Genes & Genomics

, Volume 38, Issue 11, pp 1061–1076 | Cite as

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

  • Vemulawada Chakrapani
  • Swagat K. Patra
  • Shibani D. Mohapatra
  • Kiran D. Rasal
  • Uday Deshpande
  • Swapnarani Nayak
  • Jitendra K. Sundaray
  • Pallipuram Jayasankar
  • Hirak K. BarmanEmail author
Research Article


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.


Transcriptome Macrobrachium rosenbergii Salinity Metamorphosis Illumina GAIIx 



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.

Compliance with ethical standards

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.

Supplementary material

13258_2016_452_MOESM1_ESM.xls (3 mb)
Supplementary material 1 (XLS 3064 kb)


  1. Annadurai RS, Jayakumar V, Mugasimangalam RC, Katta MA, Anand S, Gopinathan S, Sarma SP, Fernandes SJ, Mullapudi N, Murugesan S, Rao SN (2012) Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties. BMC Genomics 13:663CrossRefPubMedPubMedCentralGoogle Scholar
  2. Barman HK, Patra SK, Das V, Mohapatra SD, Jayasankar P, Mohapatra C, Mohanta R, Panda RP, Rath SN (2012) Identification and characterization of differentially expressed transcripts in the gills of freshwater prawn (Macrobrachium rosenbergii) under salt stress. ScientificWorldJournal 2012:149361CrossRefPubMedPubMedCentralGoogle Scholar
  3. Chand BK, Trivedi RK, Dubey SK, Routb SK, Beg MM, Das UK (2015) Effect of salinity on survival and growth of giant freshwater prawn Macrobrachium rosenbergii (de Man). Aquac Rep 2:26–33CrossRefGoogle Scholar
  4. Chen K, Li E, Li T, Xu C, Wang X, Lin H, Qin JG, Chen L (2015) Transcriptome and molecular pathway analysis of the hepatopancreas in the Pacific White Shrimp Litopenaeus vannamei under chronic low-salinity stress. PLoS One 10:e0131503CrossRefPubMedPubMedCentralGoogle Scholar
  5. Delattre M, Felix MA (2009) The evolutionary context of robust and redundant cell biological mechanisms. BioEssays 31:537–545CrossRefPubMedGoogle Scholar
  6. Dubey RS, Singh AK (1999) Salinity induces accumulation of soluble sugars and alters the activity of sugar metabolising enzymes in rice plants. Biol Plant 42:233–239CrossRefGoogle Scholar
  7. Duchateau PN, Pullinger CR, Cho MH, Eng C, Kane JP (2001) Apolipoprotein L gene family: tissue-specific expression, splicing, promoter regions; discovery of a new gene. J Lipid Res 42:620–630PubMedGoogle Scholar
  8. Durica DS, Schloss JA, Crain WR Jr (1980) Organization of actin gene sequences in the sea urchin: molecular cloning of an intron-containing DNA sequence coding for a cytoplasmic actin. Proc Natl Acad Sci USA 77:5683–5687CrossRefPubMedPubMedCentralGoogle Scholar
  9. FaML Le Gac (1993) Expression of insulin- like growth factor (IGF) I and action of IGF I and II in the trout testis. Reprod Nutr Dev 33:80–81Google Scholar
  10. Fischer C, Kugler A, Hoth S, Dietrich P (2013) An IQ domain mediates the interaction with calmodulin in a plant cyclic nucleotide-gated channel. Plant Cell Physiol 54:573–584CrossRefPubMedPubMedCentralGoogle Scholar
  11. Gao J, Wang X, Zou Z, Jia X, Wang Y, Zhang Z (2014) Transcriptome analysis of the differences in gene expression between testis and ovary in green mud crab (Scylla paramamosain). BMC Genomics 15:585CrossRefPubMedPubMedCentralGoogle Scholar
  12. Hu D, Pan L, Zhao Q, Ren Q (2015) Transcriptomic response to low salinity stress in gills of the Pacific white shrimp Litopenaeus vannamei. Mar Genomics 24(Pt 3):297–304CrossRefPubMedGoogle Scholar
  13. Jung H, Lyons RE, Dinh H, Hurwood DA, McWilliam S, Mather PB (2011) Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): de novo assembly, annotation and marker discovery. PLoS One 6:e27938CrossRefPubMedPubMedCentralGoogle Scholar
  14. Kitsios G, Doonan JH (2011) Cyclin dependent protein kinases and stress responses in plants. Plant Signal Behav 6:204–209CrossRefPubMedPubMedCentralGoogle Scholar
  15. Kyriakis JM, Avruch J (2001) Mammalian mitogen-activated protein kinase signal transduction pathways activated by stress and inflammation. Physiol Rev 81:807–869PubMedGoogle Scholar
  16. Larsen PF, Nielsen EE, Koed A, Thomsen DS, Olsvik PA, Loeschcke V (2008) Interpopulation differences in expression of candidate genes for salinity tolerance in winter migrating anadromous brown trout (Salmo trutta L.). BMC Genet 9:12CrossRefPubMedPubMedCentralGoogle Scholar
  17. Leise EM, Kempf S, Durham N, Gifondorwa DJ (2004) Induction of metamorphosis in the marine gastropod Ilyanassa obsoleta: 5HT, NO and programmed cell death. Acta Biol Hung 55:293–300CrossRefPubMedGoogle Scholar
  18. Lewis TS, Shapiro PS, Ahn NG (1998) Signal transduction through MAP kinase cascades. Adv Cancer Res 74:49–139CrossRefPubMedGoogle Scholar
  19. Lilius G, Holmberg N, Bulow L (1996) Enhanced NaCl stress tolerance in transgenic tobacco expressing bacterial choline dehydrogenase. Nat Biotechnol 14:177–180CrossRefGoogle Scholar
  20. Lu G, Ren S, Korge P, Choi J, Dong Y, Weiss J, Koehler C, Chen JN, Wang Y (2007) A novel mitochondrial matrix serine/threonine protein phosphatase regulates the mitochondria permeability transition pore and is essential for cellular survival and development. Genes Dev 21:784–796CrossRefPubMedPubMedCentralGoogle Scholar
  21. Lucu C, Towle DW (2003) Na(+)+K(+)-ATPase in gills of aquatic crustacea. Comp Biochem Physiol A: Mol Integr Physiol 135:195–214CrossRefGoogle Scholar
  22. Lv J, Liu P, Wang Y, Gao B, Chen P, Li J (2013) Transcriptome analysis of Portunus trituberculatus in response to salinity stress provides insights into the molecular basis of osmoregulation. PLoS One 8:e82155CrossRefPubMedPubMedCentralGoogle Scholar
  23. Lv J, Liu P, Gao B, Wang Y, Wang Z, Chen P, Li J (2014) Transcriptome analysis of the Portunus trituberculatus: de novo assembly, growth-related gene identification and marker discovery. PLoS One 9:e94055CrossRefPubMedPubMedCentralGoogle Scholar
  24. Ma K, Qiu G, Feng J, Li J (2012) Transcriptome analysis of the oriental river prawn, Macrobrachium nipponense using 454 pyrosequencing for discovery of genes and markers. PLoS One 7:e39727CrossRefPubMedPubMedCentralGoogle Scholar
  25. Madsen S, Bern H (1993) In-vitro effects of insulin-like growth factor-I on gill Na+, K+-ATPase in coho salmon, Oncorhynchus kisutch. J Endocrinol 138:23–30CrossRefPubMedGoogle Scholar
  26. McCormick SD, Sakamoto T, Hasegawa S, Hirano T (1991) Osmoregulatory actions of insulin-like growth factor-I in rainbow trout (Oncorhynchus mykiss). J Endocrinol 130:87–92CrossRefPubMedGoogle Scholar
  27. McCormick SD, Regish AM, Christensen AK (2009) Distinct freshwater and seawater isoforms of Na+/K+-ATPase in gill chloride cells of Atlantic salmon. J Exp Biol 212:3994–4001CrossRefPubMedGoogle Scholar
  28. Meng J, Zhu Q, Zhang L, Li C, Li L, She Z, Huang B, Zhang G (2013) Genome and transcriptome analyses provide insight into the euryhaline adaptation mechanism of Crassostrea gigas. PLoS One 8:e58563CrossRefPubMedPubMedCentralGoogle Scholar
  29. Mohanta R, Jayasankar P, Das Mahapatra K, Saha JN, Barman HK (2014) Molecular cloning, characterization and functional assessment of the myosin light polypeptide chain 2 (mylz2) promoter of farmed carp, Labeo rohita. Transgenic Res 23:601–607CrossRefPubMedGoogle Scholar
  30. Mohapatra C, Barman HK, Panda RP, Kumar S, Das V, Mohanta R, Mohapatra SD, Jayasankar P (2010) Cloning of cDNA and prediction of peptide structure of Plzf expressed in the spermatogonial cells of Labeo rohita. Mar Genomics 3:157–163CrossRefPubMedGoogle Scholar
  31. Mohapatra C, Patra SK, Panda RP, Mohanta R, Saha A, Saha JN, Das Mahapatra K, Jayasankar P, Barman HK (2014) Gene structure and identification of minimal promoter of Pou2 expressed in spermatogonial cells of rohu carp, Labeo rohita. Mol Biol Rep 41:4123–4132CrossRefPubMedGoogle Scholar
  32. Mohd-Shamsudin MI, Kang Y, Lili Z, Tan TT, Kwong QB, Liu H, Zhang G, Othman RY, Bhassu S (2013) In-depth tanscriptomic analysis on giant freshwater prawns. PLoS One 8:e60839CrossRefPubMedPubMedCentralGoogle Scholar
  33. Nakamura T, Liu Y, Hirata D, Namba H, Harada S, Hirokawa T, Miyakawa T (1993) Protein phosphatase type 2B (calcineurin)-mediated, FK506-sensitive regulation of intracellular ions in yeast is an important determinant for adaptation to high salt stress conditions. EMBO J 12:4063–4071PubMedPubMedCentralGoogle Scholar
  34. Nayak S, Singh SK, Ramaiah N, Sreepada RA (2010) Identification of upregulated immune-related genes in Vibrio harveyi challenged Penaeus monodon postlarvae. Fish Shellfish Immunol 29:544–549CrossRefPubMedGoogle Scholar
  35. New MB (2002) Farming freshwater prawns. A manual for the culture of the giant river prawn (Macrobrachium rosenbergii). FAO Fisheries Technical Paper 428Google Scholar
  36. New MB, Valenti WC (2000) Freshwater prawn culture. The farming of Macrobrachium rosenbergii. Aquaculture 203:399–400Google Scholar
  37. Nguyen Thanh H, Zhao L, Liu Q (2014) De novo transcriptome sequencing analysis and comparison of differentially expressed genes (DEGs) in Macrobrachium rosenbergii in China. PLoS One 9:e109656CrossRefPubMedPubMedCentralGoogle Scholar
  38. Paidhungat M, Garrett S (1997) A homolog of mammalian, voltage-gated calcium channels mediates yeast pheromone-stimulated Ca2+ uptake and exacerbates the cdc1(Ts) growth defect. Mol Cell Biol 17:6339–6347CrossRefPubMedPubMedCentralGoogle Scholar
  39. Panda RP, Barman HK, Mohapatra C (2011) Isolation of enriched carp spermatogonial stem cells from Labeo rohita testis for in vitro propagation. Theriogenology 76:241–251CrossRefPubMedGoogle Scholar
  40. Panda RP, Chakrapani V, Patra SK, Saha JN, Jayasankar P, Kar B, Sahoo PK, Barman HK (2014) First evidence of comparative responses of Toll-like receptor 22 (TLR22) to relatively resistant and susceptible Indian farmed carps to Argulus siamensis infection. Dev Comp Immunol 47:25–35CrossRefPubMedGoogle Scholar
  41. Pandit A, Rai V, Bal S, Sinha S, Kumar V, Chauhan M, Gautam RK, Singh R, Sharma PC, Singh AK, Gaikwad K, Sharma TR, Mohapatra T, Singh NK (2010) Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.). Mol Genet Genomics 284:121–136CrossRefPubMedGoogle Scholar
  42. Rajesh S, Kiruthika J, Ponniah AG, Shekhar MS (2012) Identification, cloning and expression analysis of Catechol-O-methyltransferase (COMT) gene from shrimp, Penaeus monodon and its relevance to salinity stress. Fish Shellfish Immunol 32:693–699CrossRefPubMedGoogle Scholar
  43. Robinson N, Sahoo PK, Baranski M, Das Mahapatra K, Saha JN, Das S, Mishra Y, Das P, Barman HK, Eknath AE (2012) Expressed sequences and polymorphisms in rohu carp (Labeo rohita, Hamilton) revealed by mRNA-seq. Mar Biotechnol (NY) 14:620–633CrossRefGoogle Scholar
  44. Romualdi C, Bortoluzzi S, D’Alessi F, Danieli GA (2003) IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments. Physiol Genomics 12:159–162CrossRefPubMedGoogle Scholar
  45. Ruffalo M, LaFramboise T, Koyuturk M (2011) Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 27:2790–2796CrossRefPubMedGoogle Scholar
  46. Sakamoto T, Hirano T (1993) Expression of insulin-like growth factor I gene in osmoregulatory organs during seawater adaptation of the salmonid fish: possible mode of osmoregulatory action of growth hormone. Proc Natl Acad Sci USA 90:1912–1916CrossRefPubMedPubMedCentralGoogle Scholar
  47. Sakamoto T, Ogawa S, Nishiyama Y, Godo W, Takahashi H (2013) Osmolality and ionic status of hemolymph and branchial Na+/K+-ATPase in adult mitten crab during seawater adaptation. HOAJ Biol 2:5CrossRefGoogle Scholar
  48. Santos CA, Blanck DV, de Freitas PD (2014) RNA-seq as a powerful tool for penaeid shrimp genetic progress. Front Genet 5:298CrossRefPubMedPubMedCentralGoogle Scholar
  49. Shaterian J, Georges F, Hussain A, Waterer D, De Jong H, Tanino KK (2005) Root to shoot communication and abscisic acid in calreticulin (CR) gene expression and salt-stress tolerance in grafted diploid potato clones. Environ Exp Bot 53:323–332CrossRefGoogle Scholar
  50. Sookruksawong S, Sun F, Liu Z, Tassanakajon A (2013) RNA-Seq analysis reveals genes associated with resistance to Taura syndrome virus (TSV) in the Pacific white shrimp Litopenaeus vannamei. Dev Comp Immunol 41:523–533CrossRefPubMedGoogle Scholar
  51. Tidwell JH, Coyle S, Durborow RM, Dasgupta S, Wurts WA, Wynne F, Bright LA, Van Arnum A (2002) Grow out of freshwater prawns in Kentucky Ponds. Kentucky State Univ Aqua Prog 44Google Scholar
  52. Ventura T, Manor R, Aflalo ED, Chalifa-Caspi V, Weil S, Sharabi O, Sagi A (2013) Post-embryonic transcriptomes of the prawn Macrobrachium rosenbergii: multigenic succession through metamorphosis. PLoS One 8:e55322CrossRefPubMedPubMedCentralGoogle Scholar
  53. Wood IS, Trayhurn P (2003) Glucose transporters (GLUT and SGLT): expanded families of sugar transport proteins. Br J Nutr 89:3–9CrossRefPubMedGoogle Scholar
  54. Xu Q, Liu Y (2011) Gene expression profiles of the swimming crab Portunus trituberculatus exposed to salinity stress. Mar Biol 158:2161CrossRefGoogle Scholar
  55. Xu J, Ji P, Wang B, Zhao L, Wang J, Zhao Z, Zhang Y, Li J, Xu P, Sun X (2013) Transcriptome sequencing and analysis of wild Amur Ide (Leuciscus waleckii) inhabiting an extreme alkaline-saline lake reveals insights into stress adaptation. PLoS One 8:e59703CrossRefPubMedPubMedCentralGoogle Scholar
  56. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829CrossRefPubMedPubMedCentralGoogle Scholar
  57. Zhao X, Yu H, Kong L, Li Q (2012) Transcriptomic responses to salinity stress in the Pacific oyster Crassostrea gigas. PLoS One 7:e46244CrossRefPubMedPubMedCentralGoogle Scholar
  58. Zwerger K, Hirt H (2001) Recent advances in plant MAP kinase signalling. Biol Chem 382:1123–1131CrossRefPubMedGoogle Scholar

Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2016

Authors and Affiliations

  • Vemulawada Chakrapani
    • 1
  • Swagat K. Patra
    • 1
  • Shibani D. Mohapatra
    • 1
  • Kiran D. Rasal
    • 1
  • Uday Deshpande
    • 2
  • Swapnarani Nayak
    • 1
  • Jitendra K. Sundaray
    • 1
  • Pallipuram Jayasankar
    • 1
  • Hirak K. Barman
    • 1
    Email author
  1. 1.Fish Genetics and Biotechnology DivisionICAR - Central Institute of Freshwater AquacultureBhubaneswarIndia
  2. 2.Bioserve India, (CGI Company)HyderabadIndia

Personalised recommendations