study has played a significant role in all fields of biological research (Klopfeisch and Gruber 2012). Transcriptome or the expressed part of the genome is highly variable, depend- ing upon the specifc tissue type, environmental stressors or developmental stage (Huang et al. 2016). The gene expres- sion profles provide functional mechanisms of a genotype, resulting in a particular phenotype via study of pathway analysis (Papatheodorou et al. 2015). Apart from expres- sion the variations identifed from transcripts, such as single nucleotide polymorphism (SNP) (Divya et al. 2017) may act as molecular markers for selection of individuals with diferential performance (Zou et al. 2015). Skeletal muscles cells are important for animals to deter- mine diferent behaviors for their existence in changing envi- ronment and their characterizations for in-depth investigation (Musumeci et al. 2015). The Cell signaling pathways and their regulatory factors are integrated phenotypically with skeletal muscle and also with muscle fbers (Buckingham and Rigby 2014). The studies have also reported that the changes in Online ISSN 2092-9293 Print ISSN 1976-9571 Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13258-018-0732-y) contains supplementary material, which is available to authorized users. * Vindhya Mohindra vindhyamohindra@gmail.com 1 ICAR- National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, P. O. Dilkusha, Lucknow, Uttar Pradesh 226002, India 2 Present Address: Division of Fisheries Science, Indian Council of Agricultural Research (ICAR), Krishi Anusandhan Bhawan - II, New Delhi 110 012, India