Exploring the larval transcriptome of the common sole (Solea solea L.)

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Ferraresso, Serena ^a   Bonaldo, Alessio ^b   Parma, Luca ^b   Cinotti, Stefano ^c   Massi, Paola ^c   Bargelloni, Luca ^a   Gatta, Pier Paolo ^b  

^a UNIVERSITY OF PADOVA   (Italy)

^b UNIVERSITY OF BOLOGNA   (Italy)

^c ISTITUTO ZOOPROFILATTICO SPERIMENTALE DELLA LOMBARDIA E DELL EMILIA ROMAGNA   (Italy)

Author keywords

Flatfish; Gene expression; Larval development; Metamorphosis; Solea solea; Transcriptome

Indexed keywords

DNA; FOLIC ACID; GROWTH HORMONE; OLIGONUCLEOTIDE; RETINOL; SOMATOMEDIN C; THYROID HORMONE; TRANSCRIPTOME;

ANAEROBIC CAPACITY; ANIMAL CELL; ANIMAL STRUCTURES; ANIMAL TISSUE; ARTICLE; CELL ADHESION; CELL MOTILITY; DNA MICROARRAY; GASTROINTESTINAL TRACT; GENE EXPRESSION PROFILING; GENE FUNCTION; JUVENILE ANIMAL; LARVAL DEVELOPMENT; LARVAL STAGE; METAMORPHOSIS; MOLECULAR MECHANICS; MUSCLE DEVELOPMENT; NONHUMAN; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; ONTOGENY; ORGANOGENESIS; PHYSIOLOGY; REGULATORY MECHANISM; RNA ANALYSIS; RNA SEQUENCE; SOLEA SOLEA; UPREGULATION; VISUAL SYSTEM; VITAMIN METABOLISM;

ANIMALS; FLATFISHES; GENE EXPRESSION PROFILING; INSULIN-LIKE GROWTH FACTOR I; LARVA; MOLECULAR SEQUENCE ANNOTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RECEPTORS, THYROID HORMONE; RECEPTORS, THYROTROPIN; RECEPTORS, THYROTROPIN-RELEASING HORMONE; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; TIME FACTORS; TRANSCRIPTION, GENETIC;

PLEURONECTIFORMES; SOLEA SOLEA;

EID: 84877249570     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-315     Document Type: Article

References (86)

1. 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(1):59-66. 10.1007/s004410100353, 11383887.
2. Cerdà J, Douglas S, Reith M. Genomic resources for flatfish research and their applications. J Fish Biol 2010, 77:1045-1070. 10.1111/j.1095-8649.2010.02695.x, 21039490.
3. Mazurais D, Darias M, Zambonino-Infante JL, Cahu CL. Transcriptomics for understanding marine fish larval development. Can J Zool 2011, 89:599-611.
4. Bonaldo A, Parma L, Badiani A, Serratore P, Gatta PP. Very early weaning of common sole (Solea solea L.) larvae by means of different feeding regimes and three commercial microdiets: influence on performances, metamorphosis development and tank hygiene. Acquaculture 2011, 321:237-244.
5. Agulleiro MJ, Nguis V, Cañavate JP, Martínez-Rodríguez G, Mylonas CC, Cerdà J. Induction of spawning of captive-reared Senegal sole (Solea senegalensis) using different delivery systems for gonadotropin-releasing hormone agonist. Aquaculture 2006, 257(1-4):511-524.
6. Conceição LEC, Ribeiro L, Engrola S, Aragão C, Morais S, Lacuisse M, Soares F, Dinis MT. Nutritional physiology during development of Senegalese sole (Solea senegalensis). Aquaculture 2007, 268(1-4):64-81.
7. 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.
8. 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. 10.1186/1471-2164-8-144, 1924502, 17547761.
9. Murray HM, Lall SP, Rajaselvam R, Boutilier LA, Flight RM, Blanchard B, Colombo S, Mohindra V, Yúfera M, Douglas SE. Effect of early introduction of microencapsulated diet to larval Atlantic halibut, Hippoglossus hippoglossus L. assessed by microarray analysis. Mar Biotechnol 2010, 12(2):214-229. 10.1007/s10126-009-9211-4, 19618242.
10. Cerdà J, Mercadé J, Lozano JJ, Manchado M, Tingaud-Sequeira A, Astola A, Infante C, Halm S, Viñas J, Castellana B, Asensio E, Cañavate P, Martínez-Rodríguez G, Piferrer F, Planas JV, Prat F, Yúfera M, Durany O, Subirada F, Rosell E, Maes T. 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 2008, 9:508. 10.1186/1471-2164-9-508, 2612027, 18973667.
11. Taboada X, Robledo D, Del Palacio L, Rodeiro A, Felip A, Martínez P, Viñas A. Comparative expression analysis in mature gonads, liver and brain of turbot (Scophthalmus maximus) by cDNA-AFLPS. Gene 2012, 492(1):250-261. 10.1016/j.gene.2011.10.020, 22037609.
12. Darias MJ, Boglino A, Manchado M, Ortiz-Delgado JB, Estévez A, Andree KB, Gisbert E. Molecular regulation of both dietary vitamin A and fatty acid absorption and metabolism associated with larval morphogenesis of Senegalese sole (Solea senegalensis). Comp Biochem Physiol A Mol Integr Physiol 2012, 161(2):130-139. 10.1016/j.cbpa.2011.10.001, 22008841.
13. Transcriptome Shotgun Assembly Sequence Database http://www.ncbi.nlm.nih.gov/genbank/tsa.
14. GEO database http://www.ncbi.nlm.nih.gov/geo/.
15. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci 2001, 98(9):5116-5121. 10.1073/pnas.091062498, 33173, 11309499.
16. Kawaguchi M, Yasumasu S, Hiroi J, Naruse K, Inoue M, Iuchi I. Evolution of teleostean hatching enzyme genes and their paralogous genes. Dev Genes Evol 2006, 216(12):769-784. 10.1007/s00427-006-0104-5, 17016731.
17. 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(2):447-455. 10.1016/j.ygcen.2007.07.011, 17888916.
18. Galay-Burgos M, Power DM, Llewellyn L, Sweeney GE. Thyroid hormone receptor expression during metamorphosis of Atlantic halibut (Hippoglossus hippoglossus). Mol Cell Endocrinol 2008, 281:56-63. 10.1016/j.mce.2007.10.009, 18068891.
19. Pelletier I, Bally-Cuif L, Ziegler I. Cloning and developmental expression of zebrafish GTP cyclohydrolase I. Mech Dev 2001, 109(1):99-103. 10.1016/S0925-4773(01)00516-0, 11677059.
20. Brody LC, Conley M, Cox C, Kirke PN, McKeever MP, Mills JL, Molloy AM, O'Leary VB, Parle-McDermott A, Scott JM. A polymorphism, R653Q, in the trifunctional enzyme methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase/formyltetrahydrofolate synthetase is a maternal genetic risk factor for neural tube defects: report of the Birth Defects Research Group. Am J Hum Genet 2002, 71(5):1207-1215. 10.1086/344213, 385099, 12384833.
21. Stuckenholz C, Lu L, Thakur P, Kaminski N, Bahary N. FACS-assisted microarray profiling implicates novel genes and pathways in zebrafish gastrointestinal tract development. Gastroenterology 2009, 137(4):1321-1332. 10.1053/j.gastro.2009.06.050, 2785077, 19563808.
22. Lampert JM, Holzschuh J, Hessel S, Driever W, Vogt K, von Lintig J. Provitamin A conversion to retinal via the beta, beta-carotene-15,15′-oxygenase (bcox) is essential for pattern formation and differentiation during zebrafish embryogenesis. Development 2003, 130(10):2173-2186. 10.1242/dev.00437, 12668631.
23. Darias MJ, Zambonino-Infante JL, Hugot K, Cahu CL, Mazurais D. Gene expression patterns during the larval development of European sea bass (Dicentrarchus labrax) by microarray analysis. Mar Biotechnol (NY). 2008, 10(4):416-428.
24. Sarropoulou E, Kotoulas G, Power DM, Geisler R. Gene expression profiling of gilthead sea bream during early development and detection of stress-related genes by the application of cDNA microarray technology. Physiol Genomics 2005, 23:182-191. 10.1152/physiolgenomics.00139.2005, 16046618.
25. Ferraresso S, Vitulo N, Mininni AN, Romualdi C, Cardazzo B, Negrisolo E, Reinhardt R, Canario AV, Patarnello T, Bargelloni L. Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata). BMC Genomics 2008, 9:580. 10.1186/1471-2164-9-580, 2648989, 19055773.
26. Yúfera M, Halm S, Beltran S, Fusté B, Planas JV, Martínez-Rodríguez G. Transcriptomic characterization of the larval stage in gilthead seabream (Sparus aurata) by 454 pyrosequencing. Mar Biotechnol (NY). 2012, 14(4):423-435.
27. Douglas SE, Knickle LC, Williams J, Flight RM, Reith ME. A first generation Atlantic halibut Hippoglossus hippoglossus (L.) microarray: application to developmental studies. J Fish Biol 2008, 72(9):2391-2406.
28. Pardo BG, Fernández C, Millán A, Bouza C, Vázquez-López A, Vera M, Alvarez-Dios JA, Calaza M, Gómez-Tato A, Vázquez M, Cabaleiro S, Magariños B, Lemos ML, Leiro JM, Martínez P. Expressed sequence tags (ESTs) from immune tissues of turbot (Scophthalmus maximus) challenged with pathogens. BMC Vet Res 2008, 25:4-37.
29. Adzhubei AA, Vlasova AV, Hagen-Larsen H, Ruden TA, Laerdahl JK, Høyheim B. Annotated expressed sequence tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource. BMC Genomics 2007, 8:209. 10.1186/1471-2164-8-209, 1913521, 17605782.
30. Liu Z, Li RW, Waldbieser GC. Utilization of microarray technology for functional genomics in ictalurid catfish. J Fish Biol 2008, 72:2377-2390.
31. Coppe A, Pujolar JM, Maes GE, Larsen PF, Hansen MM, Bernatchez L, Zane L, Bortoluzzi S. Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel. BMC Genomics 2010, 11:635. 10.1186/1471-2164-11-635, 3012609, 21080939.
32. Falk-Petersen IB. Comparative organ differentiation during early life stages of marine fish. Fish Shellfish Immunol 2005, 19(5):397-412. 10.1016/j.fsi.2005.03.006, 15890533.
33. Yarfitz S, Hurley JB. Transduction mechanisms of vertebrate and invertebrate photoreceptors. J Biol Chem 1994, 269(20):14329-14332.
34. Terakita A. The opsins. Genome Biol 2005, 6(3):213. 10.1186/gb-2005-6-3-213, 1088937, 15774036.
35. Bohnsack BL, Kasprick DS, Kish PE, Goldman D, Kahana A. A zebrafish model of axenfeld-rieger syndrome reveals that pitx2 regulation by retinoic acid is essential for ocular and craniofacial development. Invest Ophthalmol Vis Sci 2012, 53(1):7-22. 10.1167/iovs.11-8494, 3292384, 22125274.
36. Prabhudesai SN, Cameron DA, Stenkamp DL. Targeted effects of retinoic acid signaling upon photoreceptor development in zebrafish. Dev Biol 2005, 287(1):157-167. 10.1016/j.ydbio.2005.08.045, 2804901, 16197938.
37. Li A, Zhu X, Craft CM. Retinoic acid upregulates cone arrestin expression in retinoblastoma cells through a Cis element in the distal promoter region. Invest Ophthalmol Vis Sci 2002, 43(5):1375-1383.
38. Cammas L, Trensz F, Jellali A, Ghyselinck NB, Roux MJ, Dollé P. Retinoic acid receptor (RAR)-alpha is not critically required for mediating retinoic acid effects in the developing mouse retina. Invest Ophthalmol Vis Sci 2010, 51(6):3281-3290. 10.1167/iovs.09-3769, 20107170.
39. Matt N, Dupé V, Garnier JM, Dennefeld C, Chambon P, Mark M, Ghyselinck NB. Retinoic acid-dependent eye morphogenesis is orchestrated by neural crest cells. Development 2005, 132(21):4789-4800. 10.1242/dev.02031, 16207763.
40. Nixon SJ, Wegner J, Ferguson C, Méry PF, Hancock JF, Currie PD, Key B, Westerfield M, Parton RG. Zebrafish as a model for caveolin-associated muscle disease; caveolin-3 is required for myofibril organization and muscle cell patterning. Hum Mol Genet 2005, 14(13):1727-1743. 10.1093/hmg/ddi179, 15888488.
41. Bryantsev AL, Baker PW, Lovato TL, Jaramillo MS, Cripps RM. Differential requirements for Myocyte Enhancer Factor-2 during adult myogenesis in Drosophila. Dev Biol 2012, 361(2):191-207. 10.1016/j.ydbio.2011.09.031, 3246536, 22008792.
42. Chan J, O'Donoghue K, Gavina M, Torrente Y, Kennea N, Mehmet H, Stewart H, Watt DJ, Morgan JE, Fisk NM. Galectin-1 induces skeletal muscle differentiation in human fetal mesenchymal stem cells and increases muscle regeneration. Stem Cells 2006, 24(8):1879-1891. 10.1634/stemcells.2005-0564, 16675596.
43. Seeley M, Huang W, Chen Z, Wolff WO, Lin X, Xu X. Depletion of zebrafish titin reduces cardiac contractility by disrupting the assembly of Z-discs and A-bands. Circ Res 2007, 100(2):238-245. 10.1161/01.RES.0000255758.69821.b5, 2756513, 17170364.
44. Johnston IA. Environment and plasticity of myogenesis in teleost fish. J Exp Biol 2006, 209:2249-2264. 10.1242/jeb.02153, 16731802.
45. Campinho MA, Galay-Burgos M, Sweeney GE, Power DM. Coordination of deiodinase and thyroid hormone receptor expression during the larval to juvenile transition in sea bream (Sparus aurata, Linnaeus). Gen Comp Endocrinol 2010, 165(2):181-194. 10.1016/j.ygcen.2009.06.020, 19549532.
46. Power DM, Llewellyn L, Faustino M, Nowell MA, Björnsson BT, Einarsdottir IE, Canario AV, Sweeney GE. Thyroid hormones in growth and development of fish. Comp Biochem Physiol C Toxicol Pharmacol 2001, 130(4):447-459. 10.1016/S1532-0456(01)00271-X, 11738632.
47. Brown DD, Cai L. Amphibian metamorphosis. Dev Biol 2007, 306(1):20-33. 10.1016/j.ydbio.2007.03.021, 1945045, 17449026.
48. 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. 10.1186/1471-2199-9-19, 2270864, 18234081.
49. Köhrle J. Thyrotropin (TSH) action of thyroid hormone deiodination and secretion: One aspect of thyrotropin regulation of thyroid cell biology. Physiological Regulation and Biological Function of Thyrotropin 1990, 18-28. New York: Georg Thieme Verlag: Hormone and Metabolic Research, Supplement Series, 23, Stuttgart BG.
50. Harada M, Yoshinaga T, Ojima D, Iwata M. cDNA cloning and expression analysis of thyroid hormone receptor in the coho salmon Oncorhynchus kisutch during smoltification. Gen Comp Endocrinol 2008, 155(3):658-667. 10.1016/j.ygcen.2007.09.004, 17950735.
51. Kawakami Y, Nozaki J, Seoka M, Kumai H, Ohta H. Characterization of thyroid hormones and thyroid hormone receptors during the early development of Pacific bluefin tuna (Thunnus orientalis). Gen Comp Endocrinol 2008, 155(3):597-606. 10.1016/j.ygcen.2007.09.005, 17988667.
52. Manchado M, Infante C, Rebordinos L, Cañavate JP. Molecular characterization, gene expression and transcriptional regulation of thyroid hormone receptors in Senegalese sole. Gen Comp Endocrinol 2009, 160(2):139-147. 10.1016/j.ygcen.2008.11.001, 19028494.
53. Nakatani Y, Takeda H, Kohara Y, Morishita S. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res 2007, 17(9):1254-1265. 10.1101/gr.6316407, 1950894, 17652425.
54. Kawakami Y, Tanda M, Adachi S, Yamauchi K. Characterization of thyroid hormone receptor alpha and beta in the metamorphosing Japanese conger eel. Conger myriaster. Gen Comp Endocrinol. 2003, 132(2):321-332.
55. Reinecke M, Björnsson BT, Dickhoff WW, McCormick SD, Navarro I, Power DM, Gutiérrez J. Growth hormone and insulin-like growth factors in fish: where we are and where to go. Gen Comp Endocrinol 2005, 142(1-2):20-24.
56. Hidahl J, Sweeney G, Galay-Burgos M, Einarsdóttir IE, Björnsson BT. Cloning of Atlantic halibut growth hormone receptor genes and quantitative gene expression during metamorphosis. Gen Comp Endocrinol 2007, 151(2):143-152. 10.1016/j.ygcen.2006.10.003, 17141236.
57. Hildahl J, Galay-Burgos M, Sweeney G, Einarsdóttir IE, Björnsson BT. Identification of two isoforms of Atlantic halibut insulin-like growth factor-I receptor genes and quantitative gene expression during metamorphosis. Comp Biochem Physiol B Biochem Mol Biol 2007, 147(3):395-401. 10.1016/j.cbpb.2007.02.006, 17395512.
58. Clark RG, Robinson IC. Up and down the growth hormone cascade. Cytokine Growth Factor Rev 1996, 7(1):65-80. 10.1016/1359-6101(96)00006-8, 8864355.
59. Hildahl J, Power DM, Björnsson BT, Einarsdóttir IE. Involvement of growth hormone-insulin-like growth factor I system in cranial remodeling during halibut metamorphosis as indicated by tissue- and stage-specific receptor gene expression and the presence of growth hormone receptor protein. Cell Tissue Res 2008, 332(2):211-225. 10.1007/s00441-007-0568-2, 18335247.
60. Reinecke M. Influences of the environment on the endocrine and paracrine fish growth hormone-insulin-like growth factor-I system. J Fish Biol 2010, 76(6):1233-1254. 10.1111/j.1095-8649.2010.02605.x, 20537012.
61. Zhai W, Zhang J, Shi Z, Fu Y. Identification and expression analysis of IGFBP-1 gene from Japanese flounder (Paralichthys olivaceus). Comp Biochem Physiol B Biochem Mol Biol 2012, 161(4):413-420. 10.1016/j.cbpb.2012.01.007, 22290028.
62. Kamei H, Lu L, Jiao S, Li Y, Gyrup C, Laursen LS, Oxvig C, Zhou J, Duan C. Duplication and diversification of the hypoxia-inducible IGFBP-1 gene in zebrafish. PLoS One 2008, 3(8):e3091. 10.1371/journal.pone.0003091, 2518108, 18769480.
63. Schmid AC, Lutz I, Kloas W, Reinecke M. Thyroid hormone stimulates hepatic IGF-I mRNA expression in a bony fish, the tilapia Oreochromis mossambicus, in vitro and in vivo. Gen Comp Endocrinol 2003, 130:129-134. 10.1016/S0016-6480(02)00577-4, 12568789.
64. Xing W, Govoni KE, Donahue LR, Kesavan C, Wergedal J, Long C, Bassett JH, Gogakos A, Wojcicka A, Williams GR, Mohan S. Genetic evidence that thyroid hormone is indispensable for prepubertal insulin-like growth factor-I expression and bone acquisition in mice. J Bone Miner Res 2012, 27(5):1067-1079. 10.1002/jbmr.1551, 22513648.
65. Saele O, Smáradóttir H, Pittman K. Twisted story of eye migration in flatfish. J Morphol 2006, 267(6):730-738. 10.1002/jmor.10437, 16526052.
66. Bao B, Ke Z, Xing J, Peatman E, Liu Z, Xie C, Xu B, Gai J, Gong X, Yang G, Jiang Y, Tang W, Ren D. Proliferating cells in suborbital tissue drive eye migration in flatfish. Dev Biol 2011, 351(1):200-207. 10.1016/j.ydbio.2010.12.032, 21195706.
67. Suzuki T, Washio Y, Aritaki M, Fujinami Y, Shimizu D, Uji S, Hashimoto H. Metamorphic pitx2 expression in the left habenula correlated with lateralization of eye-sidedness in flounder. Dev Growth Differ 2009, 51(9):797-808. 10.1111/j.1440-169X.2009.01139.x, 19843151.
68. Friedl P, Wolf K. Plasticity of cell migration: a multiscale tuning model. J Cell Biol 2010, 188(1):11-19. 10.1083/jcb.200909003, 2812848, 19951899.
69. Friedl P, Wolf K. Tumour-cell invasion and migration: diversity and escape mechanisms. Nat Rev Cancer 2003, 3:362-374. 10.1038/nrc1075, 12724734.
70. Escudero-Esparza A, Jiang WG, Martin TA. Claudin-5 is involved in breast cancer cell motility through the N-WASP and ROCK signalling pathways. J Exp Clin Cancer Res 2012, 31:43. 10.1186/1756-9966-31-43, 3432004, 22559840.
71. Acloque H, Lavial F, Pain B. Astacin-like metallo-endopeptidase is dynamically expressed in embryonic stem cells and embryonic epithelium during morphogenesis. Dev Dyn 2012, 241(3):574-582. 10.1002/dvdy.23737, 22275110.
72. 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.
73. 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(3):e37. 10.1093/nar/gnh031, 373426, 14973331.
74. Shagin DA, Rebrikov DV, Kozhemyako VB, Altshuler IM, Shcheglov AS, Zhulidov PA, Bogdanova EA, Staroverov DB, Rasskazov VA, Lukyanov S. A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res 2002, 12(12):1935-1942. 10.1101/gr.547002, 187582, 12466298.
75. Sequence Read Archive (SRA) http://www.ncbi.nlm.nih.gov/sra.
76. NCBI http://www.ncbi.nlm.nih.gov/.
77. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674-3676. 10.1093/bioinformatics/bti610, 16081474.
78. Ensemble Genome Browser http://www.ensembl.org/index.html.
79. Unigene http://www.ncbi.nlm.nih.gov/unigene.
80. Ferraresso S, Milan M, Pellizzari C, Vitulo N, Reinhardt R, Canario AV, Patarnello T, Bargelloni L. Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity. BMC Genomics 2010, 11:354. 10.1186/1471-2164-11-354, 2889902, 20525278.
81. R statistical software http://www.r-project.org.
82. Newman AM, Cooper JB. AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. BMC Bioinforma 2010, 11:117.
83. Cytoscape http://www.cytoscape.org.
84. DAVID Bioinformatic Database http://david.abcc.ncifcrf.gov/.
85. Ensembl BIOMART http://www.ensembl.org/biomart/martview/.
86. Thiel T, Michalek W, Varshney RK, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 2003, 106(3):411-422.