Skip to main content

Advertisement

SpringerLink
Log in

Bivalve transcriptomics reveal pathogen sequences and a powerful immune response of the Mediterranean mussel (Mytilus galloprovincialis)

  • Original paper
  • Published:
Marine Biology Aims and scope Submit manuscript

Abstract

Bivalves have colonized the interface between land and sea for the last 500 million years. Although bivalves lack an adaptive immune system, they are extraordinarily well adapted to adverse environmental conditions. Bivalves are valuable aquaculture resources worldwide and are used as sentinels for monitoring pollution. In this work, the immune transcriptomes of mussels (Mytilus galloprovincialis and edulis) and clam (Ruditapes decussatus) were sequenced. For comparative purposes, an already published transcriptome dataset of Ruditapes philippinarum was also included in the analyses. The 454 pyrosequencing of stimulated hemocytes resulted in more than 400,000 reads for each transcriptome. The percentage of annotated sequences ranges from 50% for mussels to 30–40% for clams. Considering the 28,061 non-redundant sequences from the four transcriptomes, the four species share 785 genes. Moreover, sequences related to different putative pathogens were found in the four bivalves. A high number of bivalve herpesvirus ORFs were found, which confirms the value of NGSs as tools to detect and quantify pathogen RNA. Based on an examination of the immune-enriched transcriptomes of these four species, we can conclude that bivalves present an immune system that differs from its conventional characterization as a simple innate immune response against invading pathogens. Enrichment analyses showed that species in the Mytilus genus, especially M. galloprovincialis, possesses a significantly higher number of sequences related to immune processes and killing molecules than species in the Ruditapes genus. This could be related to the broader ecological niche occupied by mussels and the scarcity of reported mussel mass mortalities compared to the high number of mass mortalities reported for clams.

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

Similar content being viewed by others

References

  • Allam B, Pales Espinosa E (2016) Bivalve immunity and response to infections: are we looking at the right place? Fish Shellfish Immunol 53:4–12

    Article  CAS  PubMed  Google Scholar 

  • Bai Z, Zheng H, Lin J, Wang G, Li J (2013) Comparative analysis of the transcriptome in tissues secreting purple and white nacre in the pearl mussel Hyriopsis cumingii. PLoS One 8:e53617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Balseiro P, Falcó A, Romero A, Dios S, Martínez-López A, Figueras A, Estepa A, Novoa B (2011) Mytilus galloprovincialis myticin C: a chemotactic molecule with antiviral activity and immunoregulatory properties. PLoS One 6:e23140

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Batista FM, Arzul I, Pepin JF, Ruano F, Friedman CS, Boudry P, Renault T (2007) Detection of ostreid herpesvirus 1 DNA by PCR in bivalve molluscs: a critical review. J Virol Methods 139:1–11

    Article  CAS  PubMed  Google Scholar 

  • Beaz-Hidalgo R, Balboa S, Romalde JL, Figueras MJ (2010) Diversity and pathogenecity of Vibrio species in cultured bivalve molluscs. Environ Microbiol Rep 2:34–43

    Article  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 Genom 11:559

    Article  CAS  Google Scholar 

  • Bower SM (2010) Synopsis of infectious diseases and parasites of commercially exploited shellfish. Fisheries and oceans Canada. http://www.dfo-mpo.gc.ca/science/aah-saa/diseases-maladies/index-eng.html. Accessed Nov 2017

  • Carlsson J, Gauthier DT, Carlsson JEL, Coughlan JP, Dillane E, Fitzgerald RD, Keating U, McGinnity P, Mirimin L, Cross TF (2013) Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua. J Fish Biol 82:944–958

    Article  CAS  PubMed  Google Scholar 

  • Carneiro AR, Ramos RT, Barbosa HP, Schneider MP, Barh D, Azevedo V, Silva A (2012) Quality of prokaryote genome assembly: indispensable issues of factors affecting prokaryote genome assembly quality. Gene 505:365–367

    Article  CAS  PubMed  Google Scholar 

  • Cassat JE, Skaar EP (2013) Iron in infection and immunity. Cell Host Microbe 13:509–519

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chang PH, Kuo ST, Lai SH, Yang HS, Ting YY, Hsu CL, Chen HC (2005) Herpes-like virus infection causing mortality of cultured abalone Haliotis diversicolor supertexta in Taiwan. Dis Aquat Organ 65:23–27

    Article  PubMed  Google Scholar 

  • Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Coppe A, Bortoluzzi S, Murari G, Marino IA, Zane L, Papetti C (2012) Sequencing and characterization of striped venus transcriptome expand resources for clam fishery genetics. PLoS One 7:e44185

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Corbeil S, Williams LM, McColl KA, Crane MS (2016) Australian abalone (Haliotis laevigata, H. rubra and H. conicopora) are susceptible to infection by multiple abalone herpesvirus genotypes. Dis Aquat Organ 119:101–106

    Article  CAS  PubMed  Google Scholar 

  • Costa MM, Novoa B, Figueras A (2008) Influence of beta-glucans on the immune responses of carpet shell clam (Ruditapes decussatus) and Mediterranean mussel (Mytilus galloprovincialis). Fish Shellfish Immunol 24:498–505

    Article  CAS  Google Scholar 

  • Costa MM, Dios S, Alonso-Gutierrez J, Romero A, Novoa B, Figueras A (2009) Evidence of high individual diversity on myticin C in mussel (Mytilus galloprovincialis). Dev Comp Immunol 33:162–170

    Article  CAS  PubMed  Google Scholar 

  • Craft JA, Gilbert JA, Temperton B, Dempsey KE, Ashelford K, Tiwari B, Hutchinson TH, Chipman JK (2010) Pyrosequencing of Mytilus galloprovincialis cDNAs: tissue-specific expression patterns. PLoS One 5:e8875

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dame RF (1993) The role of bivalve filter feeder material fluxes in estuarine ecosystems. In: Dame RF (ed) Bivalve filter feeders. Nato ASI Series (Series G: Ecological Sciences), vol 33. Springer, Berlin, Heidelberg, pp 245–269

  • Dang LT, Koyama T, Shitara A, Kondo H, Aoki T, Hirono I (2010) Involvement of WSSV-shrimp homologs in WSSV infectivity in kuruma shrimp: Marsupenaeus japonicus. Antivir Res 88:217–226

    Article  CAS  PubMed  Google Scholar 

  • Davis HC, Loosanoff VL, Weston WH, Martin C (1954) A fungus disease in clam and oyster larvae. Science 120:36–38

    Article  CAS  PubMed  Google Scholar 

  • Dégremont L, Lamy JB, Pépin JF, Travers MA, Renault T (2015) New Insight for the genetic evaluation of resistance to ostreid herpesvirus infection, a worldwide disease, in Crassostrea gigas. PLoS One 10:e0127917

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dellagi A, Segond D, Rigault M, Fagard M, Simon C, Saindrenan P, Expert D (2009) Microbial siderophores exert a subtle role in Arabidopsis during infection by manipulating the immune response and the iron status. Plant Physiol 150:1687–1696

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dufresne M, Seva C, Fourmy D (2006) Cholecystokinin and gastrin receptors. Physiol Rev 86:805–847

    Article  CAS  PubMed  Google Scholar 

  • Estévez-Calvar N, Romero A, Figueras A, Novoa B (2011) Involvement of pore-forming molecules in immune defense and development of the Mediterranean mussel (Mytilus galloprovincialis). Dev Comp Immunol 35:1017–1031

    Article  PubMed  CAS  Google Scholar 

  • Ewen-Campen B, Shaner N, Panfilio K, Suzuki Y, Roth S, Extavour CG (2011) The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genom 12:61

    Article  CAS  Google Scholar 

  • Fino KK, Matters GL, McGovern CO, Gilius EL, Smith JP (2012) Downregulation of the CCK-B receptor in pancreatic cancer cells blocks proliferation and promotes apoptosis. Am J Physiol Gastrointest Liver Physiol 302:G1244–G1252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fisher WS (1986) Structure and functions of oyster hemocytes. In: Brehélin M (ed) Immunity in invertebrates. Proceedings in life sciences. Springer, Berlin

    Google Scholar 

  • Flajnik MF (2010) All GOD’s creatures got dedicated mucosal immunity. Nat Immunol 11:777–779

    Article  CAS  PubMed  Google Scholar 

  • Galindo J, Grahame JW, Butlin RK (2010) An EST-based genome scan using 454 sequencing in the marine snail Littorina saxatilis. J Evol Biol 23:2004–2016

    Article  CAS  PubMed  Google Scholar 

  • Gerdol M, Venier P (2015) An updated molecular basis for mussel immunity. Fish Shellfish Immunol 46:17–38

    Article  CAS  PubMed  Google Scholar 

  • Gerdol M, De Moro G, Manfrin C, Milandri A, Riccardi E, Beran A, Venier P, Pallavicini A (2014) RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum. BMC Res Notes 7:722

    Article  PubMed  PubMed Central  Google Scholar 

  • Gestal C, Costa M, Figueras A, Novoa B (2007) Analysis of differentially expressed genes in response to bacterial stimulation in hemocytes of the carpet shell clam Ruditapes decussatus: identification of new antimicrobial peptides. Gene 406:134–143

    Article  CAS  PubMed  Google Scholar 

  • Giles H, Pilditch CA, Bell DG (2006) Sedimentation from mussel (Perna canaliculus) culture in the Firth of Thames, New Zealand: impacts on sediment oxygen and nutrient fluxes. Aquaculture 261:125–140

    Article  Google Scholar 

  • Gómez-León J, Villamil L, Lemos ML, Novoa B, Figueras A (2005) Isolation of V. alginolyticus and Vibrio splendidus from aquacultured carpet shell clam (Ruditapes decussatus) larvae associated with mass mortalities. Appl Environ Microbiol 71:98–104

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Green TJ, Raftos D, Speck P, Montagnani C (2015) Antiviral immunity in marine molluscs. J Gen Virol 96:2471–2482

    Article  CAS  PubMed  Google Scholar 

  • Hallen LC, Burki Y, Ebeling M, Broger C, Siegrist F, Oroszlan-Szovik K, Bohrmann B, Certa U, Foser S (2007) Antiproliferative activity of the human IFN-alpha-inducible protein IFI44. J Interferon Cytokine Res 27:675–680

    Article  CAS  PubMed  Google Scholar 

  • Heinonen MT, Kanduri K, Lähdesmäki HJ, Lahesmaa R, Henttinen TA (2015) Tubulin- and actin-associating GIMAP4 is required for IFN-γ secretion during Th cell differentiation. Immunol Cell Biol 93:158–166

    Article  CAS  PubMed  Google Scholar 

  • Hertel LA, Bayne CJ, Loker ES (2002) The symbiont Capsaspora owczarzaki, nov. gen. nov. sp., isolated from three strains of the pulmonate snail Biomphalaria glabrata is related to members of the Mesomycetozoea. Int J Parasitol 32:1183–1191

    Article  CAS  PubMed  Google Scholar 

  • Hotamisligil GS, Erbay E (2008) Nutrient sensing and inflammation in metabolic diseases. Nat Rev Immunol 8:923–934

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu H, Bandyopadhyay PK, Olivera BM, Yandell M (2011) Characterization of the Conus bullatus genome and its venom-duct transcriptome. BMC Genom 12:60

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Huang XD, 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 5:253–264

    Article  CAS  Google Scholar 

  • Huang G, Huang S, Yan X, Yang P, Li J, Xu W, Zhang L, Wang R, Yu Y, Yuan S, Chen S, Luo G, Xu A (2014) Two apextrin-like proteins mediate extracellular and intracellular bacterial recognition in amphioxus. Proc Natl Acad Sci USA 111:13469–13474

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iyer A, Brown L, Whitehead JP, Prins JB, Fairlie DP (2015) Nutrient and immune sensing are obligate pathways in metabolism, immunity, and disease. FASEB J 29:3612–3625

    Article  CAS  PubMed  Google Scholar 

  • Jeffroy F, Brulle F, Paillard C (2013) Differential expression of genes involved in immunity and biomineralization during brown ring disease development and shell repair in the Manila clam, Ruditapes philippinarum. J Invertebr Pathol 113:129–136

    Article  CAS  PubMed  Google Scholar 

  • Jiang JZ, Zhang W, Guo ZX, Cai CC, Su YL, Wang RX, Wang JY (2011) Functional annotation of an expressed sequence tag library from Haliotis diversicolor and analysis of its plant-like sequences. Mar Genom 4:189–196. https://doi.org/10.1016/j.margen.2011.05.001

    Article  Google Scholar 

  • Kawai T, Akira S (2011) Regulation of innate immune signalling pathways by the tripartite motif (TRIM) family proteins. EMBO Mol Med 3:513–527

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kinoshita S, Wang N, Inoue H, Maeyama K, Okamoto K, Nagai K, Kondo H, Hirono I, Asakawa S, Watabe S (2011) Deep sequencing of ESTs from nacreous and prismatic layer producing tissues and a screen for novel shell formation-related genes in the pearl oyster. PLoS One 6:e21238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kurelec B, Pivčević B (1991) Evidence for a multixenobiotic resistance mechanism in the mussel Mytilus galloprovincialis. Aquat Toxicol 19:291–301

    Article  CAS  Google Scholar 

  • Le Roux F, Wegner KM, Baker-Austin C, Vezzulli L, Osorio CR, Amaro C, Ritchie JM, Defoirdt T, Destoumieux-Garzón D, Blokesch M, Mazel D, Jacq A, Cava F, Gram L, Wendling CC, Strauch E, Kirschner A, Huehn S (2015) The emergence of Vibrio pathogens in Europe: ecology, evolution, and pathogenesis. Front Microbiol 6:830

    PubMed  PubMed Central  Google Scholar 

  • Leite RB, Milan M, Coppe A, Bortoluzzi S, dos Anjos A, Reinhardt R, Saavedra C, Patarnello T, Cancela ML, Bargelloni L (2013) mRNA-Seq and microarray development for the Grooved Carpet shell clam, Ruditapes decussatus: a functional approach to unravel host–parasite interaction. BMC Genom 14:741

    Article  CAS  Google Scholar 

  • Lemer S, González VL, Bieler R, Giribet G (2016) Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach. Proc Biol Sci 283:20160857

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Leoni G, De Poli A, Mardirossian M, Gambato S, Florian F, Venier P, Wilson DN, Tossi A, Pallavicini A, Gerdol M (2017) Myticalins: a novel multigenic family of linear, cationic antimicrobial peptides from marine mussels (Mytilus spp.). Mar Drugs 15:261

    Article  PubMed Central  Google Scholar 

  • Liao Z, Wang XC, Liu HH, Fan MH, Sun JJ, Shen W (2013) Molecular characterization of a novel antimicrobial peptide from Mytilus coruscus. Fish Shellfish Immunol 34:610–616

    Article  CAS  PubMed  Google Scholar 

  • Marteil L (1976) Shellfish culture in France. Part 2. Oyster and mussel biology. Original title: La conchyliculture française. Biologie de l’huître et de la moule. Revue des Travaux de l´institut des Pêches maritimes. France: IFREMER 40:149–345. http://archimer.ifremer.fr/doc/00000/1796/. Accessed Nov 2017

  • Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:1

    Article  Google Scholar 

  • McDowell IC, Modak TH, Lane CE, Gomez-Chiarri M (2016) Multi-species protein similarity clustering reveals novel expanded immune gene families in the eastern oyster Crassostrea virginica. Fish Shellfish Immunol 53:13–23

    Article  CAS  PubMed  Google Scholar 

  • McNab FW, Rajsbaum R, Stoye JP, O’Garra A (2011) Tripartite-motif proteins and innate immune regulation. Curr Opin Immunol 23:46–56

    Article  CAS  PubMed  Google Scholar 

  • Meyer E, Aglyamova G, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genom 10:219

    Article  CAS  Google Scholar 

  • Milan M, Coppe A, Reinhardt R, Cancela LM, Leite RB, 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 Genom 12:234

    Article  CAS  Google Scholar 

  • Milan M, Ferraresso S, Ciofi C, Chelazzi G, Carrer C, Ferrari G, Pavan L, Patarnello T, Bargelloni L (2013) Exploring the effects of seasonality and chemical pollution on the hepatopancreas transcriptome of the Manila clam. Mol Ecol 22:2157–2172

    Article  CAS  PubMed  Google Scholar 

  • Mitta G, Vandenbulcke F, Noël T, Romestand B, Beauvillain JC, Salzet M, Roch P (2000a) Differential distribution and defence involvement of antimicrobial peptides in mussel. J Cell Sci 113:2759–2769

    CAS  PubMed  Google Scholar 

  • Mitta G, Vandenbulcke F, Roch P (2000b) Original involvement of antimicrobial peptides in mussel innate immunity. FEBS Lett 486:185–190

    Article  CAS  PubMed  Google Scholar 

  • Moreira R, Balseiro P, Romero A, Dios S, Posada D, Novoa B, Figueras A (2012a) Gene expression analysis of clams Ruditapes philippinarum and Ruditapes decussatus following bacterial infection yields molecular insights into pathogen resistance and immunity. Dev Comp Immunol 36:140–149

    Article  CAS  PubMed  Google Scholar 

  • Moreira R, Balseiro P, Planas JV, Fuste B, Beltran S, Novoa B, Figueras A (2012b) Transcriptomics of in vitro immune-stimulated hemocytes from the Manila clam Ruditapes philippinarum using high-throughput sequencing. PLoS One 7:e35009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moreira R, Pereiro P, Canchaya C, Posada D, Figueras A, Novoa B (2015) RNA-seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues. BMC Genom 16:728

    Article  CAS  Google Scholar 

  • Morton B (1981) The anomalodesmata. Malacologia 21:35–60

    Google Scholar 

  • Mount AS, Wheeler AP, Paradkar RP, Snider D (2004) Hemocyte-mediated shell mineralization in the eastern oyster. Science 304:297–300

    Article  CAS  PubMed  Google Scholar 

  • Murgarella M, Puiu D, Novoa B, Figueras A, Posada D, Canchaya C (2016) A first insight into the genome of the filter-feeder mussel Mytilus galloprovincialis. PLoS One 11:e0151561

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nairz M, Haschka D, Demetz E, Weiss G (2014) Iron at the interface of immunity and infection. Front Pharmacol 5:152

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Newell RIE (2004) Ecosystem influences of natural and cultivated populations of suspension-feeding bivalve molluscs: a review. J Shellfish Res 23:51–61

    Google Scholar 

  • Novoa B, Romero A, Álvarez ÁL, Moreira R, Pereiro P, Costa MM, Dios S, Estepa A, Parra F, Figueras A (2016) Antiviral activity of myticin C peptide from mussel: an ancient defence against herpesviruses. J Virol 90(7692):7702

    Google Scholar 

  • Pallavicini A, del Mar Costa M, Gestal C, Dreos R, Figueras A, Venier P, Novoa B (2008) High sequence variability of myticin transcripts in hemocytes of immune-stimulated mussels suggests ancient host–pathogen interactions. Dev Comp Immunol 32:213–226

    Article  CAS  PubMed  Google Scholar 

  • Philipp EE, 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:e33091

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pinkenburg O, Meyer T, Bannert N, Norley S, Bolte K, Czudai-Matwich V, Herold S, Gessner A, Schnare M (2016) The human antimicrobial protein bactericidal/permeability-increasing protein (BPI) inhibits the infectivity of influenza a virus. PLoS One 11:e0156929

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Plazzi F, Passamonti M (2010) Towards a molecular phylogeny of Molluscs: bivalves’ early evolution as revealed by mitochondrial genes. Mol Phylogenet Evol 57:641–657

    Article  CAS  PubMed  Google Scholar 

  • Ponder WF, Lindberg DR (2008) Phylogeny and evolution of the mollusca. University of California Press, Oakland

    Book  Google Scholar 

  • Power D, Santoso N, Dieringer M, Yu J, Huang H, Simpson S, Seth I, Miao H, Zhu J (2015) IFI44 suppresses HIV-1 LTR promoter activity and facilitates its latency. Virology 481:142–150

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qin CL, Huang W, Zhou SQ, Wang XC, Liu HH, Fan MH, Wang RX, Gao P, Liao Z (2014) Characterization of a novel antimicrobial peptide with chitin-biding domain from Mytilus coruscus. Fish Shellfish Immunol 41:362–370

    Article  CAS  PubMed  Google Scholar 

  • Ren W, Chen H, Renault T, Cai Y, Bai C, Wang C, Huang J (2013) Complete genome sequence of acute viral necrosis virus associated with massive mortality outbreaks in the Chinese scallop, Chlamys farreri. Virol J 10:110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ren Y, Xue J, Yang H, Pan B, Bu W (2017) Transcriptome analysis of Ruditapes philippinarum hepatopancreas provides insights into immune signaling pathways under Vibrio anguillarum infection. Fish Shellfish Immunol 64:14–23

    Article  CAS  PubMed  Google Scholar 

  • Riesgo A, Andrade SC, Sharma P, Novo M, Pérez-Porro AR, Vahtera V, González VL, Kawauchi GY, Giribet G (2012) Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Front Zool 9:33

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Romero A, Dios S, Poisa-Beiro L, Costa MM, Posada D, Figueras A, Novoa B (2011) Individual sequence variability and functional activities of fibrinogen-related proteins (FREPs) in the Mediterranean mussel (Mytilus galloprovincialis) suggest ancient and complex immune recognition models in invertebrates. Dev Comp Immunol 35:334–344

    Article  CAS  PubMed  Google Scholar 

  • Romero A, Costa Md, Forn-Cuni G, Balseiro P, Chamorro R, Dios S, Figueras A, Novoa B (2014) Occurrence, seasonality and infectivity of Vibrio strains in natural populations of mussels Mytilus galloprovincialis. Dis Aquat Organ 108:149–163

    Article  PubMed  Google Scholar 

  • Rosani U, Varotto L, Rossi A, Roch P, Novoa B, Figueras A, Pallavicini A, Venier P (2011) Massively parallel amplicon sequencing reveals isotype-specific variability of antimicrobial peptide transcripts in Mytilus galloprovincialis. PLoS One 6:e26680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rosani U, Varotto L, Gerdol M, Pallavicini A, Venier P (2015) IL-17 signaling components in bivalves: comparative sequence analysis and involvement in the immune responses. Dev Comp Immunol 52:255–268

    Article  CAS  PubMed  Google Scholar 

  • Ruano F, Batista FM, Arcangeli G (2015) Perkinsosis in the clams Ruditapes decussatus and R. philippinarum in the Northeastern Atlantic and Mediterranean Sea: a review. J Invertebr Pathol 131:58–67

    Article  PubMed  Google Scholar 

  • Sánchez-Pla A, Reverter F, Ruíz de Villa MC, Comabella M (2012) Transcriptomics: mRNA and alternative splicing. J Neuroimmunol 248:23–31

    Article  PubMed  CAS  Google Scholar 

  • Schmieder R, Edwards R (2011) Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 6:e17288

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Segarra A, Pepin JF, Arzul I, Morga B, Faury N, Renault T (2010) Detection and description of a particular Ostreid herpesvirus 1 genotype associated with massive mortality outbreaks of Pacific oysters, Crassostrea gigas, in France in 2008. Virus Res 153:92–99

    Article  CAS  PubMed  Google Scholar 

  • Shagin DA, Rebrikov DV, Kozhemyako VB, Altshuler IM, Shcheglov AS, Zhulidov PA, Bogdanova EA, Staroverov DB, Rasskazov VA, Lukyanov S (2002) A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res 12:1935–1942

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shi Y, Yu C, Gu Z, Zhan X, Wang Y, Wang A (2013) Characterization of the pearl oyster (Pinctada martensii) mantle transcriptome unravels biomineralization genes. Mar Biotechnol 15:175–187

    Article  CAS  PubMed  Google Scholar 

  • Sillanpää JK, Ramesh K, Melzner F, Sundh H, Sundell K (2016) Calcium mobilisation following shell damage in the Pacific oyster, Crassostrea gigas. Mar Genom 27:75–83

    Article  Google Scholar 

  • Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212

    Article  PubMed  CAS  Google Scholar 

  • Sun Y, Zhang Y, Fu X, Zhang R, Zou J, Wang S, Hu X, Zhang L, Bao Z (2014) Identification of two secreted ferritin subunits involved in immune defense of Yesso scallop Patinopecten yessoensis. Fish Shellfish Immunol 37:53–59

    Article  CAS  PubMed  Google Scholar 

  • Suttle CA (2007) Marine viruses—major players in the global ecosystem. Nat Rev Microbiol 5:801–812

    Article  CAS  PubMed  Google Scholar 

  • Tornatore L, Thotakura AK, Bennett J, Moretti M, Franzoso G (2012) The nuclear factor kappa B signaling pathway: integrating metabolism with inflammation. Trends Cell Biol 22:557–566

    Article  CAS  PubMed  Google Scholar 

  • Toubiana M, Gerdol M, Rosani U, Pallavicini A, Venier P, Roch P (2013) Toll-like receptors and MyD88 adaptors in Mytilus: complete cds and gene expression levels. Dev Comp Immunol 40:158–166

    Article  CAS  PubMed  Google Scholar 

  • van der Meer JW, Joosten LA, Riksen N, Netea MG (2015) Trained immunity: a smart way to enhance innate immune defence. Mol Immunol 68:40–44

    Article  PubMed  CAS  Google Scholar 

  • van Diepen MT, Spencer GE, van Minnen J, Gouwenberg Y, Bouwman J, Smit AB, van Kesteren RE (2005) The molluscan RING-finger protein L-TRIM is essential for neuronal outgrowth. Mol Cell Neurosci 29:74–81

    Article  PubMed  CAS  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 17:1636–1647

    Article  CAS  PubMed  Google Scholar 

  • Villalba A, Reece KS, Ordas MC, Casas SM, Figueras A (2004) Perkinsosis in molluscs: a review. Aquat Living Res 17:411e32

    Article  Google Scholar 

  • Wang J, Wang L, Yang C, Jiang Q, Zhang H, Yue F, Huang M, Sun Z, Song L (2013) The response of mRNA expression upon secondary challenge with Vibrio anguillarum suggests the involvement of C-lectins in the immune priming of scallop Chlamys farreri. Dev Comp Immunol 40:142–147

    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 15:230–243

    Article  CAS  PubMed  Google Scholar 

  • Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J (2016) Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions. Nature 529:496–501

    Article  CAS  PubMed  Google Scholar 

  • Yarra T, Gharbi K, Blaxter M, Peck LS, Clark MS (2016) Characterization of the mantle transcriptome in bivalves: Pecten maximus, Mytilus edulis and Crassostrea gigas. Mar Genom 27:9–15

    Article  Google Scholar 

  • Zhao J, Li C, Chen A, Li L, Su X, Li T (2010) Molecular characterization of a novel big defensin from clam Venerupis philippinarum. PLoS One 5:e13480

    Article  PubMed  PubMed Central  CAS  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 14:730–739

    Article  CAS  PubMed  Google Scholar 

  • Zhulidov PA, Bogdanova EA, Shcheglov AS, Vagner LL, Khaspekov GL, Kozhemyako VB, Matz MV, Meleshkevitch E, Moroz LL, Lukyanov SA, Shagin DA (2004) Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res 32:e37

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zorita I, Apraiz I, Ortiz-Zarragoitia M, Orbea A, Cancio I, Soto M, Marigómez I, Cajaraville MP (2007) Assessment of biological effects of environmental pollution along the NW Mediterranean Sea using mussels as sentinel organisms. Environ Pollut 148:236–250

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work has been funded by the EU Project REPROSEED (245119) and 10 PXIB 402 096 PR from Xunta de Galicia; and partially supported by Ministerio de Economía y Competitividad through Intramural 201640E024 and MYTIPEP (AGL2015-65705-R). We also acknowledge the support of Xunta de Galicia to our group (IN607B 2016/12). RM wishes to acknowledge the Spanish MICINN for her FPI Spanish research Grant (BES-2009-029765) and the EU H2020 funded Project VIVALDI (678589). We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI). We would also like to thank Ainhoa Blanco for the supply of the blue mussel, Mytilus edulis.

Author information

Author notes

  1. Pablo Balseiro

    Present address: Uni Research Environment, Uni Research AS, Bergen, Norway

Authors and Affiliations

  1. Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Eduardo Cabello 6, 36208, Vigo, Spain

    Rebeca Moreira, Pablo Balseiro, Gabriel Forn-Cuní, Beatriz Novoa & Antonio Figueras

  2. Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, PD, Italy

    Massimo Milan & Luca Bargelloni

Authors
  1. Rebeca Moreira
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pablo Balseiro
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gabriel Forn-Cuní
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Massimo Milan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Luca Bargelloni
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Beatriz Novoa
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Antonio Figueras
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

BN, LB and AF conceived and designed the project. PB and MM performed the annotation step. RM and PB made the functional annotation analyses. GFC did the BUSCO analyses. BN and RM made the analysis of pathogen sequences. RM wrote the manuscript. All listed authors revised, edited, read and approved the manuscript.

Corresponding authors

Correspondence to Rebeca Moreira or Antonio Figueras.

Ethics declarations

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Additional information

Responsible Editor: T. Reusch.

Reviewed by Undisclosed experts.

Electronic supplementary material

Below is the link to the electronic supplementary material.

227_2018_3308_MOESM1_ESM.tif

Figure S1. Read distribution per species. Raw data before (blue) and after (red and green) filtering obtained for the 454 GS FLX platform for the three species (TIFF 66 kb)

227_2018_3308_MOESM2_ESM.tif

Figure S2. Quality control per species. Quality score per base position in the filtered reads under 600 bp (A, C and E) and over 600 bp (B, D, F) (TIFF 1176 kb)

File S1. Bioanalyzer results for the sequenced samples (RAR 3286 kb)

227_2018_3308_MOESM4_ESM.rar

File S2 Nucleotidic sequences in fasta format of contigs and singletons of M. edulis, M. galloprovincialis and R. decussatus (RAR 41811 kb)

227_2018_3308_MOESM5_ESM.xlsx

File S3 List of annotated contigs of M. edulis, M. galloprovincialis and R. decussatus. The file includes among other relevant information: sequence name, length, subject mapping, e value, GO (XLSX 29038 kb)

File S4. Enrichment analysis between Mytilus and Ruditapes genus (XLSX 288 kb)

File S5. Viral sequences found in the four transcriptomes (XLSX 31 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Moreira, R., Balseiro, P., Forn-Cuní, G. et al. Bivalve transcriptomics reveal pathogen sequences and a powerful immune response of the Mediterranean mussel (Mytilus galloprovincialis). Mar Biol 165, 61 (2018). https://doi.org/10.1007/s00227-018-3308-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00227-018-3308-0

Search

Navigation