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De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing

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Abstract

Labeo rohita, one of the Indian major carps, is the most popular culture species in Indian subcontinent due to its consumer preference and delicacy. A selective breeding program for harvest body weight has resulted in an average genetic gain of 17% per generation. Transcriptome resource for this species is scanty. Here, we have characterized the liver and muscle transcriptomes of rohu using Roche 454 GS-FLX next generation sequencing platform. In total, 1.2 million reads were generated, de novo assembly and clustering resulted in 4171 transcripts. Out of these, 4171 had significant blast hit against NCBI nr database, and 2130 transcripts were successfully annotated. In total, 289 SSRs were identified with an identification rate of 5.8%, and dinucleotide repeat motifs were observed to be the most abundant SSRs. Further, 2231 putative SNPs were identified with high confidence. Validation of eight putative SNPs using Sanger sequencing resulted in 100% true SNPs. Significant allelic imbalance of M1, M4 and M5 loci between growth selected and control individual were observed. Furthermore, 13 transcription factors were identified in the present study belonging to six different transcription factor families. The present study demonstrated the utility of RNAseq to develop genomics resources in non-model fish species, and the marker resources developed would support the genetic improvement program of this species.

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Data availability

The RNA-seq data were submitted in the GenBank with Biosample accession number SAMN15062925, SAMN15062926, SAMN15062927, SAMN15062928.

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Acknowledgements

The authors are thankful to the Director, ICAR-Central Institute of Freshwater Aquaculture for providing the laboratory facilities. Acknowledgements are due to selective breeding team of ICAR-CIFA and Anand Agricultural University, Anand, India for providing samples and sequencing facility, respectively.

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Authors and Affiliations

  1. Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, Odisha, India

    L. Sahoo, A. Bit, G. Das & P. Das

  2. Amity Institute of Marine Science and Technology, Amity University, Noida, 201313, India

    S. P. Das

  3. Department of Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore

    S. Patnaik

  4. Barcode Biosciences, Dr. Shivaram Karanth Nagar, Bengaluru, 560077, India

    M. Mohanty

Authors
  1. L. Sahoo
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  2. S. P. Das
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  3. A. Bit
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  4. S. Patnaik
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  5. M. Mohanty
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  6. G. Das
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  7. P. Das
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Contributions

PD and LS conceived the project; SPD, AB, SP, MM and GD collected the samples, isolated total RNA; SPD, AB and LS analyzed the data; MM, SP and GD performed the PCR; LS and PD wrote and reviewed the MS. All authors read and approved the manuscript.

Corresponding author

Correspondence to P. Das.

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The authors declare that they have no conflict of interest.

Ethical approval

All handling of fish was carried out following the guidelines for control and supervision of experiments on animals by the Government of India and approved by Institutional Animal Ethics Committee (IAEC) of ICAR-CIFA.

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Sahoo, L., Das, S.P., Bit, A. et al. De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing. Genetica 150, 59–66 (2022). https://doi.org/10.1007/s10709-021-00141-7

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  • DOI: https://doi.org/10.1007/s10709-021-00141-7

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