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Muscle Transcriptome Sequencing Revealed Thermal Stress–Responsive Regulatory Genes in Farmed Rohu, Labeo rohita (Hamilton, 1822)

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Abstract

Rohu, Labeo rohita, is one of the most important aquaculture species in the Indian subcontinent. Understanding the molecular-level physiological responses to thermal stress or climate change is essential. In the present work, transcriptome sequencing was carried out in the muscle tissue of the rohu in response to heat stress (35 °C) in comparison with the control (28 °C). A total of 125 Gb of sequence data was generated, and the raw-reads were filtered and trimmed, which resulted in 484 million quality reads. Reference-based assembly of reads was performed using L. rohita genome, and a total of 90.17% of reads were successfully mapped. A total of 37,462 contigs were assembled with an N50 value of 1854. The differential expression analysis revealed a total of 107 differentially expressed genes (DEGs) (15 up-, 37 down-, and 55 neutrally regulated) as compared to the control group (Log2FC > 2, P < 0.05). Gene enrichment analysis of DEGs indicates that transcripts were associated with molecular, biological, and cellular activities. The randomly selected differentially expressed transcripts were validated by RT-qPCR and found consistent expression patterns in line with the RNA-seq data. Several transcripts such as SERPINE1(HSP47), HSP70, HSP90alpha, Rano class II histocompatibility A beta, PGC-1 and ERR-induced regulator, proto-oncogene c-Fos, myozenin2, alpha-crystallin B chain-like protein, angiopoietin-like protein 8, and acetyl-CoA carboxylases have been identified in muscle tissue of rohu that are associated with stress/immunity. This study identified the key biomarker SERPINE1 (HSP47), which showed significant upregulation (~ 2- to threefold) in muscle tissue of rohu exposed to high temperature. This study can pave a path for the identification of stress-responsive biomarkers linked with thermal adaptations in the farmed carps.

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Data Availability

The data have been deposited to the National Center for Biotechnology Information (NCBI) under accession numbers SRR23215594, SRR23215970, SRR23216425, and SRR23217297.

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Acknowledgements

The authors are thankful to the Director, Indian Council of Agricultural Research—NIASM, Baramati, Pune, India, for providing the research facilities and the Director, Indian Council of Agricultural Research –CIFE, Mumbai, for providing the facility for data analysis.

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Authors and Affiliations

  1. ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India

    Pokanti Vinay Kumar, Kiran D. Rasal, Arpit Acharya, Diganta Dey, Arvind A. Sonwane, Dhalongsaih Reang, R. Rajeshkannan, Kishore K. Krishnani, Naresh S. Nagpure & Manoj P. Brahmane

  2. School of Atmospheric Stress Management, ICAR – National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India

    Sachin S. Pawar, Nitin P. Kurade, Mukesh P. Bhendarkar, Kishore K. Krishnani & Manoj P. Brahmane

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  1. Pokanti Vinay Kumar
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Contributions

Conceptualization: Kishore K. Krishnani, Manoj P. Brahmane; Methodology: Kiran D. Rasal, Kishore K. Krishnani, Manoj P. Brahmane, Dhalongsaih Reang, Sachin S. Pawar, Arvind A. Sonwane, R Rajeshkannan; Investigation: Pokanti Vinay Kumar, Arvind A. Sonwane, Nitin P. Kurade, Mukesh P. Bhendarkar, Dhalongsaih Reang, Data processing: Pokanti Vinay Kumar; Writing—original draft preparation: Pokanti Vinay Kumar, Kiran D. Rasal, Manoj P. Brahmane, R Rajeshkannan; Writing—review and editing: Pokanti Vinay Kumar, Kiran D. Rasal, Dhalongsaih Reang, Arvind A. Sonwane, Naresh S. Nagpure, Manoj P. Brahmane, Kishore K. Krishnani; Result validation: Pokanti Vinay Kumar, Arpit Acharya, Diganta Dey; Lab Work: Pokanti Vinay Kumar; Resources: Naresh S. Nagpure, Arvind A. Sonwane, Nitin P. Kurade; Supervision: Manoj P. Brahmane.

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Correspondence to Manoj P. Brahmane.

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Kumar, P.V., Rasal, K.D., Acharya, A. et al. Muscle Transcriptome Sequencing Revealed Thermal Stress–Responsive Regulatory Genes in Farmed Rohu, Labeo rohita (Hamilton, 1822). Mar Biotechnol 25, 1057–1075 (2023). https://doi.org/10.1007/s10126-023-10259-8

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