Advances in genomics for flatfish aquaculture

Aanes H, Winata CL, Lin CH, Chen JP, Srinivasan KG, Lee SG, Lim AY, Hajan HS, Collas P, Bourque G, Gong Z, Korzh V, Alestrom P, Mathavan S (2011) Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. Genome Res 21(8):1328–1338 Agulleiro MJ, Anguis V, Cañavate JP, Martínez-Rodríguez G, Mylonas CC, Cerdà J (2006) Induction of spawning of captive-reared Senegal sole (Solea senegalensis) using different delivery systems for gonadotropin-releasing hormone agonist. Aquaculture 257(1–4):511–524 Ardura A, Horreo JL, Hernandez E, Jardon A, Pola IG, Martinez JL, Garcia-Vazquez E (2012) Forensic DNA analysis reveals use of high trophic level marine fish in commercial aquaculture fish meals. Fish Res 115–116:115–120 Asociación Empresarial de Productores de Cultivos Marinos de España (APROMAR) (2011) La Acuicultura Marina de Peces en España. Ministerio de Medio Ambiente y Medio Rural y Marino, 76 pp (in Spanish) Begemann G (2008) MicroRNAs and RNA interference in zebrafish development. Zebrafish 5(2):111–119 Bengtson D, Nardi G (2010) Culture of summer flounder. In: Daniels HV, Watanabe WO (eds) Practical flatfish culture and stock enhancement. Wiley, New York, pp 65–81 Blencowe BJ, Ahmad S, Lee LJ (2009) Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev 23(12):1379–1386 Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA (2009) Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics 10:221 Bouza C, Sanchez L, Martinez P (1994) Karyotypic characterization of turbot (Scophthalmus maximus) with conventional, fluorochrome, and restriction endonuclease banding techniques. Mar Biol 120(4):609–613 Bouza C, Hermida M, Pardo BG, Fernandez C, Fortes GG, Castro J, Sanchez L, Presa P, Pérez M, Sanjuan A, de Carlos A, Alvarez-Dios JA, Ezcurra S, Cal RM, Piferrer F, Martínez P (2007) A microsatellite genetic map of the turbot (Scophthalmus maximus). Genetics 177(4):2457–2467 Bradford JR, Hey Y, Yates T, Li Y, Pepper SD, Miller CJ (2010) A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics 11:282 Bromage N, Mazorra C, Bruce M, Brown N, Shields R (2000) Halibut culture. In: Stickney RR (ed) Encyclopedia of aquaculture. Wiley, New York, pp 425–432 Brown NP, Bromage NR, Penman DJ, Shields RJ (1997) The karyotype of the Atlantic halibut, Hippoglossus hippoglossus (Linnaeus). Aquac Res 28(7):489–491 Brunskill EW, Lai HL, Jamison DC, Potter SS, Patterson LT (2011) Microarrays and RNA-Seq identify molecular mechanisms driving the end of nephron production. BMC Dev Biol 11:15 Canario AVM, Bargelloni L, Volckaert F, Houston RD, Massault C, Guiguen Y (2008) Genomics toolbox for farmed fish. Rev Fish Sci 16(Supp 1):3–15 Cañavate JP, Zerolo R, Fernández-Diaz C (2006) Feeding and development of Senegal sole (Solea senegalensis) larvae reared in different photoperiods. Aquaculture 258(1–4):368–377 Canovas A, Rincon G, Islas-Trejo A, Wickramasinghe S, Medrano JF (2010) SNP discovery in the bovine milk transcriptome using RNA-Seq technology. Mamm Genome 21(11–12):592–598 Castaño-Sanchez C, Fuji K, Ozaki A, Hasegawa O, Sakamoto T, Morishima K, Nakayama I, Fujiwara A, Masaoka T, Okamoto H, Hayashida K, Tagami M, Kawai J, Hayashizaki Y, Okamoto N (2010) A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus). BMC Genomics 11:554 Cerdà J, Bobe J, Babin PJ, Admon A, Lubzens E (2008) Functional genomics and proteomic approaches for the study of gamete formation and viability in farmed finfish. Rev Fish Sci 16(Supp 1):54–70 Cerdà J, Douglas S, Reith M (2010) Genomic resources for flatfish research and their applications. J Fish Biol 77(5):1045–1070 Chen SL, Li J, Deng SP, Tian YS, Wang QY, Zhuang ZM, Sha ZX, Xu JY (2007) Isolation of female-specific AFLP markers and molecular identification of genetic sex in half-smooth tongue sole (Cynoglossus semilaevis). Marine Biotechnol 9(2):273–280 Choi SM, Wang X, Park GJ, Lim SR, Kim KW, Bai SC, Shin IS (2004) Dietary dehulled soybean meal as a replacement for fish meal in fingerling and growing olive flounder Paralichthys olivaceus (Temminck et Schlegel). Aquac Res 35(4):410–418 Christodoulou DC, Gorham JM, Herman DS, Seidman JG (2011) Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease. Curr Protoc Mol Biol Chapter 4 Unit 4 12 Cifuentes A (2009) Food analysis and foodomics. J Chromatogr A 1216(43):7109 Conceição LCE, Ribeiro L, Engrola S, Aragão C, Morais S, Lacuisse M, Soares F, Dinis MT (2007) Nutritional physiology during development of Senegalese sole (Solea senegalensis). Aquaculture 268(1–4):64–81 Coppe A, Pujolar JM, Maes GE, Larsen PF, Hansen MM, Bernatchez L, Zane L, Bortoluzzi S (2010) 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 11:635 Crawford JE, Guelbeogo WM, Sanou A, Traore A, Vernick KD, Sagnon N, Lazzaro BP (2010) De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology. PLoS ONE 5(12):e14202 Cross I, Merlo A, Manchado M, Infante C, Canavate JP, Rebordinos L (2006) Cytogenetic characterization of the sole Solea senegalensis (Teleostei: Pleuronectiformes: Soleidae): Ag-NOR, (GATA)n, (TTAGGG)n and ribosomal genes by one-color and two-color FISH. Genetica 128(1–3):253–259 Cuñado N, Terrones J, Sanchez L, Martinez P, Santos JL (2001) Synaptonemal complex analysis in spermatocytes and oocytes of turbot, Scophthalmus maximus (Pisces, Scophthalmidae). Genome 44(6):1143–1147 Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Le Blomberg A, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S et al (2010) Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol 8(9):e1000475 Day OJ, Plascencia-González HG (2000) Soybean protein concentrate as a protein source for turbot Scophthalmus maximus L. Aquac Nutr 6(4):221–228 de Groot SJ (1971) On the interrelationships between morphology of the alimentary tract, food and feeding behaviour in flatfishes (Pisces: Pleuronectiformes). Nether J Sea Res 5(2):121–196 Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK (2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 25(24):3207–3212 Dixon JM, Lubomirski M, Amaratunga D, Morrison TB, Brenan CJ, Ilyin SE (2009) Nanoliter high-throughput RT-qPCR: a statistical analysis and assessment. Biotechniques 46(6):2–8 Duarte CM, Holmer M, Olsen Y, Soto D, Marba N, Guiu J, Black K, Karakassis I (2009) Will the oceans help feed humanity? Bioscience 59(11):967–976 Elling AA, Deng XW (2009) Next-generation sequencing reveals complex relationships between the epigenome and transcriptome in maize. Plant Signal Behav 4(8):760–762 FEAP (2010) Production and Price reports of member associations of the FEAP. Federation of European Aquaculture Producers. http://www.aquamedia.org/home/default2_en.asp Forné I, Abián J, Cerdà J (2010) Fish proteome analysis: model organisms and non-sequenced species. Proteomics 10(4):858–872 Frith MC, Pheasant M, Mattick JS (2005) The amazing complexity of the human transcriptome. Eur J Hum Genet 13(8):894–897 Fu Y, Shi Z, Wu M, Zhang J, Jia L, Chen X (2011) Identification and differential expression of microRNAs during metamorphosis of the Japanese flounder (Paralichthys olivaceus). PLoS ONE 6(7):e22957 Fuji K, Kobayashi K, Hasegawa O, Coimbra M, Sakamoto T, Okamoto N (2006) Identification of a single major genetic locus controlling the resistance to lymphocystis disease in Japanese flounder (Paralichthys olivaceus). Aquaculture 254(1–4):203–210 Fuji K, Hasegawa O, Honda K, Kumasaka K, Sakamoto T, Okamoto N (2007) Marker-assisted breeding of a lymphocystis disease-resistant Japanese flounder (Paralichthys olivaceus). Aquaculture 272(1–4):291–295 Gatlin DM III, Barrows FT, Brown P, Dabrowski K, Gaylord TG, Hardy RW, Herman E, Hu G, Krogdahl Å, Nelson R, Overturf K, Rust M, Sealey W, Skonberg D, Souza EJ, Stone D, Wilson R, Wurtele E (2007) Expanding the utilization of sustainable plant products in aquafeeds: a review. Aquac Res 38:551–579 Glenn TC (2011) Field guide to next-generation DNA sequencers. Mol Ecol Res 11(5):759–769 Grisdale-Helland B, Helland SJ, Baeverfjord G, Berge GM (2002) Full-fat soybean meal in diets for Atlantic halibut: growth, metabolism and histology. Aquac Nutr 8(4):265–270 Hardie DC, Hebert PDN (2004) Genome-size evolution in fishes. Can J Fish Aquat Sci 61:1636–1646 Hibbeln JR, Nieminen LRG, Blasbalg TL, Riggs JA, Lands WEM (2006) Healthy intakes of n-3 and n-6 fatty acids: estimations considering worldwide diversity. Am J Clin Nutr 83(6):1483S–1493S Hoarau G, Boon E, Jongma DN, Ferber S, Palsson J, Van der Veer HW, Rijnsdorp AD, Stam WT, Olsen JL (2005) Low effective population size and evidence for inbreeding in an overexploited flatfish, plaice (Pleuronectes platessa L.). Proc R Soc B 272:497–503 Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J et al (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41(12):1275–1281 Huss HH (1995) Quality and quality changes in fresh fish. FAO Fisheries Technical Paper 348, pp 195 Hwang SD, Fuji K, Takano T, Sakamoto T, Kondo H, Hirono I, Aoki T (2011) Linkage Mapping of Toll-Like Receptors (TLRs) in Japanese Flounder, Paralichthys olivaceus. Mar Biotechnol 13(6):1086–1091 ICES (2008) Report of the study group on mixed fisheries management (SGMixMan). ICES CM 2008/ACOM:23 Imsland AK, Foss A, Conceição LEC, Dinis MT, Delbare D, Schram E, Kamstra A, Rema P, White P (2003) A review of the culture potential of Solea solea and S. senegalensis. Rev Fish Biol Fish 13(4):379–407 Kolakowska A, Olley J, Dunstan GA (2003) Fish lipids. In: Sikorski ZE, Kolakowska A (eds) Chemical and functional properties of food lipids. CRC press, New York, pp 228–271 Lall SP, Lewis-McCrea LM (2007) Role of nutrients in skeletal metabolism and pathology in fish—an overview. Aquaculture 267(1–4):3–19 Langdon C (2003) Microparticle types for delivering nutrients to marine fish larvae. Aquaculture 227(1–4):259–275 Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 7(9):709–715 Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W et al (2010) The sequence and de novo assembly of the giant panda genome. Nature 463(7279):311–317 Liao X, Ma HY, Xu GB, Shao CW, Tian YS, Ji XS, Yang JF, Chen SL (2009) Construction of a genetic linkage map and mapping of a female-specific DNA marker in half-smooth tongue sole (Cynoglossus semilaevis). Mar Biotechnol 11(6):699–709 Malone JH, Oliver B (2011) Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol 9:34 Manchado M, Infante C, Asensio E, Planas JV, Cañavate JP (2008) Thyroid hormones down-regulate thyrotropin beta subunit and thyroglobulin during metamorphosis in the flatfish Senegalese sole (Solea senegalensis Kaup). Gen Comp Endocrinol 155(2):447–455 Manchado M, Infante C, Ponce M, Planas JV, Cañavate JP (2011) Massive transcriptome sequencing in sole. In: Howell B (ed) Sole Workshop V. CCMAR, University of the Algarve, Faro, Portugal Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18(9):1509–1517 Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12(10):671–682 Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z (2010) Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics 11:663 Martinez P, Bouza C, Hermida M, Fernandez J, Toro MA, Vera M, Pardo B, Millan A, Fernandez C, Vilas R, Viñas A, Sanchez L, Felip A, Piferre F, Ferreiro I, Cabaleiro S (2009) Identification of the major sex-determining region of turbot (Scophthalmus maximus). Genetics 183(4):1443–1452 Mechaly AS, Viñas J, Murphy C, Reith M, Piferrer F (2010) Gene structure of the Kiss1 receptor-2 (Kiss1r-2) in the Atlantic halibut: insights into the evolution and regulation of Kiss1r genes. Mol Cell Endocrinol 317(1–2):78–89 Meijer AH, Verbeek FJ, Salas-Vidal E, Corredor-Adamez M, Bussman J, van der Sar AM, Otto GW, Geisler R, Spaink HP (2005) Transcriptome profiling of adult zebrafish at the late stage of chronic tuberculosis due to Mycobacterium marinum infection. Mol Immunol 42(10):1185–1203 Metzker ML (2010) Sequencing technologies - the next generation. Nat Rev Genet 11(1):31–46 Millán A, Gomez-Tato A, Fernandez C, Pardo BG, Alvarez-Dios JA, Calaza M, Bouza C, Vázquez M, Cabaleiro S, Martinez P (2010) Design and performance of a turbot (Scophthalmus maximus) oligo-microarray based on ESTs from immune tissues. Mar Biotechnol 12(4):452–465 Millán A, Gómez-Tato A, Pardo BG, Fernández C, Bouza C, Vera M, Alvarez-Dios JA, Cabaleiro S, Lamas J, Lemos ML, Martínez P (2011) Gene expression profiles of the spleen, liver, and head kidney in turbot (Scophthalmus maximus) along the infection process with Aeromonas salmonicida using an immune-enriched oligo-microarray. Mar Biotechnol 13(6):1099–1114 Millner R, Walsh SJ, Díaz de Astarloa JM (2005) Atlantic flatfish fisheries. In: Gibson RN (ed) Flatfishes: biology and exploitation. Blackwell Publishing, Oxford, pp 240–271 Miwa S, Tagawa M, Inui Y, Hirano T (1988) Thyroxine surge in metamorphosing flounder larvae. Gen Comp Endocrinol 70:158–163 Mollet FM, Kraak SBM, Rijnsdorp AD (2007) Fisheries-induced evolutionary changes in maturation reaction norms in North Sea sole Solea solea. Mar Ecol Prog Ser 351:189–199 Morrison T, Hurley J, Garcia J, Yoder K, Katz A, Roberts D, Cho J, Kanigan T, Ilyin SE, Horowitz D, Dixon JM, Brenan CJ (2006) Nanoliter high throughput quantitative PCR. Nucleic Acids Res 34(18):e123 Mu Y, Ding F, Cui P, Ao J, Hu S, Chen X (2010) Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection. BMC Genomics 11:506 Munroe TA (2005) Systematic diversity of the Pleuronectiformes. In: Gibson RN (ed) Flatfishes: biology and exploitation. Blackwell Publishing, Oxford, pp 10–41 Murray HM, Lall SP, Rajaselvam R, Boutilier LA, Blanchard B, Flight RM, Colombo S, Mohindra V, Douglas SE (2009) A nutrigenomic analysis of intestinal response to partial soybean meal replacement in diets for juvenile Atlantic halibut, Hippoglossus hippoglossus L. Aquaculture 298(3–4):282–293 Murray HM, Lall SP, Rajaselvam R, Boutilier LA, Flight RM, Blanchard B, Colombo S, Mohindra V, Yúfera M, Douglas SE (2010) Effect of early introduction of microencapsulated diet to larval Atlantic halibut, Hippoglossus hippoglossus L. assessed by microarray analysis. Mar. Biotechnol 12(2):214–229 Naylor R, Burke M (2005) Aquaculture and ocean resources: raising tigers of the sea. Annu Rev Environ Resour 30:185–218 Naylor RL, Hardy RW, Bureau DP, Chiu A, Elliott M, Farrell AP, Forster I, Gatlin DM, Goldburg RJ, Hua K, Nichols PD (2009) Feeding aquaculture in an era of finite resources. Proc Natl Acad Sci USA 106:15103–15110 Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461(7261):272–276 Ota T, Chihara Y, Itabashi Y, Takagi T (1994) Occurrence of all-cis-6, 9, 12, 15, 18, 21-Tetracosahexaenoic acid in flatfish lipids. Fish Sci 60:171–175 Pareek CS, Smoczynski R, Tretyn A (2011) Sequencing technologies and genome sequencing. J Appl Genet 52(4):413–435 Ponce M, Salas-Leiton E, Garcia-Cegarra A, Boglino A, Coste O, Infante C, Gisbert E, Rebordinos L, Manchado M (2011) Genomic characterization, phylogeny and gene regulation of g-type lysozyme in sole (Solea senegalensis). Fish Shellfish Immunol 31(6):925–937 Power DM, Einarsdóttir IE, Pittman K, Sweeney GE, Hildahl J, Campinho MA, Silva N, Sæle Ø, Galay-Burgos M, Smáradóttir H, Björnsson BT (2008) The molecular and endocrine basis of flatfish metamorphosis. Rev Fish Sci 16(Supp 1):95–111 Reid DP, Smith CA, Rommens M, Blanchard B, Martin-Robichaud D, Reith M (2007) A genetic linkage map of Atlantic halibut (Hippoglossus hippoglossus L.). Genetics 177:1193–1205 Rodríguez-Ramilo ST, Toro MA, Bouza C, Hermida M, Pardo BG, Cabaleiro S, Martínez P, Fernández J (2011) QTL detection for Aeromonas salmonicida resistance related traits in turbot (Scophthalmus maximus). BMC Genomics 12:541 Ruan X, Wang W, Kong J, Yu F, Huang X (2010) Genetic linkage mapping of turbot (Scophthalmus maximus L.) using microsatellite markers and its application in QTL analysis. Aquaculture 308(3–4):89–100 Sánchez-Molano E, Cerna A, Toro MA, Bouza C, Hermida M, Pardo BG, Cabaleiro S, Fernández J, Martinez P (2011) Detection of growth-related QTL in turbot (Scophthalmus maximus). BMC Genomics 12:473 Sarropoulou E, Nousdili D, Magoulas A, Kotoulas G (2008) Linking the genomes of nonmodel teleosts through comparative genomics. Mar Biotechnol 10(3):227–233 Schadt EE, Turner S, Kasarskis A (2010) A window into third-generation sequencing. Human Mol Genet 19(R2):R227–R240 Schulte D, Ariyadasa R, Shi B, Fleury D, Saski C, Atkins M, deJong P, Wu CC, Graner A, Langridge P, Stein N (2011) BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.). BMC Genomics 12:247 Sha Z, Wang S, Zhuang Z, Wang Q, Wang Q, Li P, Ding H, Wang N, Liu Z, Chen S (2010) Generation and analysis of 10,000 ESTs from the half-smooth tongue sole Cynoglossus semilaevis and identification of microsatellite and SNP markers. J Fish Biol 76(5):1190–1204 Solbakken JS, Norberg B, Watanabe K, Pittman K (1999) Thyroxine as a mediator of metamorphosis of Atlantic halibut (Hippoglossus hippoglossus L.). Environ Biol Fish 56:53–65 Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Fave MJ et al (2011) The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet 7(2):e1002007 Surget-Groba Y, Montoya-Burgos JI (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res 20(10):1432–1440 Suzuki M, Hayashizaki Y (2004) Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs. BioEssays 26(8):833–843 Tacon AGJ, Metian M (2008) Global overview on the use of fish meal and fish oil in industrially compounded aquafeeds: trends and future prospects. Aquaculture 285(1–4):146–158 Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A (2011) Differential expression in RNA-seq: a matter of depth. Genome Res 21(12):2213–2223 Valente LMP, Linares F, Villanueva JLR, Silva JMG, Espe M, Escorcio C, Pires MA, Saavedra MJ, Borges P, Medale F, Alvárez-Blázquez B, Peleteiro JB (2011) Dietary protein source or energy levels have no major impact on growth performance, nutrient utilization or flesh fatty acids composition of market-sized Senegalese sole. Aquaculture 318(1–2):128–137 van Walraven L, Mollet FM, van Damme CJG, Rijnsdorp AD (2010) Fisheries-induced evolution in growth, maturation and reproductive investment of the sexually dimorphic North Sea plaice (Pleuronectes platessa L.). J Sea Res 64(1–2):85–93 Vesterlund L, Jiao H, Unneberg P, Hovatta O, Kere J (2011) The zebrafish transcriptome during early development. BMC Dev Biol 11(1):30 Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55(4):641–658 Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63 Welch A, Hoenig R, Stieglitz J, Benetti D, Tacon A, Sims N, O’Hanlon B (2010) From fishing to the sustainable farming of carnivorous marine finfish. Rev Fish Sci 18:235–247 Weltzien FA, Andersson E, Andersen Ø, Shalchian-Tabrizi K, Norberg B (2004) The brain-pituitary-gonad axis in male teleosts, with special emphasis on flatfish (Pleuronectiformes). Comp Biochem Physiol A Mol Integr Physiol 137(3):447–477 Wong CE, Zhao YT, Wang XJ, Croft L, Wang ZH, Haerizadeh F, Mattick JS, Singh MB, Carroll BJ, Bhalla PL (2011) MicroRNAs in the shoot apical meristem of soybean. J Exp Bot 62(8):2495–2506 Woycicki R, Witkowicz J, Gawronski P, Dabrowska J, Lomsadze A, Pawelkowicz M, Siedlecka E, Yagi K, Plader W, Seroczynska A, Smiech M, Gutman W, Niemirowicz-Szczytt K et al (2011) The genome sequence of the North-European cucumber (Cucumissativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS ONE 6(7):e22728 Xu TJ, Chen SL, Ji XS, Tian YS (2008) MHC polymorphism and disease resistance to Vibrio anguillarum in 12 selective Japanese flounder (Paralichthys olivaceus) families. Fish Shellfish Immunol 25(3):213–221 Yang SS, Tu ZJ, Cheung F, Xu WW, Lamb JF, Jung HJ, Vance CP, Gronwald JW (2011) Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 12:199 Yúfera M, Fernández-Diaz C, Pascual E (2005) Food microparticles for larval fish prepared by internal gelation. Aquaculture 248(1–4):253–262 Zhang J, Chiodini R, Badr A, Zhang G (2011a) The impact of next-generation sequencing on genomics. J Genet Genomics 38(3):95–109 Zhang Y, Stupka E, Henkel CV, Jansen HJ, Spaink HP, Verbeek FJ (2011b) Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq Data. J Integr Bioinform 8(2):169 Zhuang ZM, Wu D, Zhang SC, Pang QX, Wang CL, Wan RJ (2006) G-banding patterns of the chromosomes of tonguefish Cynoglossus semilaevis Günther, 1873. J App Ichthyol 22(5):437–440