MytiBase: A knowledgebase of mussel (M. galloprovincialis) transcribed sequences

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Venier, Paola ^a   De Pittà, Cristiano ^a   Bernante, Filippo ^a   Varotto, Laura ^a   De Nardi, Barbara ^b   Bovo, Giuseppe ^c   Roch, Philippe ^d   Novoa, Beatriz ^e   Figueras, Antonio ^e   Pallavicini, Alberto ^f   Lanfranchi, Gerolamo ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b Council for Research and Experimentation in Agriculture ^*  (Italy)

^c Institue of Veterinary Sciences (IZSVe)   (Italy)

^d UNIVERSITÉ MONTPELLIER 2   (France)

^e INSTITUTO DE INVESTIGACIONES MARINAS   (Spain)

^f UNIVERSITY OF TRIESTE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MICROSATELLITE DNA;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BACTERIUM; BIOINFORMATICS; BLOOD CELL; CONTROLLED STUDY; DNA LIBRARY; EXOCRINE GLAND; EXPRESSED SEQUENCE TAG; GENETIC TRANSCRIPTION; GILL; KNOWLEDGE BASE; LINKAGE ANALYSIS; MICROSATELLITE MARKER; MOLECULAR CLONING; MYTIBASE; MYTILUS GALLOPROVINCIALIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLLUTANT; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; TEMPERATURE; ANIMAL; BIOLOGY; CLUSTER ANALYSIS; COMPUTER INTERFACE; DNA SEQUENCE; GENE LIBRARY; GENETIC DATABASE; GENETIC MARKER; GENETICS; MYTILUS;

BIVALVIA; MYTILUS GALLOPROVINCIALIS;

ANIMALS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENETIC MARKERS; KNOWLEDGE BASES; MICROSATELLITE REPEATS; MYTILUS; SEQUENCE ANALYSIS, DNA; USER-COMPUTER INTERFACE;

EID: 62749109661     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-72     Document Type: Article

References (90)

1. Gosling EM Bivalve molluscs: Biology, ecology and culture Oxford; Malden, MA: Fishing News Books 2003
2. FAO - Fisheries and Aquaculture Information and Statistics Service http://www.fao.org
3. Whitfield J Vital signs Nature 2001, 411(6841):989-990 11429567
4. Gaitanaki C Kefaloyianni E Marmari A Beis I Various stressors rapidly activate the p38-MAPK signaling pathway in Mytilus galloprovincialis (Lam.) Mol Cellular Biochem 2004, 260(1-2):119-127 15228093
5. Cajaraville MP Bebianno MJ Blasco J Porte C Sarasquete C Viarengo A The use of biomarkers to assess the impact of pollution in coastal environments of the Iberian Peninsula: A practical approach The Science of the total environment 2000, 247(2-3):295-311 10803557
6. Riginos C Cunningham CW Local adaptation and species segregation in two mussel (Mytilus edulis × Mytilus trossulus) hybrid zones Molecular ecology 2005, 14(2):381-400 15660932
7. Saavedra C Bachere E Bivalve genomics Aquaculture 2006, 256(1-4):1-14
8. Anisimova AA Genome sizes of some Bivalvia species of the Peter the Great Bay of the Sea of Japan Comparative Cytogenetics 2007, 1:63-69
9. Food Standards Agency http://www.food.gov.uk
10. Cunningham C Hikima J Jenny MJ Chapman RW Fang GC Saski C Lundqvist ML Wing RA Cupit PM Gross PS Warr GW Tomkins JP New resources for marine genomics: Bacterial artificial chromosome libraries for the Eastern and Pacific oysters (Crassostrea virginica and C. gigas) Marine biotechnology 2006, 8(5):521-533 16896533
11. 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 et al.: The genome of the sea urchin Strongylocentrotus purpuratus Science 2006, 314(5801):941-952 17095691
12. Putnam NH Srivastava M Hellsten U Dirks B Chapman J Salamov A Terry A Shapiro H Lindquist E Kapitonov VV Jurka J Genikhovich G Grigoriev IV Lucas SM Steele RE Finnerty JR Technau U Martindale MQ Rokhsar DS Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization Science 2007, 317(5834):86-94 17615350
13. Riginos C Wang D Abrams AJ Geographic variation and positive selection on M7 lysin, an acrosomal sperm protein in mussels (Mytilus spp.) Mol Biol Evol 2006, 23(10):1952-1965 16855010
14. Dreyer H Steiner G The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica - and the first record for a putative Atpase subunit 8 gene in marine bivalves Frontiers in zoology 2006, 3:13 1570459 16948842
15. Serb JM Lydeard C Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): An examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca) Mol Biol Evol 2003, 20(11):1854-1866 12949150
16. Cao L Kenchington E Zouros E Rodakis GC Evidence that the large noncoding sequence is the main control region of maternally and paternally transmitted mitochondrial genomes of the marine mussel (Mytilus spp.) Genetics 2004, 167(2):835-850 1470915 15238532
17. Mizi A Zouros E Moschonas N Rodakis GC The complete maternal and paternal mitochondrial genomes of the Mediterranean mussel Mytilus galloprovincialis: Implications for the doubly uniparental inheritance mode of mtDNA Mol Biol Evol 2005, 22(4);952-967 15647523
18. Hoffmann RJ Boore JL Brown WM A novel mitochondrial genome organization for the blue mussel, Mytilus edulis Genetics 1992, 131(2):397-412 1205014 1386586
19. Boore JL Medina M Rosenberg LA Complete sequences of the highly rearranged molluscan mitochondrial genomes of the Scaphopod Graptacme eborea and the bivalve Mytilus edulis Mol Biol Evol 2004, 21(8):1492-1503 15014161
20. Breton S Burger G Stewart DT Blier PU Comparative analysis of gender-associated complete mitochondrial genomes in marine mussels (Mytilus spp.) Genetics 2006, 172(2):1107-19 1456209 16322521
21. Milbury CA Gaffney PM Complete mitochondrial DNA sequence of the eastern oyster Crassostrea virginica Marine biotechnology 2005, 7(6):69- 712 16132463
22. Yu Z Wei Z Kong X Shi W Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis - a case of "Tandem duplication-random loss" for genome rearrangement in Crassostrea? BMC Genomics 2008, 9:477 18847502 2576254
23. Sato M Nagashima K Molecular characterization of a mitochondrial DNA segment from the Japanese scallop (Patinopecten yessoensis): demonstration of a region showing sequence polymorphism in the population Marine biotechnology 2001, 3(4):370-379 14961353
24. La Roche J Snyder M Cook DI Fuller K Zouros E Molecular characterization of a repeat element causing large-scale size variation in the mitochondrial DNA of the sea scallop Placopecten magellanicus Mol Biol Evol 1990, 7(1):45-64 2299981
25. Zouros E Oberhauser Ball A Saavedra C Freeman KR An unusual type of mitochondrial DNA inheritance in the blue mussel Mytilus Proc Natl Acad Sci U S A 1994, 91(16):7463-7467 8052604 44421
26. Skibinski DO Gallagher C Beynon CM Mitochondrial DNA inheritance Nature 1994, 368(6474):817-818 8159240
27. Ladoukakis ED Zouros E Direct evidence for homologous recombination in mussel (Mytilus galloprovincialis) mitochondrial DNA Mol Biol Evol 2001, 18(7):1168-1175 11420358
28. Velculescu VE Zhang L Vogelstein B Kinzler KW Serial analysis of gene expression Science 1995, 270(5235):484-487 7570003
29. Liang P Pardee AB Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction Science 1992, 257(5072):967-971 1354393
30. Adams MD Kerlavage AR Fields C Venter JC 3,400 new expressed sequence tags identify diversity of transcripts in human brain Nature genetics 1993, 4(3):256-267 8358434
31. Poustka AJ Groth D Hennig S Thamm S Cameron A Beck A Reinhardt R Herwig R Panopoulou G Lehrach H Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters Genome research 2003, 13(12):2736-2746 403816 14656975
32. Tassanakajon A Klinbunga S Paunglarp N Rimphanitchayakit V Udomkit A Jitrapakdee S Sritunyalucksana K Phongdara A Pongsomboon S Supungul P Tang S Kuphanumart K Pichyangkura R Lursinsap C Penaeus monodon gene discovery project: The generation of an EST collection and establishment of a database Gene 2006, 384:104-112 16945489
33. De Pitta C Bertolucci C Mazzotta GM Bernante F Rizzo G De Nardi B Pallavicini A Lanfranchi G Costa R Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature BMC genomics 2008, 9:45 2270838 18226200
34. Romualdi C Bortoluzzi S D'Alessi F Danieli GA IDEG6: A web tool for detection of differentially expressed genes in multiple tag sampling experiments Physiological genomics 2003, 12(2):159-162 12429865
35. Okubo K Hori N Matoba R Niiyama T Fukushima A Kojima Y Matsubara K Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression Nature genetics 1992, 2(3):173-179 1345164
36. He C Chen L Simmons M Li P Kim S Liu ZJ Putative SNP discovery in interspecific hybrids of catfish by comparative EST analysis Animal genetics 2003, 34(6):445-448 14687075
37. Serapion J Waldbieser GC Wolters W Liu ZJ Development of type I markers in channel catfish through intron sequencing Animal genetics 2004, 35(6):463-466 15566471
38. Serapion J Kucuktas H Feng J Liu Z Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus) Marine biotechnology 2004, 6(4):364-377 15136916
39. 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 JF 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(1-2):27-36 18054177
40. Gueguen Y Cadoret JP Flament D Barreau-Roumiguiere C Girardot AL Garnier J Hoareau A Bachere E Escoubas JM Immune gene discovery by expressed sequence tags generated from hemocytes of the bacteria-challenged oyster, Crassostrea gigas Gene 2003, 303:139-145 12559575
41. Hedgecock D Lin JZ DeCola S Haudenschild CD Meyer E Manahan DT Bowen B Transcriptomic analysis of growth heterosis in larval Pacific oysters (Crassostrea gigas) Proc Natl Acad Sci U S A 2007, 104(7):2313-2318 17277080 1790866
42. Jenny MJ Ringwood AH Lacy ER Lewitus AJ Kempton JW Gross PS Warr GW Chapman RW Potential indicators of stress response identified by expressed sequence tag analysis of hemocytes and embryos from the American oyster, Crassostrea virginica Marine biotechnology 2002, 4(1):81-93 14961291
43. Quilang J Wang S Li P Abernathy J Peatman E Wang Y Wang L Shi Y Wallace R Guo X Liu Z Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers BMC genomics 2007, 8:157 1919373 17559679
44. Jenny MJ Chapman RW Mancia A Chen YA McKillen DJ Trent H Lang P Escoubas JM Bachere E Boulo V Liu ZJ Gross PS Cunningham C Cupit PM Tanguy A Guo X Moraga D Boutet I Huvet A De Guise S Almeida JS Warr GW A cDNA microarray for Crassostrea virginica and C. gigas Marine biotechnology 2007, 9(5):577-591 17668266
45. Venier P Pallavicini A De Nardi B Lanfranchi G Towards a catalogue of genes transcribed in multiple tissues of Mytilus galloprovincialis Gene 2003, 314:29-40 14527715
46. Venier P De Pitta C Pallavicini A Marsano F Varotto L Romualdi C Dondero F Viarengo A Lanfranchi G Development of mussel mRNA profiling: Can gene expression trends reveal coastal water pollution? Mutation research 2006, 602(1-2):121-134 17010391
47. Pallavicini A del Mar Costa M Gestal C Dreos R Figueras A Venier P Novoa B High sequence variability of myticin transcripts in hemocytes of immune-stimulated mussels suggests ancient host-pathogen interactions Dev Comp Immunol 2008, 32(3): 213-226 17628673
48. Parkinson J Anthony A Wasmuth J Schmid J Hedley A Blaxter M PartiGene - constructing partial genomes Bioinformatics 2004, 20:1398-1404 14988115
49. Parkinson J Guiliano DB Blaxter M Making sense of EST sequences by CLOBBing them BMC Bioinformatics 2002, 3:31 137596 12398795
50. Phrap software http://www.phrap.org
51. The National Center for Biotechnology Information ftp://ftp.ncbi.nih.gov/ blast/db
52. UniProtKB database http://www.pir.uniprot.org/database/download.shtml
53. Wasmuth JD Blaxter ML prot4EST: Translating expressed sequence tags from neglected genomes BMC Bioinformatics 2004, 5:187 543579 15571632
54. Quevillon E Silventoinen V Pillai S Harte N Mulder N Apweiler R Lopez R InterProScan: Protein domains identifier Nucleic Acids Res 2005, 33:W116-20 1160203 15980438
55. M. galloprovincialis database http://mussel.cribi.unipd.it
56. 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. The Gene Ontology Consortium Nat Genet 2000, 25(1):l25-9 10802651
57. MISA software http://pgrc.ipk-gatersleben.de/misa/;
58. Li P Peatman E Wang S Feng J He C Baoprasertkul P Xu P Kucuktas H Nandi S Somridhivej B Serapion J Simmons M Turan C Liu L Muir W Dunham R Brady Y Grizzle J Liu Z Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs BMC Genomics 2007, 8:177 1906771 17577415
59. Bultelle F Panchout M Leboulenger F Danger JM Identification of differentially expressed genes in Dreissena polymorpha exposed to contaminants Mar Environ Res 2002, 54(3-5):385-9 12408591
60. Huvet A Herpin A Dégremont L Labreuche Y Samain JF Cunningham C The identification of genes from the oyster Crassostrea gigas that are differentially expressed in progeny exhibiting opposed susceptibility to summer mortality Gene 2004, 343(1):211-20 15563847
61. Wilson R Chen C Ratcliffe NA Innate immunity in insects: The role of multiple, endogenous serum lectins in the recognition of foreign invaders in the cockroach, Blaberus discoidalis J Immunol 1999, 162(3):1590-1596 9973417
62. Silverman HG Roberto FF Understanding marine mussel adhesion Mar Biotechnol 2007, 9(6):661-81 2100433 17990038
63. Bull PC Cox DW Wilson disease and Menkes disease: New handles on heavy-metal transport Trends Genet 1994, 10(7):246-52 8091505
64. Bard JBL Rhee SY Ontologies in biology: Design, applications and future challenges Nat Rev Genet 2004, 5:213-222 14970823
65. Salvesen GS Riedl SJ Caspase mechanisms Adv Exp Med Biol 2008, 615:13-23 18437889
66. Zinkel S Gross A Yang E BCL2 family in DNA damage and cell cycle control Cell Death Differ 2006, 13(8):1351-9 16763616
67. Lai EC Notch signaling: Control of cell communication and cell fate Development 2004, 131:965-973 14973298
68. Stenmark H Olkkonen VM The Rab GTPase family Genome Biol 2001, 2:5 REVIEWS3007 138937 11387043
69. Konstantinova IM Tsimokha AS Mittenberg AG Role of proteasomes in cellular regulation Int Rev Cell Mol Biol 2008, 267:59-124 18544497
70. Andrews SC Arosio P Bottke W Briat JF von Darl M Harrison PM Laulhère JP Levi S Lobreaux S Yewdall SJ Structure, function, and evolution of ferritins J Inorg Biochem 1992, 47(3-4):161-74 1431878
71. Durand JP Goudard F Pieri J Escoubas JM Schreiber N Cadoret JP Crassostrea gigas ferritin: CDNA sequence analysis for two heavy chain type subunits and protein purification Gene 2004, 338(2):187-95 15315822
72. Zhang Y Meng Q Jiang T Wang H Xie L Zhang R A novel ferritin subunit involved in shell formation from the pearl oyster (Pinctada fucata) Comp Biochem Physiol B Biochem Mol Biol 2003, 135(1):43-54 12781972
73. Bauman JW Liu J Klaassen CD Production of metallothionein and heat-shock proteins in response to metals Fundam Appl Toxicol 1993, 21(1):15-22 8365580
74. Jenny MJ Warr GW Ringwood AH Baltzegar DA Chapman RW Regulation of metallothionein genes in the American oyster (Crassostrea virginica): ontogeny and differential expression in response to different stressors Gene 2006, 379:156-65 16846698
75. Bebianno MJ Lopes B Guerra L Hoarau P Ferreira AM Glutathione S-tranferases and cytochrome P450 activities in Mytilus galloprovincialis from the South coast of Portugal: Effect of abiotic factors Environ Int 2007, 33(4):550-8 17175024
76. Porte C Biosca X Solé M Albaigés J The integrated use of chemical analysis, cytochrome P450 and stress proteins in mussels to assess pollution along the Galician coast (NW Spain) Environ Pollut 2001, 112(2):261-8 11234544
77. Sheehan D Meade G Foley VM Dowd CA Structure, function and evolution of glutathione transferases: Implications for classification of non-mammalian members of an ancient enzyme superfamily Biochem J 2001, 360(Pt 1):1-16 1222196 11695986
78. de Lafontaine Y Gagné F Blaise C Costan G Gagnon P Chan HM Biomarkers in zebra mussels (Dreissena polymorpha) for the assessment and monitoring of water quality of the St Lawrence River (Canada) Aquat Toxicol 2000, 50(1-2):51-71 10930650
79. Vlahogianni T Dassenakis M Scoullos MJ Valavanidis A Integrated use of biomarkers (superoxide dismutase, catalase and lipid peroxidation) in mussels Mytilus galloprovincialis for assessing heavy metals' pollution in coastal areas from the Saronikos Gulf of Greece Mar Pollut Bull 2007, 54(9):1361-71 17624376
80. Mannello F Canesi L Gazzanelli G Gallo G Biochemical properties of metalloproteinases from the hemolymph of the mussel Mytilus galloprovincialis Lam Comp Biochem Physiol B Biochem Mol Biol 2001, 128(3):507-15 11250546
81. Zane L Bargelloni L Patarnello T Strategies for microsatellite isolation: A review Mol Ecol 2002, 11(1):1-16 11903900
82. Lucas JM Vaccaro E Waite JH A molecular, morphometric and mechanical comparison of the structural elements of byssus from Mytilus edulis and Mytilus galloprovincialis J Exp Biol 2002, 205(Pt 12):1807-17 12042339
83. Yu H Li Q Development of EST-SSRs in the Mediterranean blue mussel, Mytilus galloproviancialis Molecular Ecology Notes 2007, 7(6):1308-1310
84. Harrington MJ Waite JH Holdfast heroics: Comparing the molecular and mechanical properties of Mytilus californianus byssal threads J Exp Biol 2007, 210(Pt 24):4307-18 18055620
85. Martinez-Lage A Rodriguez F Gonzalez-Tizon A Prats E Cornudella L Mendez J Comparative analysis of different satellite DNAs in four Mytilus species Genome 2002, 45(5):922-929 12416625
86. McDonald JH Seed R Koehn RK Allozyme and morphometric characters of three species of Mytilus in the northern and southern hemispheres Mar Biol 1991, 11:1323-335
87. Hohe WR Stewart DT Saavedra C Sutherland BW Zouros E Phylogenetic evidence for role-associated mitochondrial DNA in Mytilus (Bivalvia: Mytilidae) Mol Biol Evol 1997, 14:959-967 9287429
88. Kenchington E Landry D Bird CJ Comparison of taxa of the mussel Mytilus (Bivalvia) by analysis of the nuclear small-subunit rRNA gene sequence Can J Fish Aquat Sci 1995, 52:2613-2620
89. Rudd S Expressed sequence tags: Alternative or complement to whole genome sequences? Trends Plant Sci 2003, 8(7):321-329 12878016
90. Jackson RB Linder CR Lynch M Purugganan M Somerville S Thayer SS Linking molecular insight and ecological research Trends Ecol Evol 2002, 17:409-414