Skip to main content
SpringerLink
Log in

Transcriptome Analysis Reveals a Rich Gene Set Related to Innate Immunity in the Eastern Oyster (Crassostrea virginica)

  • Original Article
  • Published:
Marine Biotechnology Aims and scope Submit manuscript

Abstract

As a benthic filter-feeder of estuaries, the eastern oyster, Crassostrea virginica, faces tremendous exposure to microbial pathogens. How eastern oysters without adaptive immunity survive in pathogen-rich environments is of fundamental interest, but studies on its immune system are hindered by the lack of genomic resources. We sequenced the transcriptome of an adult oyster with short Illumina reads and assembled 66,229 contigs with a N50 length of 1,503 bp. The assembly covered 89.4 % of published ESTs and 97.9 % of mitochondrial genes demonstrating its quality. A set of 39,978 contigs and unigenes (>300 bp) were identified and annotated by searching public databases. Analysis of the gene set yielded a diverse set of 657 genes related to innate immunity, including many pertaining to pattern recognition, effectors, signal transduction, cytokines, and apoptosis. Gene families encoding C1q domain containing proteins, CTLD, IAPs, Ig_I-set, and TRAFs expanded in C. virginica and Crassostrea gigas. Many key genes of the apoptosis system including IAP, BAX, BAC-2, caspase, FADD, and TNFR were identified, suggesting C. virginica posses advanced apoptosis and apoptosis-regulating systems. Our results show that short Illumina reads can produce transcriptomes of highly polymorphic genomes with coverage and integrity comparable to that from longer 454 reads. The expansion and high diversity in gene families related to innate immunity, point to a complex defense system in the lophotrochozoan C. virginica, probably in adaptation to a pathogen-rich environment.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

Abbreviations

TLR:

Toll-like receptor

SRCR:

Scavenger domain containing protein

CD36-like:

Cluster of differentiation 36 like gene

PGRP:

Peptidoglycan recognition protein

GNBP:

Gram-negative binding protein

CTLD:

C type lectin domain containing protein

C1qDC:

C1q domain containing protein

NOS:

Nitric oxide synthase

BPI:

Bactericidal permeability-increasing protein

SOD:

Superoxide dismutase

IKK:

IκB kinase

Rel/NF-κB:

Rel or nuclear factor kappa B

TBK:

Serine/threonine-protein kinase TBK1

TRAF:

TNF receptor-associated factor

IRAK:

Interleukin-1 receptor-associated kinase

TRIAD:

E3 ubiquitin-protein ligase ARIH

MyD88:

Myeloid differentiation primary response gene (88)

SARM:

Sterile alpha and TIR motif-containing protein

MIF:

Macrophage migration inhibitory factor

TNF:

Tumor necrosis factor

TNFR:

Tumor necrosis factor receptor

FADD:

FAS-associated death domain protein

IAP:

Inhibitor of apoptosis protein

Bcl-2:

Apoptosis regulator Bcl-2

Bax:

Apoptosis regulator Bax

References

  • Arancibia SA, Beltran CJ, Aguirre IM, Silva P, Peralta AL, Malinarich F, Hermoso MA (2007) Toll-like receptors are key participants in innate immune responses. Biol Res 40(2):97–112

    Article  CAS  PubMed  Google Scholar 

  • Bell JK, Mullen GE, Leifer CA, Mazzoni A, Davies DR, Segal DM (2003) Leucine-rich repeats and pathogen recognition in Toll-like receptors. Trends Immunol 24(10):528–533

    Article  CAS  PubMed  Google Scholar 

  • Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27(2):573–580

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bettencourt R, Pinheiro M, Egas C, Gomes P, Afonso M, Shank T, Santos RS (2010) High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus. BMC Genomics 11:559

    Article  PubMed Central  PubMed  Google Scholar 

  • Carland TM, Gerwick L (2010) The C1q domain containing proteins: where do they come from and what do they do? Dev Comp Immunol 34(8):785–790

    Article  CAS  PubMed  Google Scholar 

  • Clark MS, Thorne MA, Vieira FA, Cardoso JC, Power DM, Peck LS (2010) Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing. BMC Genomics 11:362

    Article  PubMed Central  PubMed  Google Scholar 

  • Devasagayam TP, Tilak JC, Boloor KK, Sane KS, Ghaskadbi SS, Lele RD (2004) Free radicals and antioxidants in human health: current status and future prospects. J Assoc Physicians India 52:794–804

    CAS  PubMed  Google Scholar 

  • Dodds AW, Law SK (1988) Structural basis of the binding specificity of the thioester-containing proteins, C4, C3 and alpha-2-macroglobulin. Complement 5(2):89–97

    CAS  PubMed  Google Scholar 

  • Drivenes Ø, Taranger GL, Edvardsen RB (2012) Gene expression profiling of Atlantic cod (Gadus morhua) embryogenesis using microarray. Mar Biotechnol 14(2):167–176

    Article  CAS  PubMed  Google Scholar 

  • Emrich SJ, Barbazuk WB, Li L, Schnable PS (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 17(1):69–73

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Endo Y, Nakazawa N, Iwaki D, Takahashi M, Matsushita M, Fujita T (2009) Interactions of ficolin and mannose-binding lectin with fibrinogen/fibrin augment the lectin complement pathway. J Innate Immun 2(1):33–42

    Article  PubMed  Google Scholar 

  • Feldmeyer B, Wheat C, Krezdorn N, Rotter B, Pfenninger M (2011) Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics 12(1):317

    Article  PubMed Central  PubMed  Google Scholar 

  • Ford SE, Tripp MR (1996) Diseases and defence mechanisms. In: Kennedy VS, Newell RIE, Eble AF (eds) The eastern oyster, Crassostrea virginica. Maryland Sea Grant, College Park, pp 581–660

  • Franchini P, van der Merwe M, Roodt-Wilding R (2011) Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis. BMC Res Notes 4:59

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gerwick L, Reynolds WS, Bayne CJ (2000) A precerebellin-like protein is part of the acute phase response in rainbow trout, Oncorhynchus mykiss. Dev Comp Immunol 24(6–7):597–607

    Article  CAS  PubMed  Google Scholar 

  • Gerwick L, Corley-Smith G, Nakao M, Watson J, Bayne C (2005) Intracranial injections induce local transcription of a gene encoding precerebellin-like protein. Fish Physiol Biochem 31(4):363–372

    Article  CAS  Google Scholar 

  • Ghai R, Waters P, Roumenina LT, Gadjeva M, Kojouharova MS, Reid KB, Sim RB, Kishore U (2007) C1q and its growing family. Immunobiology 212(4–5):253–266

    Article  CAS  PubMed  Google Scholar 

  • Goedken M, Morsey B, Sunila I, Dungan C, De Guise S (2005) The effects of temperature and salinity on apoptosis of Crassostrea virginica hemocytes and Perkinsus marinus. J Shellfish Res 24(1):177–183

    Article  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gueguen Y, Cadoret JP, Flament D, Barreau-Roumiguiere C, Girardot AL, Garnier J, Hoareau A, Bachere E, Escoubas JM (2003) Immune gene discovery by expressed sequence tags generated from hemocytes of the bacteria-challenged oyster, Crassostrea gigas. Gene 303:139–145

    Article  CAS  PubMed  Google Scholar 

  • Guo X, Wang Y, Wang L, Lee J-H (2008) Oysters. In: Kocher TD, Kole C (eds) Genome mapping and genomics in fishes and aquatic animals, vol 2. Springer, Heidelberg, pp 163–175

  • He Y, Yu H, Bao Z, Zhang Q, Guo X (2012) Mutation in promoter region of a serine protease inhibitor confers Perkinsus marinus resistance in the eastern oyster (Crassostrea virginica). Fish Shellfish Immunol 33(2):411–417

    Google Scholar 

  • Hedgecock D, Gaffney PM, Goulletquer P, Guo X, Reece K, Warr GW (2005) The case for sequencing the Pacific oyster genome. J Shellfish Res 24(2):429–441

    Article  Google Scholar 

  • Hibino T, Loza-Coll M, Messier C, Majeske AJ, Cohen AH, Terwilliger DP, Buckley KM, Brockton V, Nair SV, Berney K, Fugmann SD, Anderson MK, Pancer Z, Cameron RA, Smith LC, Rast JP (2006) The immune gene repertoire encoded in the purple sea urchin genome. Dev Biol 300(1):349–365

    Article  CAS  PubMed  Google Scholar 

  • Hou R, Bao Z, Wang S, Su H, Li Y, Du H, Hu J, Hu X (2011) Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX. PLoS One 6(6):e21560

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Huan P, Wang H, Liu B (2012) Transcriptomic analysis of the clam Meretrix meretrix on different larval stages. Mar Biotechnol 14(1):69–78

    Article  CAS  PubMed  Google Scholar 

  • Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9(9):868–877

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Huang X-D, Zhao M, Liu WG, Guan YY, Shi Y, Wang Q, Wu SZ, He MX (2013) Gigabase-scale transcriptome analysis on four species of pearl oysters. Mar Biotechnol 15(3):253–264

    Google Scholar 

  • Hughes FM, Foster B, Grewal S, Sokolova IM (2010) Apoptosis as a host defense mechanism in Crassostrea virginica and its modulation by Perkinsus marinus. Fish Shellfish Immunol 29(2):247–257

    Article  CAS  PubMed  Google Scholar 

  • Jenny MJ, Ringwood AH, Lacy ER, Lewitus AJ, Kempton JW, Gross PS, Warr GW, Chapman RW (2002) Potential indicators of stress response identified by expressed sequence tag analysis of hemocytes and embryos from the American oyster, Crassostrea virginica. Mar Biotechnol 4(1):81–93

    Article  CAS  PubMed  Google Scholar 

  • Joubert C, Piquemal D, Marie B, Manchon L, Pierrat F, Zanella-Cleon I, Cochennec-Laureau N, Gueguen Y, Montagnani C (2010) Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization. BMC Genomics 11:613

    Article  PubMed Central  PubMed  Google Scholar 

  • Kashi Y, King D, Soller M (1997) Simple sequence repeats as a source of quantitative genetic variation. Trends Genet 13(2):74–78

    Article  CAS  PubMed  Google Scholar 

  • Kiss T (2010) Apoptosis and its functional significance in molluscs. Apoptosis 15(3):313–321

    Article  PubMed  Google Scholar 

  • Kuchel RP, Aladaileh S, Birch D, Vella N, Raftos DA (2010) Phagocytosis of the protozoan parasite, Marteilia sydneyi, by Sydney rock oyster (Saccostrea glomerata) hemocytes. J Invertebr Pathol 104(2):97–104

    Article  PubMed  Google Scholar 

  • La Peyre JF, Xue QG, Itoh N, Li Y, Cooper RK (2010) Serine protease inhibitor cvSI-1 potential role in the eastern oyster host defense against the protozoan parasite Perkinsus marinus. Dev Comp Immunol 34(1):84–92

    Article  PubMed  Google Scholar 

  • Macagno E, Gaasterland T, Edsall L, Bafna V, Soares M, Scheetz T, Casavant T, Da Silva C, Wincker P, Tasiemski A, Salzet M (2010) Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. BMC Genomics 11(1):407

    Article  PubMed Central  PubMed  Google Scholar 

  • MacKenzie C Jr (1996) History of oystering in the United States and Canada, featuring the eight greatest oyster estuaries. Mar Fish Rev 58(4):1–78

    Google Scholar 

  • Martín-Gómez L, Villalba A, Carballal MJ, Abollo E (2013) Identification of relevant cancer related-genes in the flat oyster Ostrea edulis affected by Disseminated neoplasia. Mar Biotechnol 15(2):159–174

    Article  PubMed  Google Scholar 

  • Micallef G, Bickerdike R, Reiff C, Fernandes JM, Bowman AS, Martin SA (2012) Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defense organ. Mar Biotechnol 14(5):559–569

    Article  CAS  PubMed  Google Scholar 

  • Milan M, Coppe A, Reinhardt R, Cancela L, Leite R, Saavedra C, Ciofi C, Chelazzi G, Patarnello T, Bortoluzzi S, Bargelloni L (2011) Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring. BMC Genomics 12(1):234

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Nakamura O, Wada Y, Namai F, Saito E, Araki K, Yamamoto A, Tsutsui S (2009) A novel C1q family member with fucose-binding activity from surfperch, Neoditrema ransonnetii (Perciformes, Embiotocidae). Fish Shellfish Immunol 27(6):714–720

    Article  CAS  PubMed  Google Scholar 

  • Nonaka M, Kimura A (2006) Genomic view of the evolution of the complement system. Immunogenetics 58(9):701–713

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Nonaka M, Yoshizaki F (2004) Evolution of the complement system. Mol Immunol 40(12):897–902

    Article  CAS  PubMed  Google Scholar 

  • Oberst A, Bender C, Green DR (2008) Living with death: the evolution of the mitochondrial pathway of apoptosis in animals. Cell Death Differ 15(7):1139–1146

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Paris M, Brunet F, Markov GV, Schubert M, Laudet V (2008) The amphioxus genome enlightens the evolution of the thyroid hormone signaling pathway. Dev Genes Evol 218(11–12):667–680

    Article  CAS  PubMed  Google Scholar 

  • Peatman E, Wei X, Feng J, Liu L, Kucuktas H, Li P, He C, Rouse D, Wallace R, Dunham R (2004) Development of expressed sequence tags from eastern oyster (Crassostrea virginica): lessons learned from previous efforts. Mar Biotechnol 6:S491–S496

    Google Scholar 

  • Philipp EER, Kraemer L, Melzner F, Poustka AJ, Thieme S, Findeisen U, Schreiber S, Rosenstiel P (2012) Massively parallel RNA sequencing identifies a complex immune gene repertoire in the lophotrochozoan Mytilus edulis. PLoS One 7(3):e33091

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Prado-Alvarez M, Rotllant J, Gestal C, Novoa B, Figueras A (2009) Characterization of a C3 and a factor B-like in the carpet-shell clam, Ruditapes decussatus. Fish Shellfish Immunol 26(2):305–315

    Article  CAS  PubMed  Google Scholar 

  • Quilang J, Wang S, Li P, Abernathy J, Peatman E, Wang Y, Wang L, Shi Y, Wallace R, Guo X (2007) Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers. BMC Genomics 8(1):157

    Article  PubMed Central  PubMed  Google Scholar 

  • Ren J, Liu X, Jiang F, Guo X, Liu B (2010) Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia. BMC Evol Biol 10:394. doi:10.1186/1471-2148-10-394

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Roberts S, Gueguen Y, de Lorgeril J, Goetz F (2008) Rapid accumulation of an interleukin 17 homolog transcript in Crassostrea gigas hemocytes following bacterial exposure. Dev Comp Immunol 32(9):1099–1104

    Article  CAS  PubMed  Google Scholar 

  • Robinson N, Sahoo PK, Baranski M, Mahapatra KD, 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 14(5):620–633

    Article  CAS  PubMed  Google Scholar 

  • Rosenberg SH (2011) Mammalian apoptosis in a parasitic worm. Proc Natl Acad Sci U S A 108(17):6695–6696

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Schmitt P, Gueguen Y, Desmarais E, Bachere E, de Lorgeril J (2010) Molecular diversity of antimicrobial effectors in the oyster Crassostrea gigas. BMC Evol Biol 10:23

    Article  PubMed Central  PubMed  Google Scholar 

  • Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28(8):1086–1092

    Google Scholar 

  • Seo JK, Crawford JM, Stone KL, Noga EJ (2005) Purification of a novel arthropod defensin from the American oyster, Crassostrea virginica. Biochem Biophys Res Commun 338(4):1998–2004

    Article  CAS  PubMed  Google Scholar 

  • Shi Y, Yu C, Gu Z, Zhan X, Wang Y, Wang A (2012) Characterization of the pearl oyster (Pinctada martensii) mantle transcriptome unravels biomineralization genes. Mar Biotechnol 15(2):175–187

    Google Scholar 

  • Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Belle R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Geneviere AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallbook F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Rottinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R (2006) The genome of the sea urchin Strongylocentrotus purpuratus. Science 314(5801):941–952

    Article  PubMed  Google Scholar 

  • Sokolova I (2009) Apoptosis in molluscan immune defense. Invertebrate Surviv J 6:49–58

    Google Scholar 

  • Sontheimer RD, Racila E, Racila DM (2005) C1q: its functions within the innate and adaptive immune responses and its role in lupus autoimmunity. J Invest Dermatol 125(1):14–23

    Article  CAS  PubMed  Google Scholar 

  • Sunila I, LaBanca J (2003) Apoptosis in the pathogenesis of infectious diseases of the eastern oyster Crassostrea virginica. Dis Aquat Organ 56(2):163–170

    Article  PubMed  Google Scholar 

  • Takeda K, Akira S (2004) TLR signaling pathways. Semin Immunol 16(1):3–9

    Article  CAS  PubMed  Google Scholar 

  • Tanguy A, Guo X, Ford SE (2004) Discovery of genes expressed in response to Perkinsus marinus challenge in Eastern (Crassostrea virginica) and Pacific ( C. gigas) oysters. Gene 338(1):121–131

    Article  CAS  PubMed  Google Scholar 

  • Tasumi S, Vasta GR (2007) A galectin of unique domain organization from hemocytes of the Eastern oyster (Crassostrea virginica) is a receptor for the protistan parasite Perkinsus marinus. J Immunol 179(5):3086–3098

    Article  CAS  PubMed  Google Scholar 

  • Terahara K, Takahashi KG (2008) Mechanisms and immunological roles of apoptosis in molluscs. Curr Pharm Des 14(2):131–137

    Article  CAS  PubMed  Google Scholar 

  • Thompson CB (1995) Apoptosis in the pathogenesis and treatment of disease. Science 267(5203):1456–1462

    Article  CAS  PubMed  Google Scholar 

  • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Venier P, Varotto L, Rosani U, Millino C, Celegato B, Bernante F, Lanfranchi G, Novoa B, Roch P, Figueras A, Pallavicini A (2011) Insights into the innate immunity of the Mediterranean mussel Mytilus galloprovincialis. BMC Genomics 12:69

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17(7):1636–1647

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Shi Y, Guo X (2009) Identification and characterization of 66 EST-SSR markers in the eastern oyster Crassostrea virginica (Gmelin). J Shellfish Res 28(2):227–234

    Article  Google Scholar 

  • Wang S, Peatman E, Liu H, Bushek D, Ford SE, Kucuktas H, Quilang J, Li P, Wallace R, Wang Y, Guo X, Liu Z (2010) Microarray analysis of gene expression in eastern oyster (Crassostrea virginica) reveals a novel combination of antimicrobial and oxidative stress host responses after dermo (Perkinsus marinus) challenge. Fish Shellfish Immunol 29(6):921–929

    Article  CAS  PubMed  Google Scholar 

  • Werner GD, Gemmell P, Grosser S, Hamer R, Shimeld SM (2013) Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes. Mar Biotechnol 15(2):230–243

    Article  CAS  PubMed  Google Scholar 

  • Xue Q-G, Waldrop GL, Schey KL, Itoh N, Ogawa M, Cooper RK, Losso JN, La Peyre JF (2006) A novel slow-tight binding serine protease inhibitor from eastern oyster (Crassostrea virginica) plasma inhibits perkinsin, the major extracellular protease of the oyster protozoan parasite Perkinsus marinus. Comp Biochem Physiol B: Biochem Mol Biol 145(1):16–26

    Article  Google Scholar 

  • Xue QG, Itoh N, Schey KL, Li YL, Cooper RK, La Peyre JF (2007) A new lysozyme from the eastern oyster (Crassostrea virginica) indicates adaptive evolution of i-type lysozymes. Cell Mol Life Sci 64(1):82–95

    Article  CAS  PubMed  Google Scholar 

  • Yu H, He Y, Wang X, Zhang Q, Bao Z, Guo X (2011) Polymorphism in a serine protease inhibitor gene and its association with disease resistance in the eastern oyster (Crassostrea virginica Gmelin). Fish Shellfish Immunol 30(3):757–762

    Article  CAS  PubMed  Google Scholar 

  • Yúfera M, Halm S, Beltran S, Fusté B, Planas JV, Martínez-Rodríguez G (2012) Transcriptomic characterization of the larval stage in gilthead seabream (Sparus aurata) by 454 pyrosequencing. Mar Biotechnol 14(4):423–435

    Article  PubMed  Google Scholar 

  • Zeng D, Chen X, Xie D, Zhao Y, Yang C, Li Y, Ma N, Peng M, Yang Q, Liao Z (2013) Transcriptome analysis of pacific white shrimp (Litopenaeus vannamei) hepatopancreas in response to taura syndrome virus (TSV) experimental infection. PLoS One 8(2):e57515

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zhang L, Guo X (2010) Development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea virginica Gmelin by mining ESTs and resequencing. Aquaculture 302:124–129

    Article  CAS  Google Scholar 

  • Zhang H, Song L, Li C, Zhao J, Wang H, Qiu L, Ni D, Zhang Y (2008) A novel C1q-domain-containing protein from Zhikong scallop Chlamys farreri with lipopolysaccharide binding activity. Fish Shellfish Immunol 25(3):281–289

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Li L, Zhang G (2011a) A Crassostrea gigas Toll-like receptor and comparative analysis of TLR pathway in invertebrates. Fish Shellfish Immunol 30(2):653–660

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Li L, Zhang G (2011b) Gene discovery, comparative analysis and expression profile reveal the complexity of the Crassostrea gigas apoptosis system. Dev Comp Immunol 35(5):603–610

    Article  CAS  PubMed  Google Scholar 

  • Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H, Xiong Z, Que H, Xie Y, Holland PW, Paps J, Zhu Y, Wu F, Chen Y, Wang J, Peng C, Meng J, Yang L, Liu J, Wen B, Zhang N, Huang Z, Zhu Q, Feng Y, Mount A, Hedgecock D, Xu Z, Liu Y, Domazet-Loso T, Du Y, Sun X, Zhang S, Liu B, Cheng P, Jiang X, Li J, Fan D, Wang W, Fu W, Wang T, Wang B, Zhang J, Peng Z, Li Y, Li N, Chen M, He Y, Tan F, Song X, Zheng Q, Huang R, Yang H, Du X, Chen L, Yang M, Gaffney PM, Wang S, Luo L, She Z, Ming Y, Huang W, Huang B, Zhang Y, Qu T, Ni P, Miao G, Wang Q, Steinberg CE, Wang H, Qian L, Liu X, Yin Y (2012) The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490(7418):49–54

    Article  CAS  PubMed  Google Scholar 

  • Zhao X, Wang Q, Jiao Y, Huang R, Deng Y, Wang H, Du X (2012) Identification of genes potentially related to biomineralization and immunity by transcriptome analysis of pearl sac in pearl oyster Pinctada martensii. Mar Biotechnol 14(6):730–739

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Laodong Aquaculture Breeding Company for providing oysters. Thanks also to Ping Zhang, Zengfang Zhao in high-performance computing center of Institute of Oceanology, CAS, for providing computing resources. This research was supported in part by National Basic Research Program of China (973 Program, No. 2010CB126401), National High Technology Research and Development Program (863 program, 2012AA10A405), the National Natural Science Foundation of China (no. 40730845), Molluscan Research and Development Center, CARS, Taishan Scholars Climbing Program of Shandong and Taishan Oversea Scholar Program of Shandong, US NSF EID award (OCE-0622672), and RAPID award (OCE-1136530).

Author information

Authors and Affiliations

  1. Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China

    Linlin Zhang, Li Li & Guofan Zhang

  2. University of Chinese Academy of Sciences, Beijing, 100039, China

    Linlin Zhang

  3. BGI-Shenzhen, Shenzhen, 518083, China

    Yabing Zhu

  4. Haskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ, 08349, USA

    Ximing Guo

Authors
  1. Linlin Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Li Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yabing Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Guofan Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ximing Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Guofan Zhang or Ximing Guo.

Additional information

Authors’ contributions

Conceived and designed experiments: LZ, XG, LL, and GZ. Performed experiments: LZ. Analyzed data: LZ, XG, and YZ. Contributed reagents/materials: GZ, XG, and LL. Wrote the paper: LZ and XG. All authors read and approved the paper.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file 1

Cross-mapping statistics among different assemblies of Crassostrea virginica transcriptome. (DOC 51 kb)

Supplementary file 2

Mapping of assembled contigs with BLASTN against the 12 Crassostrea virginica mitochondrial protein coding genes at a cut-off E value of 1E-5. (DOC 35 kb)

Supplementary file 3

Simple sequence repeats (SSRs) identified in the transcriptome of Crassostrea virginica. (DOC 30 kb)

Supplementary file 4

Annotation by top hits from BLASTX of Crassostrea virginica unigenes against the nr protein database with a cut-off E value of 1E-5. (TXT 2231 kb)

Supplementary file 5

Crassostrea virginica transcriptome protein set based on the Oases k-mer 23 assembly. Only proteins longer than 100 amino acids are included. (FA 11414 kb)

Supplementary file 6

InterProScan annotation of predicted Crassostrea virginica genes. (TXT 4688 kb)

Supplementary file 7

GO annotation of predicted Crassostrea virginica genes. (TXT 5304 kb)

Supplementary file 8

KEGG pathway mapping of Crassostrea virginica genes. (TXT 1508 kb)

Supplementary file 9

Complete list of immunity-related unigenes found in Crassostrea virginica transcriptome (with predicted unigene IDs). (DOC 94 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhang, L., Li, L., Zhu, Y. et al. Transcriptome Analysis Reveals a Rich Gene Set Related to Innate Immunity in the Eastern Oyster (Crassostrea virginica). Mar Biotechnol 16, 17–33 (2014). https://doi.org/10.1007/s10126-013-9526-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10126-013-9526-z

Keywords

Search

Navigation