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Comparative transcriptomic profiling of larvae and post-larvae of Macrobrachium rosenbergii in response to metamorphosis and salinity exposure

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Abstract

The high-throughput sequencing technology provides a platform for revealing the expressed genes within a tissue at a specific time. The giant freshwater prawn, Macrobrachium rosenbergii, is an economically important species, which is surviving in a wide-range of salinity. In this study, to understand the physiological mechanism of adaptability with respect to moulting and salinity; transcriptome sequencing of larvae and post-larvae of M. rosenbergii was performed using the Illumina GAIIx platform. The generated raw read-data comprised 71,391,946 and 75,276,622 paired-end reads (PE) for larvae and post-larvae respectively. Using CLC bio Genomic Workbench version 7.5 (CGWB), 71.39 million and 75.27 million of each 72 base paired-end, high quality reads were assembled into 43,383 (N50 1852) and 44,960 (N50 1874) transcripts, respectively, for larvae and post-larvae. The nucleotide level annotation of both transcriptomes showed significant similarity with unigenes of closely related species. The Gene Ontology analysis suggested enrichment of transcripts involving several biological processes linked to transcriptional regulation, signal transduction, immune response, ion-binding. Differential gene expression analysis using CGWB and DESeq identified 9680 deregulated genes of which 3454 unigenes were up-regulated and 3068 down-regulated by ≥1.5 fold (p < 0.05) in larval stage compared to post-larval stage. However, in larval stage 938 genes were down regulated and 1599 genes up-regulated by ≥3 fold with p < 0.05. GO enrichment of differentially expressed genes was shown several molecular functions for maintaining homeostasis against salinity stress. To validate the expression patterns, few transcripts were chosen for quantitative real-time PCR that showed the consistency and exactness of our analysis. In addition, we also speculated the enzymatic pathway using KEGG, which depicted that up-regulated genes are involved in several significant metabolic pathways and those are critical for maintaining osmoregulation and linked with metamorphosis. Therefore, we have generated valuable information of salinity tolerant genes in the larval and post larval stage of M. rosenbergii during salt- and freshwater compliances, which will be further harnessed for gene targeting. The present finding would provide the basis for further screening of salt tolerant genes associated markers for selective breeding.

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Acknowledgments

We thank M/s Genotypic Technology Private Limited, Bangalore, India for providing us Illumina GAIIx platform and data analysis pipeline. Thanks are due to the Director, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, India for providing facilities.

Author contribution

Conceived and designed experiments HKB, PJ and JKS. Performed the experiment and analyzed data: VC, SKP, SDM, KDR, SN, and UD. Wrote the manuscript VC, SKP, KDR and HKB.

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Authors and Affiliations

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

    Vemulawada Chakrapani, Swagat K. Patra, Shibani D. Mohapatra, Kiran D. Rasal, Swapnarani Nayak, Jitendra K. Sundaray, Pallipuram Jayasankar & Hirak K. Barman

  2. Bioserve India, (CGI Company), Hyderabad, Telangana, India

    Uday Deshpande

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  1. Vemulawada Chakrapani
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  2. Swagat K. Patra
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  3. Shibani D. Mohapatra
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  4. Kiran D. Rasal
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  5. Uday Deshpande
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  6. Swapnarani Nayak
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  7. Jitendra K. Sundaray
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  8. Pallipuram Jayasankar
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  9. Hirak K. Barman
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Correspondence to Hirak K. Barman.

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Conflict of interest

Vemulawada Chakrapani, Swagat K. Patra, Shibani D. Mohapatra, Kiran D. Rasal, Uday Deshpande, Swapnarani Nayak, Jitendra K. Sundaray, Pallipuram Jayasankar, and Hirak K. Barman declares that they have no conflict of interest.

Ethical approval

All experiments involving prawns (M. rosenbergii) were approved by the Ethical Committee of the ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India.

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Chakrapani, V., Patra, S.K., Mohapatra, S.D. et al. Comparative transcriptomic profiling of larvae and post-larvae of Macrobrachium rosenbergii in response to metamorphosis and salinity exposure. Genes Genom 38, 1061–1076 (2016). https://doi.org/10.1007/s13258-016-0452-0

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