Directed sequencing and annotation of three Dicentrarchus labrax L. chromosomes by applying Sanger- and pyrosequencing technologies on pooled DNA of comparatively mapped BAC clones

Genomics

Volumn 98, Issue 3, 2011, Pages 202-212

  Kuhl, Heiner ^a   Tine, Mbaye ^a   Beck, Alfred ^a   Timmermann, Bernd ^a   Kodira, Chinnappa ^b   Reinhardt, Richard ^c  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b 454 Life Sciences/Roche ^*  (United States)

^c MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH   (Germany)

Author keywords

Comparative mapping; Genome annotation; Genome evolution; Next generation sequencing; Teleost

Indexed keywords

DNA;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME; CONTROLLED STUDY; EUROPEAN SEA BASS; EXON; GENE FUNCTION; GENETIC LINKAGE; INTRON; MOLECULAR CLONING; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PYROSEQUENCING; TELEOST; UNINDEXED SEQUENCE;

ANIMALS; BASS; CHROMOSOME MAPPING; CHROMOSOMES; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLONING, MOLECULAR; EXONS; GENETIC LINKAGE; GENOME; INTRONS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

DICENTRARCHUS LABRAX; SERRANIDAE; TELEOSTEI;

EID: 80052165529     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2011.06.004     Document Type: Article

References (45)

1. Aparicio S., Chapman J., Stupka E., Putnam N., Chia J.M., Dehal P., Christoffels A., Rash S., Hoon S., Smit A., Gelpke M.D., Roach J., Oh T., Ho I.Y., Wong M., Detter C., Verhoef F., Predki P., Tay A., Lucas S., Richardson P., Smith S.F., Clark M.S., Edwards Y.J., Doggett N., Zharkikh A., Tavtigian S.V., Pruss D., Barnstead M., Evans C., Baden H., Powell J., Glusman G., Rowen L., Hood L., Tan Y.H., Elgar G., Hawkins T., Venkatesh B., Rokhsar D., Brenner S. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 2002, 297:1301-1310.
2. Jaillon O., Aury J.M., Brunet F., Petit J.L., Stange-Thomann N., Mauceli E., Bouneau L., Fischer C., Ozouf-Costaz C., Bernot A., Nicaud S., Jaffe D., Fisher S., Lutfalla G., Dossat C., Segurens B., Dasilva C., Salanoubat M., Levy M., Boudet N., Castellano S., Anthouard V., Jubin C., Castelli V., Katinka M., Vacherie B., Biemont C., Skalli Z., Cattolico L., Poulain J., De Berardinis V., Cruaud C., Duprat S., Brottier P., Coutanceau J.P., Gouzy J., Parra G., Lardier G., Chapple C., McKernan K.J., McEwan P., Bosak S., Kellis M., Volff J.N., Guigo R., Zody M.C., Mesirov J., Lindblad-Toh K., Birren B., Nusbaum C., Kahn D., Robinson-Rechavi M., Laudet V., Schachter V., Quetier F., Saurin W., Scarpelli C., Wincker P., Lander E.S., Weissenbach J., Roest Crollius H. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 2004, 431:946-957.
3. Jekosch K. The zebrafish genome project: sequence analysis and annotation. Methods Cell Biol. 2004, 77:225-239.
4. Kasahara M., Naruse K., Sasaki S., Nakatani Y., Qu W., Ahsan B., Yamada T., Nagayasu Y., Doi K., Kasai Y., Jindo T., Kobayashi D., Shimada A., Toyoda A., Kuroki Y., Fujiyama A., Sasaki T., Shimizu A., Asakawa S., Shimizu N., Hashimoto S., Yang J., Lee Y., Matsushima K., Sugano S., Sakaizumi M., Narita T., Ohishi K., Haga S., Ohta F., Nomoto H., Nogata K., Morishita T., Endo T., Shin I.T., Takeda H., Morishita S., Kohara Y. The medaka draft genome and insights into vertebrate genome evolution. Nature 2007, 447:714-719.
5. Johansen S.D., Coucheron D.H., Andreassen M., Karlsen B.O., Furmanek T., Jorgensen T.E., Emblem A., Breines R., Nordeide J.T., Moum T., Nederbragt A.J., Stenseth N.C., Jakobsen K.S. Large-scale sequence analyses of Atlantic cod. N. Biotechnol. 2009, 25:263-271.
6. Kuhl H., Beck A., Wozniak G., Canario A.V., Volckaert F.A., Reinhardt R. The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. BMC Genomics 2010, 11:68.
7. Quinn N.L., Levenkova N., Chow W., Bouffard P., Boroevich K.A., Knight J.R., Jarvie T.P., Lubieniecki K.P., Desany B.A., Koop B.F., Harkins T.T., Davidson W.S. Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics 2008, 9:404.
8. Shirak A., Grabherr M., Di Palma F., Lindblad-Toh K., Hulata G., Ron M., Kocher T.D., Seroussi E. Identification of repetitive elements in the genome of Oreochromis niloticus: Tilapia repeat masker. Mar. Biotechnol. 2010, 12:121-125.
9. Wang S., Peatman E., Abernathy J., Waldbieser G., Lindquist E., Richardson P., Lucas S., Wang M., Li P., Thimmapuram J., Liu L., Vullaganti D., Kucuktas H., Murdock C., Small B.C., Wilson M., Liu H., Jiang Y., Lee Y., Chen F., Lu J., Wang W., Somridhivej B., Baoprasertkul P., Quilang J., Sha Z., Bao B., Wang Y., Wang Q., Takano T., Nandi S., Liu S., Wong L., Kaltenboeck L., Xu P., Quiniou S., Bengten E., Miller N., Trant J., Rokhsar D., Liu Z., Catfish Genome T. Consortium, Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol. 2010, 11:R8.
10. Young A.L., Abaan H.O., Zerbino D., Mullikin J.C., Birney E., Margulies E.H. A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Res. 2010, 20:249-256.
11. Huang S., Li R., Zhang Z., Li L., Gu X., Fan W., Lucas W.J., Wang X., Xie B., Ni P., Ren Y., Zhu H., Li J., Lin K., Jin W., Fei Z., Li G., Staub J., Kilian A., van der Vossen E.A., Wu Y., Guo J., He J., Jia Z., Tian G., Lu Y., Ruan J., Qian W., Wang M., Huang Q., Li B., Xuan Z., Cao J., Asan, Wu Z., Zhang J., Cai Q., Bai Y., Zhao B., Han Y., Li Y., Li X., Wang S., Shi Q., Liu S., Cho W.K., Kim J.Y., Xu Y., Heller-Uszynska K., Miao H., Cheng Z., Zhang S., Wu J., Yang Y., Kang H., Li M., Liang H., Ren X., Shi Z., Wen M., Jian M., Yang H., Zhang G., Yang Z., Chen R., Ma L., Liu H., Zhou Y., Zhao J., Fang X., Fang L., Liu D., Zheng H., Zhang Y., Qin N., Li Z., Yang G., Yang S., Bolund L., Kristiansen K., Li S., Zhang X., Wang J., Sun R., Zhang B., Jiang S., Du Y. The genome of the cucumber, Cucumis sativus L. Nat. Genet. 2009, 41:1275-1281.
12. Steuernagel B., Taudien S., Gundlach H., Seidel M., Ariyadasa R., Schulte D., Petzold A., Felder M., Graner A., Scholz U., Mayer K.F., Platzer M., Stein N. De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics 2009, 10:547.
13. Palmer L.E., Dejori M., Bolanos R., Fasulo D. Improving sequence assembly using machine learning and comparative genomics for overlap correction. BMC Bioinforma. 2010, 11:33.
14. Korf I., Flicek P., Duan D., Brent M.R. Integrating genomic homology into gene structure prediction. Bioinformatics 2001, 17(Suppl. 1):S140-S148.
15. Parra G., Agarwal P., Abril J.F., Wiehe T., Fickett J.W., Guigo R. Comparative gene prediction in human and mouse. Genome Res. 2003, 13:108-117.
16. Pedersen J.S., Hein J. Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics 2003, 19:219-227.
17. Brown R.H., Gross S.S., Brent M.R. Begin at the beginning: predicting genes with 5′ UTRs. Genome Res. 2005, 15:742-747.
18. Carter D., Durbin R. Vertebrate gene finding from multiple-species alignments using a two-level strategy. Genome Biol. 2006, 7(Suppl. 1):1-12. S6.
19. Gross S.S., Do C.B., Sirota M., Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol. 2007, 8:R269.
20. Burge C., Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 1997, 268:78-94.
21. Gotoh O. Direct mapping and alignment of protein sequences onto genomic sequence. Bioinformatics 2008, 24:2438-2444.
22. Dolbeth M., Martinho F., Viegas I., Cabral H., Pardal M.A. Estuarine production of resident and nursery fish species: conditioning by drought events?. Estuarine Coastal Shelf Sci. 2008, 78:51-60.
23. Kelley D.F. The importance of estuaries for sea-bass, Dicentrarchus labrax (L.). J. Fish Biol. 1998, 33:25-33.
24. Martinho F., Leitao R., Neto J.M., Cabral H.N., Marques J.C., Pardal M.A. The use of nursery areas by juvenile fish in a temperate estuary, Portugal. Hydrobiologia 2007, 587:281-290.
25. Chistiakov D.A., Tsigenopoulos C.S., Lagnel J., Guo Y.M., Hellemans B., Haley C.S., Volckaert F.A., Kotoulas G. A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L. Anim. Genet. 2008, 39:623-634.
26. Whitaker H.A., McAndrew B.J., Taggart J.B. Construction and characterization of a BAC library for the European sea bass Dicentrarchus labrax. Anim. Genet. 2006, 37:526.
27. Martins R.S., Deloffre L.A., Mylonas C.C., Power D.M., Canario A.V. Developmental expression of DAX1 in the European sea bass, Dicentrarchus labrax: lack of evidence for sexual dimorphism during sex differentiation. Reprod. Biol. Endocrinol. 2007, 5:19.
28. Massault C., Hellemans B., Louro B., Batargias C., Van Houdt J.K., Canario A., Volckaert F.A., Bovenhuis H., Haley C., de Koning D.J. QTL for body weight, morphometric traits and stress response in European sea bass Dicentrarchus labrax. Anim. Genet. 2010, 41:337-345.
29. Navarro-Martin L., Blazquez M., Piferrer F. Masculinization of the European sea bass (Dicentrarchus labrax) by treatment with an androgen or aromatase inhibitor involves different gene expression and has distinct lasting effects on maturation. Gen. Comp. Endocrinol. 2009, 160:3-11.
30. Navarro-Martin L., Galay-Burgos M., Sweeney G., Piferrer F. Different sox17 transcripts during sex differentiation in sea bass. Dicentrarchus Labrax. Mol. Cell. Endocrinol. 2009, 299:240-251.
31. Guyon R., Senger F., Rakotomanga M., Sadequi N., Volckaert F.A., Hitte C., Galibert F. A radiation hybrid map of the European sea bass (Dicentrarchus labrax) based on 1581 markers: synteny analysis with model fish genomes. Genomics 2010, 96:228-238.
32. Harris M.A., Clark J., Ireland A., Lomax J., Ashburner M., Foulger R., Eilbeck K., Lewis S., Marshall B., Mungall C., Richter J., Rubin G.M., Blake J.A., Bult C., Dolan M., Drabkin H., Eppig J.T., Hill D.P., Ni L., Ringwald M., Balakrishnan R., Cherry J.M., Christie K.R., Costanzo M.C., Dwight S.S., Engel S., Fisk D.G., Hirschman J.E., Hong E.L., Nash R.S., Sethuraman A., Theesfeld C.L., Botstein D., Dolinski K., Feierbach B., Berardini T., Mundodi S., Rhee S.Y., Apweiler R., Barrell D., Camon E., Dimmer E., Lee V., Chisholm R., Gaudet P., Kibbe W., Kishore R., Schwarz E.M., Sternberg P., Gwinn M., Hannick L., Wortman J., Berriman M., Wood V., de la Cruz N., Tonellato P., Jaiswal P., Seigfried T., White R. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004, 32:D258-D261.
33. Guiliano D.B., Hall N., Jones S.J., Clark L.N., Corton C.H., Barrell B.G., Blaxter M.L. Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes. Genome Biol. 2002, 3:10.
34. Kuhl H., Tine M., Hecht J., Knaust F., Reinhardt R. Analysis of single nucleotide polymorphisms in three chromosomes of European sea bass Dicentrarchus labrax. Comp. Biochem. Physiol. Part D Genomics Proteomics 2011, 6:70-75.
35. Hare M.P., Palumbi S.R. High intron sequence conservation across three mammalian orders suggests functional constraints. Mol. Biol. Evol. 2003, 20:969-978.
36. Seo H.C., Kube M., Edvardsen R.B., Jensen M.F., Beck A., Spriet E., Gorsky G., Thompson E.M., Lehrach H., Reinhardt R., Chourrout D. Miniature genome in the marine chordate Oikopleura dioica. Science 2001, 294:2506.
37. Dehal P., Satou Y., Campbell R.K., Chapman J., Degnan B., De Tomaso A., Davidson B., Di Gregorio A., Gelpke M., Goodstein D.M., Harafuji N., Hastings K.E., Ho I., Hotta K., Huang W., Kawashima T., Lemaire P., Martinez D., Meinertzhagen I.A., Necula S., Nonaka M., Putnam N., Rash S., Saiga H., Satake M., Terry A., Yamada L., Wang H.G., Awazu S., Azumi K., Boore J., Branno M., Chin-Bow S., DeSantis R., Doyle S., Francino P., Keys D.N., Haga S., Hayashi H., Hino K., Imai K.S., Inaba K., Kano S., Kobayashi K., Kobayashi M., Lee B.I., Makabe K.W., Manohar C., Matassi G., Medina M., Mochizuki Y., Mount S., Morishita T., Miura S., Nakayama A., Nishizaka S., Nomoto H., Ohta F., Oishi K., Rigoutsos I., Sano M., Sasaki A., Sasakura Y., Shoguchi E., Shin-i T., Spagnuolo A., Stainier D., Suzuki M.M., Tassy O., Takatori N., Tokuoka M., Yagi K., Yoshizaki F., Wada S., Zhang C., Hyatt P.D., Larimer F., Detter C., Doggett N., Glavina T., Hawkins T., Richardson P., Lucas S., Kohara Y., Levine M., Satoh N., Rokhsar D.S. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 2002, 298:2157-2167.
38. Sakharkar M.K., Chow V.T., Kangueane P. Distributions of exons and introns in the human genome. In Silico Biol. 2004, 4:387-393.
39. Ewing B., Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998, 8:186-194.
40. Chou H.H., Holmes M.H. DNA sequence quality trimming and vector removal. Bioinformatics 2001, 17:1093-1104.
41. Miller J.R., Delcher A.L., Koren S., Venter E., Walenz B.P., Brownley A., Johnson J., Li K., Mobarry C., Sutton G. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 2008, 24:2818-2824.
42. Gordon D. Viewing and editing assembled sequences using Consed. Curr. Protoc. Bioinformatics 2003, Chapter 11, Chapter 11, Unit11.2.
43. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
44. Itoh M., Watanabe H. CGAS: comparative genomic analysis server. Bioinformatics 2009, 25:958-959.
45. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.