Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Cerdà, Joan ^a   Mercadé, Jaume ^b   Lozano, Juan Jose ^c   Manchado, Manuel ^d   Tingaud Sequeira, Angèle ^a   Astola, Antonio ^e   Infante, Carlos ^d   Halm, Silke ^e   Viñas, Jordi ^a   Castellana, Barbara ^b   Asensio, Esther ^d   Cañavate, Pedro ^d   Martínez Rodríguez, Gonzalo ^e   Piferrer, Francesc ^a   Planas, Josep V ^b   Prat, Francesc ^e   Yúfera, Manuel ^e   Durany, Olga ^b   Subirada, Francesc ^b   Rosell, Elisabet ^b   Maes, Tamara ^b   more..

^a INSTITUT DE CIÈNCIES DEL MAR   (Spain)

^b UNIVERSITY OF BARCELONA   (Spain)

^c HOSPITAL CLÍNIC   (Spain)

^d IFAPA CENTRO EL TORUÑO   (Spain)

^e INSTITUTO DE CIENCIAS MARINAS DE ANDALUCÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; OLIGONUCLEOTIDE;

3' UNTRANSLATED REGION; ANIMAL EXPERIMENT; ANIMAL TISSUE; AQUACULTURE; ARTICLE; BIOINFORMATICS; BRAIN TISSUE; CONTROLLED STUDY; DEVELOPMENTAL STAGE; DNA LIBRARY; DNA MICROARRAY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; FEMALE; FISH; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENOMICS; GONAD DEVELOPMENT; INTESTINE; LARVAL STAGE; LIVER; MALE; METAMORPHOSIS; MICROARRAY ANALYSIS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OVARY; STOMACH; TESTIS; TISSUE SECTION; TRANSCRIPTION REGULATION; UNINDEXED SEQUENCE; ANIMAL; BIOLOGY; FLATFISH; GENE LIBRARY; GENETICS; GENOME; METHODOLOGY;

PLEURONECTIFORMES; SOLEA SENEGALENSIS;

ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; FLATFISHES; GENE LIBRARY; GENOME; GENOMICS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 58149299281     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-508     Document Type: Article

References (63)

1. Crollius HR Weissenbach J Fish genomics and biology Genome Res 2005, 15:1675-1682. 10.1101/gr.3735805 16339365
2. Meyer A Peer van de Y From 2R to 3R: Evidence for a fish-specific genome duplication (FSGD) Bioessays 2005, 27:937-945. 10.1002/bies.20293 16108068
3. Rise ML von Schalburg KR Brown GD Mawer MA Devlin RH Kuipers N Busby M Beetz-Sargent M Alberto R Gibbs AR Hunt P Shukin R Zeznik JA Nelson C Jones SR Smailus DE Jones SJ Schein JE Marra MA Butterfield YS Stott JM Ng SH Davidson WS Koop BF Development and application of a salmonid EST database and cDNA microarray: Data mining and interspecific hybridization characteristics Genome Res 2004, 14:478-490. 353236 14962987 10.1101/gr.1687304
4. Von Schalburg K Rise ML Cooper GA Brown GD Gibbs AR Nelson CC Davidson WS Koop BF Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray BMC Genomics 2005, 6:126. 1239916 16164747 10.1186/1471-2164-6-126
5. Govoroun M Le Gac F Guiguen Y Generation of a large scale repertoire of Expressed Sequence Tags (ESTs) from normalised rainbow trout cDNA libraries BMC Genomics 2006, 7:196. 1564016 16887034 10.1186/ 1471-2164-7-196
6. Bobe J Montfort J Nguyen T Fostier A Identification of new participants in the rainbow trout (Oncorhynchus mykiss) oocyte maturation and ovulation processes using cDNA microarrays Reprod Biol Endocrinol 2006, 4:39. 1570352 16872517 10.1186/1477-7827-4-39
7. Adzhubei AA Vlasova AV Hagen-Larsen H Ruden TA Laerdahl JK Hoyheim B Annotated expressed sequence tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource BMC Genomics 2007, 8:209. 1913521 17605782 10.1186/1471-2164-8-209
8. Von Schalburg KR Leong J Cooper GA Robb A Beetz-Sargent MR Lieph R Holt RA Moore R Ewart KV Driedzic WR Ten Hallers BF Zhu B de Jong PJ Davidson WS Koop BF Rainbow Smelt (Osmerus mordax) genomic library and EST resources Mar Biotechnol (NY) 2008, 10(5):487-491. 2516299 18386095 10.1007/s10126-008-9089-6
9. Gong Z Hu Z Gong ZQ Kitching R Hew CL Bulk isolation and identification of fish genes by cDNA clone tagging Mol Mar Biol Biotechnol 1994, 3:243-251. 7881511
10. Inoue S Nam B-H Hirono I Aoki T A survey of expressed genes in Japanese flounder (Paralychthys olivaceus) liver and spleen Mol Mar Biol Biotechnol 1997, 6:376-380. 9418294
11. Douglas SE Gallant JW Bullerwell CE Wolff C Munholland J Reith ME Winter flounder expressed sequence tags: Establishment of an EST database and identification of novel fish genes Mar Biotechnol 1999, 1:458-464. 10.1007/PL00011802 10525680
12. Douglas SE Knickle LC Kimball J Reith ME Comprehensive EST analysis of Atlantic halibut (Hippoglossus hippoglossus), a commercially relevant aquaculture species BMC Genomics 2007, 8:144. 1924502 17547761 10.1186/ 1471-2164-8-144
13. Sarropoulou E Power ME Magoulas A Geisler R Kotoulas G Comparative analysis and characterization of expressed sequence tags in gilthead sea bream (Sparus aurata) liver and embryos Aquaculture 2005, 243:69-81. 10.1016/j.aquaculture.2004.10.012
14. Zhou L Yao B Xia W Li C-J Wang Y Shi Y-H Gui J-F EST-based identification of genes expressed in the hypothalamus of male orange-spotted grouper (Epinephelus coioides) Aquaculture 2006, 256:129-139. 10.1016/j.aquaculture.2006.01.022
15. Chini V Rimoldi S Terova G Saroglia M Rossi F Bernardini G Gornati R EST-based identification of genes expressed in the liver of adult seabass (Dicentrarchus labrax L.) Gene 2006, 376:102-106. 10.1016/ j.gene.2006.02.010 16616996
16. Nelson JS Fishes of the World New Yor: John Wiley & Sons 4 2006.
17. Okada N Takagi Y Seikai T Tanaka M Tagawa M Asymmetrical development of bones and soft tissues during eye migration of metamorphosing Japanese flounder, Paralichthys olivaceus Cell Tissue Res 2001, 304:59-66. 10.1007/s004410100353 11383887
18. Power DM Llewellyn L Faustino M Nowell MA Bjornsson BT Einarsdottir IE Canario AV Sweeney GE Thyroid hormones in growth and development of fish Comp Biochem Physiol Part C Toxicol Pharmacol 2001, 130:447-459. 10.1016/ S1532-0456(01)00271-X
19. Schreiber AM Asymmetric craniofacial remodeling and lateralized behavior in larval flatfish J Exp Biol 2006, 209:610-621. 10.1242/jeb.02056 16449556
20. Worm B Barbier EB Beaumont N Duffy JE Folke C Halpern BS Jackson JB Lotze HK Micheli F Palumbi SR Sala E Selkoe KA Stachowicz JJ Watson R Impacts of biodiversity loss on ocean ecosystem services Science 2006, 314:787-790. 10.1126/science.1132294 17082450
21. Dinis MT Ribeiro L Soares F Sarasquete C A review on the cultivation potential of Solea senegalensis in Spain and in Portugal Aquaculture 1999, 176:27-38. 10.1016/S0044-8486(99)00047-2
22. Imsland AK Foss A Conceiçao LEC Dinis MT Delbare D Schram E Kamstra A Rema P White P A review of the culture potential of Solea solea and S. senegalensis Rev Fish Biol Fish 2003, 13:379-407. 10.1007/ s11160-004-1632-6
23. Pleurogene http://www.pleurogene.ca
24. Cerdà J Douglas SE Buesa C Cañavate P López-Barea J Manchado M Martínez G Navas JI Piferrer F Planas J Prat F Reith M Ruíz-Rejón M Yúfera M PLEUROGENE: Flatfish genomics and proteomics for aquaculture Comp Biochem Physiol 2005, 141A:s87.
25. UniGene database, National Centre for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/UniGene
26. Smith TP Grosse WM Freking BA Roberts AJ Stone RT Casas E Wray JE White J Cho J Fahrenkrug SC Bennett GL Heaton MP Laegreid WW Rohrer GA Chitko-McKown CG Pertea G Holt I Karamycheva S Liang F Quackenbush J Keele JW Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle Genome Res 2001, 11:626-30. 311058 11282978 10.1101/gr.170101
27. Zhulidov PA Bogdanova EA Shcheglov AS Vagner LL Khaspekov GL Kozhemyako VB Matz MV Meleshkevitch E Moroz LL Lukyanov SA Shagin DA Simple cDNA normalization using kamchatka crab duplex-specific nuclease Nucleic Acids Res 2004, 32:e37. 373426 14973331 10.1093/nar/gnh031
28. Fernández-Díaz C Yúfera M Cañavate JP Moyano FJ Alarcón FJ Díaz M Growth and physiological changes during metamorphosis of Senegal sole reared in the laboratory J Fish Biol 2001, 58:1086-1097. 10.1111/j.1095-8649.2001.tb00557.x
29. Manchado M Infante C Asensio E Cañavate JP Douglas SE Comparative sequence analysis of the complete set of 40S ribosomal proteins in the Senegalese sole (Solea senegalensis Kaup) and Atlantic halibut (Hippoglossus Pippoglossus L.) (Teleostei: Pleuronectiformes): phylogeny and tissue- and development-specific expression BMC Evol Biol 2007, 7:107. 1933418 17608926 10.1186/1471-2148-7-107
30. Manchado M Infante C Asensio E Planas JV Cañavate JP Thyroid hormones down-regulate thyrotropin beta subunit and thyroglobulin during metamorphosis in the flatfish Senegalese sole (Solea senegalensis Kaup) Gen Comp Endocrinol 2008, 155:447-455. 10.1016/j.ygcen.2007.07.011 17888916
31. Infante C Asensio E Cañavate JP Manchado M Molecular characterization and expression analysis of five different elongation factor 1 alpha genes in the flatfish Senegalese sole (Solea senegalensis Kaup): Differential gene expression and thyroid hormones dependence during metamorphosis BMC Mol Biol 2008, 9:19. 2270864 18234081 10.1186/ 1471-2199-9-19
32. Matsuoka MP Infante C Reith M Cañavate JP Douglas SE Manchado M Translational Machinery of Senegalese Sole (Solea senegalensis Kaup) and Atlantic Halibut (Hippoglossus hippoglossus L.): Comparative Sequence Analysis of the Complete Set of 60S Ribosomal Proteins and their Expression Mar Biotechnol (NY) 2008. doi: 10.1007/s10126-008-9104-y. 18478294
33. Babin PJ Carnevali O Lubzens E Schneider WJ Molecular aspects of oocyte vitellogenesis in fish The Fish Oocyte: From Basic Studies to Biotechnological Applications The Netherlands: Springer Babin P, Cerdà J, Lubzens E 2007:39-76.
34. Modig C Westerlund L Olsson P-E Oocyte zona pellucida proteins The Fish Oocyte: From Basic Studies to Biotechnological Applications The Netherlands: Springer Babin P, Cerdà J, Lubzens E 2007:113-139.
35. Zheng S Gong Z Expressed sequence tag analysis of expression profiles of zebrafish testis and ovary Gene 2002, 294:45-53. 10.1016/ S0378-1119(02)00791-6 12234666
36. Knoll-Gellida A Andre M Gattegno T Forgue J Admon A Babin PJ Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals BMC Genomics 2006, 7:46. 1488847 16526958 10.1186/1471-2164-7-46
37. Poltronieri C Maccatrozzo L Simontacchi C Bertotto D Funkenstein B Patruno M Radaelli G Quantitative RT-PCR analysis and immunohistochemical localization of HSP70 in sea bass Dicentrarchus labrax exposed to transport stress Eur J Histochem 2007, 51:125-135. 17664163
38. Geist J Werner I Eder KJ Leutenegger CM Comparisons of tissue-specific transcription of stress response genes with whole animal endpoints of adverse effect in striped bass (Morone saxatilis) following treatment with copper and esfenvalerate Aquat Toxicol 2007, 85:28-39. 10.1016/ j.aquatox.2007.07.011 17767966
39. Bermejo-Nogales A Benedito-Palos L Saera-Vila A Calduch-Giner JA Sitjà-Bobadilla A Pérez-Sánchez J Confinement exposure induces glucose regulated protein 75 (GRP75/mortalin/mtHsp70/ PBP74/HSPA9B) in the hepatic tissue of gilthead sea bream (Sparus aurata L.) Comp Biochem Physiol Part B Biochem Mol Biol 2008, 149:428-438. 10.1016/j.cbpb.2007.11.003
40. Manchado M Infante C Asensio E Canavate JP Differential gene expression and dependence on thyroid hormones of two glyceraldehyde-3-phosphate dehydrogenases in the flatfish Senegalese sole (Solea senegalensis Kaup) Gene 2007, 400:1-8. 10.1016/j.gene.2007.05.008 17590286
41. Cerdà J Chauvigne F Agulleiro MJ Marin E Halm S Martínez-Rodríguez G Prat F Molecular cloning of Senegalese sole (Solea senegalensis) follicle-stimulating hormone and luteinizing hormone subunits and expression pattern during spermatogenesis Gen Comp Endocrinol 2008, 156:470-481. 10.1016/ j.ygcen.2008.02.006 18353326
42. Brennan C Zhang Y Leo C Feng B Cauwels C Aguirre AJ Kim M Protopopov A Chin L High-resolution global profiling of genomic alterations with long oligonucleotide microarray Cancer Res 2004, 64:4744-4748. 10.1158/ 0008-5472.CAN-04-1241 15256441
43. Van Gelder RN von Zastrow ME Yool A Dement WC Barchas JD Eberwine JH Amplified RNA synthesized from limited quantities of heterogeneous cDNA Proc Natl Acad Sci USA 1990, 87:1663-1667. 53542 1689846 10.1073/ pnas.87.5.1663
44. Edinburgh Mouse Atlas Project (emap) http://genex.hgu.mrc.ac.uk/
45. The Zebrafish Model Organism Database (ZFIN) http://zfin.org
46. The Soleamold bioinformatic platform http://inb.bsc.es/pleurogene/
47. Mercadé J Espinosa A Adsuara JE Adrados R Segura J Puigdomenech P Maes T Orymold: Ontology based gene expression data integration and analysis tool applied to rice BMC Bioinformatics.
48. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215:403-410. 2231712
49. Anguis V Cañavate P Spawning of captive Senegal sole (Solea senegalensis) under a naturally fluctuating temperature regime Aquaculture 2005, 243:133-145. 10.1016/j.aquaculture.2004.09.026
50. Ewing B Hillier L Wendl MC Green P Base-calling of automated sequencer traces using Phred. I. Accuracy assessment Genome Res 1998, 8:175-185. 9521921
51. Ewing B Green P Base-calling of automated sequencer traces using phred. II. Error probabilities Genome Res 1998, 8:186-194. 9521922
52. Laboratory of Phil Green, Genome Sciences Department, University of Washington http://www.phrap.org
53. Gordon D Abajian C Green P Consed: A graphical tool for sequence finishing Genome Res 1998, 8:195-202. 9521923
54. Altschul SF Madden TL Schäffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25:3389-3402. 146917 9254694 10.1093/nar/25.17.3389
55. Bioinformatics Centro de Investigación Príncipe Felipe CIPF, Centro de Genomica Instituto Valenciano de Investigaciones Agrarias, Universidad Politécnica de Valencia http://www.Blast2GO.de
56. Conesa A Gotz S García-Gómez JM Terol J Talon M Robles M Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research Bioinformatics 2005, 21:3674-3676. 10.1093/ bioinformatics/bti610 16081474
57. Schroeder A Mueller O Stocker S Salowsky R Leiber M Gassmann M Lightfoot S Menzel W Granzow M Ragg T The RIN: An RNA integrity number for assigning integrity values to RNA measurements BMC Mol Biol 2006, 7:3. 1413964 16448564 10.1186/1471-2199-7-3
58. Workman C Jensen LJ Jarmer H Berka R Gautier L Nielsen HB Saxild H-H Nielsen C Brunak S Knudsen S A new non-linear normalization method for reducing variability in DNA microarray experiments Genome Biol 2002, 3:rEsearch0048. 126873 12225587 10.1186/gb-2002-3-9-research0048
59. Baldi P Long AD A Bayesian framework for the analysis of microarray expression data: Regularized t -test and statistical inferences of gene changes Bioinformatics 2001, 17:509-519. 10.1093/bioinformatics/17.6.509 11395427
60. Tusher VG Tibshirani R Chu G Significance analysis of microarrays applied to the ionizing radiation response Proc Natl Acad Sci USA 2001, 98:5116-5121. 33173 11309499 10.1073/pnas.091062498
61. Cui X Hwang JT Qiu J Blades NJ Churchill GA Improved statistical tests for differential gene expression by shrinking variance components estimates Biostatistics 2005, 6:59-75. 10.1093/biostatistics/kxh018 15618528
62. Java Programming Language http://www.java.com
63. MySQL http://www.mysql.com