High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Bettencourt, Raul ^a,b   Pinheiro, Miguel ^c   Egas, Conceição ^d,e   Gomes, Paula ^d   Afonso, Mafalda ^b   Shank, Timothy ^f   Santos, Ricardo S ^a,b  

^a UNIVERSITY OF THE AZORES   (Portugal)

^b UNIVERSITY OF COIMBRA   (Portugal)

^c Bioinformatics Unit   (Portugal)

^d Advanced Services Unit   (Portugal)

^e UNIVERSITY OF COIMBRA   (Portugal)

^f WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA 2 MACROGLOBULIN; CADHERIN; CHITIN; CONTACTIN; CONTACTIN 2; EPIDERMAL GROWTH FACTOR RECEPTOR; FIBRINOGEN; FICOLIN; GALECTIN 4; GLYCOSIDASE; INTERLEUKIN 1 RECEPTOR ASSOCIATED KINASE; LAMININ; LIPOPOLYSACCHARIDE BINDING PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE; MYELOID DIFFERENTIATION FACTOR 88; NOTCH RECEPTOR; PEPTIDOGLYCAN RECOGNITION PROTEIN; RHAMNOSE; SCAVENGER RECEPTOR; SERINE PROTEINASE INHIBITOR; SOMATOMEDIN B RECEPTOR; SYNAPTOPHYSIN; SYNTENIN; THROMBOSPONDIN; TISSUE INHIBITOR OF METALLOPROTEINASE; TOLL LIKE RECEPTOR ADAPTOR MOLECULE 1; TRANSCRIPTOME; TUMOR NECROSIS FACTOR RECEPTOR; TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED FACTOR; UNCLASSIFIED DRUG; FRESH WATER;

AMINO ACID SEQUENCE; ANIMAL TISSUE; ARTICLE; BATHYMODUOLUS AZORICUS; CONTIG MAPPING; CONTROLLED STUDY; DEEP SEA SPECIES; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; GENETIC CONSERVATION; GENETIC DATABASE; GILL; HIGH THROUGHPUT SCREENING; INFLAMMATION; INNATE IMMUNITY; MUSSEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DATABASE; PROTEIN DOMAIN; QUANTITATIVE STUDY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA TRANSCRIPTION; RNA TRANSLATION; ANIMAL; BACTERIAL GENE; BIVALVE; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT NUCLEOTIDE SEQUENCING; IMMUNITY; IMMUNOLOGY; METABOLISM; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; PHYSIOLOGICAL STRESS; SEA; THERMAL SPRING;

ANIMALIA; BATHYMODIOLUS AZORICUS;

AMINO ACID SEQUENCE; ANIMALS; BIVALVIA; CONTIG MAPPING; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; FRESH WATER; GENE EXPRESSION PROFILING; GENES, BACTERIAL; GILLS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOT SPRINGS; IMMUNITY; INFLAMMATION; MOLECULAR SEQUENCE ANNOTATION; OCEANS AND SEAS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; STRESS, PHYSIOLOGICAL;

EID: 77957675520     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-559     Document Type: Article

References (29)

1. Childress JJ, Fisher CR. The biology of hydrothermal vent animals: physiology, biochemistry, and autotrophic symbioses. Oceanogr Mar Biol Annu Rev 1992, 30:337-441.
2. Desbruyères D, Biscoito M, Caprais JC, Colaço A, Comtet T, Crassous P, Fouquet Y, Khripounoff A, Le Bris N, Olu K, Riso R, Sarradin PM, Segonzac M, Vangriesheim A. Variations in deep-sea hydrothermal vent communities on the Mid-Atlantic Ridge near the Azores plateau. Deep Sea Res Pt I 2001, 48:1325-1346.
3. Salerno JL, Macko SA, Hallam SJ, Bright M, Won YJ, McKiness Z, Van Dover CL. Characterization of Symbiont Populations in Life-History Stages of Mussels From Chemosynthetic Environments. Biol Bull 2005, 208:145-155. 10.2307/3593123, 15837964.
4. Won YJ, Hallam SJ, O'Mullan GD, Pan IL, Buck KR, Vrijenhoek RC. Environmental Acquisition of Thiotrophic Endosymbionts by Deep-Sea Mussels of the Genus Bathymodiolus. Appl Environ Microbiol 2003, 69:6785-6792. 10.1128/AEM.69.11.6785-6792.2003, 262266, 14602641.
5. Duperron S, Bergin C, Zielinski F, Blazejak A, Pernthaler A, McKiness ZP, Dechaine E, Cavanaugh CM, Dubilier N. A dual symbiosis shared by two mussel species, Bathymodiolus azoricus and Bathymodiolus puteoserpentis (Bivalvia: Mytilidae), from hydrothermal vents along the northern Mid-Atlantic Ridge. Environ Microbiol 2006, 8:1441-47. 10.1111/j.1462-2920.2006.01038.x, 16872406.
6. Fiala-Medioni A, McKiness ZP, Dando P, Boulegue J, Mariotti A, Alayse-Danet AM, Robinson JJ, Cavanaugh CM. Ultrastructural, biochemical, and immunological characterization of two populations of the mytilid mussel Bathymodiolus azoricus from the Mid-Atlantic Ridge: evidence for a dual symbiosis. Mar Biol 2002, 141:1035-1043.
7. Distel DL, Lee HKW, Cavanaugh CM. Intracellular coexistence of methanotrophic and thioautotrophic bacteria in a hydrothermal vent mussel. Proc Natl Acad Sci USA 1995, 92:9598-9602. 10.1073/pnas.92.21.9598, 40849, 7568180.
8. Bettencourt R, Roch P, Stefanni S, Rosa D, Colaço A, Serrão R. Deep sea immunity: unveiling immune constituents from the hydrothermal vent mussel Bathymodiolus azoricus. Mar Environ Res 2007, 64:108-27. 10.1016/j.marenvres.2006.12.010, 17291578.
9. Kadar E, Powell J. Post-capture investigation of the hydrothermal vent macro-invertebrates to study adaptation to extreme environments. Rev Env Sci Biotechnol 2006, 5:193-201.
10. Tanguy A, Bierne N, Saavedra C, Pina B, Bachère E, Kube M, Bazin E, Bonhomme F, Boudry P, Boulo V, Boutet I, Cancela L, Dossat C, Favrel P, Huvet A, Jarque S, Jollivet D, Klages S, Lapègue S, Leite R, Moal J, Moraga D, Reinhardt R, Samain J-F, Zouros E, Canario A. Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution. Gene 2008, 408:27-36. 10.1016/j.gene.2007.10.021, 18054177.
11. Boutet I, Jollivet D, Shillito B, Moraga D, Tanguy A. Molecular identification of differentially regulated genes in the hydrothermal-vent species Bathymodiolus thermophilus and Paralvinella pandorae in response to temperature. BMC Genomics 2009, 10:222. 10.1186/1471-2164-10-222, 2689276, 19439073.
12. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-10.
13. Iseli C, Jongeneel CV, Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 1999:138-48.
14. Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Phan I, Zdobnov E. Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes. Nucleic Acids Res 2001, 29:44-48. 10.1093/nar/29.1.44, 29822, 11125045.
15. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res 2008, 37:211-215.
16. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene Ontology: tool for the unification of biology. Nature Genet 2000, 25:25-29. 10.1038/75556, 10802651.
17. Rast JP, Smith LC, Loza-Coll M, Hibino T, Litman GW. Genomic insights into the immune system of the sea urchin. Science 2006, 10:952-956.
18. Iwanaga S, Lee BL. Recent Advances in the Innate Immunity of Invertebrate Animals. J Biochem Mol Bio 2005, 38:128-150.
19. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 2009, 10:219. 10.1186/1471-2164-10-219, 2689275, 19435504.
20. Kadar E, Tschuschke IG, Checa A. Post-capture hyperbaric stimulations to study the mechanism of shell regeneration of the deep-sea hydrothermal vent mussel Bathymodiolus azoricus (Bivalvia: Mytilidae). J Exp Mar Biol Ecol 2008, 364:80-90.
21. Bettencourt R, Costa V, Laranjo M, Rosa D, Pires L, Colaço A, Lopes H, Serrão R. Out of the deep sea into a land-based aquarium environment: investigating physiological adaptations in the hydrothermal vent mussel Bathymodiolus azoricus. ICES J Mar Sci 2010, (first published online August 16, 2010).
22. Stuart R, Rolff J. Immune function keeps endosymbionts under control. J Biol 2008, 7:28. 10.1186/jbiol88, 2776399, 18947377.
23. Venier P, De Pitta C, Bernante F, Varotto L, De Nardi B, Bovo RG, Novoa B, Figueras A, Pallavicini A, Lanfranchi G. MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences. BMC genomics 2009, 10:72. 10.1186/1471-2164-10-72, 2657158, 19203376.
24. Shcheglov A, Zhulidov P, Bogdanova E, Shagin D. Normalization of cDNA Libraries. Nucleic Acids Hybridization: Modern Applications 2007, 97-124. Dordrecht, Springer, Buzdin A, Lukyanov S.
25. Zhulidov PA, Bogdanova EA, Shcheglov AS, Shagina IA, Wagner LL, Khazpekov GL, Kozhemyako VV, Lukyanov SA, Shagin DA. A method for the preparation of normalized cDNA libraries enriched with full-length sequences. Bioorg Khim 2005, 31:186-94.
26. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S. Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs. Genome Res 2004, 14:1147-59. 10.1101/gr.1917404, 419793, 15140833.
27. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12:1611-1618. 10.1101/gr.361602, 187536, 12368254.
28. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-86.
29. Bettencourt R, Dando P, Collins P, Costa V, Allam B, Serrão R. Innate Immunity in the deep sea hydrothermal vent mussel Bathymodiolus azoricus. Comp Biochem Physiol A 2009, 152:278-89.