Sequencing and assembly of highly heterozygous genome of Vitis vinifera L. cv Pinot Noir: Problems and solutions

Journal of Biotechnology

Volumn 136, Issue 1-2, 2008, Pages 38-43

  Zharkikh, Andrey ^b   Troggio, Michela ^a   Pruss, Dmitry ^b   Cestaro, Alessandro ^a   Eldrdge, Glenn ^b   Pindo, Massimo ^a   Mitchell, Jeff T ^b   Vezzulli, Silvia ^a   Bhatnagar, Satish ^b   Fontana, Paolo ^a   Viola, Roberto ^a   Gutin, Alexander ^b   Salamini, Francesco ^c   Skolnick, Mark ^b   Velasco, Riccardo ^a  

^a RESEARCH AND INNOVATION CENTRE   (Italy)

^b Myriad Genetic Laboratories   (United States)

^c NONE   (Italy)

Author keywords

Genome assembly; Heterozygosity; Polymorphism; Sanger sequencing; Sequencing by synthesis; Whole genome shotgun

Indexed keywords

CHLORINE COMPOUNDS; COMPLEXATION; DECODING; FRUITS;

CONTIGS; GENOME ASSEMBLY; HETEROZYGOSITY; LINKAGE GROUPS; NEW APPROACHES; PINOT NOIR; POLYMORPHISM; SANGER SEQUENCING; SEQUENCING BY SYNTHESIS; VITIS VINIFERA; VITIS VINIFERA L.; WHOLE-GENOME SHOTGUN;

AGRICULTURAL PRODUCTS;

ARTICLE; GENETIC ALGORITHM; GENETIC LINKAGE; GENOME ANALYSIS; GRAPE; HETEROZYGOSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; UNINDEXED SEQUENCE;

BASE SEQUENCE; CHROMOSOME MAPPING; CORYNEBACTERIUM; GENOME, PLANT; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PLANT PROTEINS; SEQUENCE ANALYSIS, DNA; VITIS;

VITACEAE; VITIS VINIFERA;

EID: 50249102714     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2008.04.013     Document Type: Article

References (13)

1. Adam-Blondon A.F., Bernole A., Faes G., Lamoureux D., Pateyron S., Grando M.S., Caboche M., Velasco R., and Chalhoub B. Construction and characterization of BAC libraries from major grapevine cultivars. Theor. Appl. Genet. 110 (2005) 1363-1371
2. Fang Z., Polacco M., Chen S., Schroeder S., Hancock D., Sanchez H., and Coe E. cMap: the comparative genetic map viewer. Bioinformatics 19 3 (2003) 416-417
3. Jaillon O., Aury J.M., Noel B., Policriti A., Clepet C., Casagrande A., Choisne N., Aubourg S., Vitulo N., Jubin C., Vezzi A., Legeai F., Hugueney P., Dasilva C., Horner D., Mica E., Jublot D., Poulain J., Bruyere C., Billault A., Segurens B., Gouyvenoux M., Ugarte E., Cattonaro F., Anthouard V., Vico V., Del Fabbro C., Alaux M., Di Gaspero G., Dumas V., Felice N., Paillard S., Juman I., Moroldo M., Scalabrin S., Canaguier A., Le Clainche I., Malacrida G., Durand E., Pesole G., Laucou V., Chatelet P., Merdinoglu D., Delledonne M., Pezzotti M., Lecharny A., Scarpelli C., Artiguenave F., Pe M.E., Valle E., Morgante M., Caboche M., Adam-Blondon A.F., Wessenbach J., Quetier F., and Wincker P. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449 (2007) 463-467
4. Goff S.A., Ricke D., Lan T.H., Presting G., Wang R., Dunn M., Glazebrook J., Sessions A., Oeller P., Varma H., Hadley D., Hutchison D., Martin C., Katagiri F., Lange B.M., Moughamer T., Xia Y., Budworth P., Zhong J., Miguel T., Paszkowski U., Zhang S., Colbert M., Sun W.L., Chen L., Cooper B., Park S., Wood T.C., Mao L., Quail P., Wing R., Dean R., Yu Y., Zharkikh A., Shen R., Sahasrabudhe S., Thomas A., Cannings R., Gutin A., Pruss D., Reid J., Tavtigian S., Mitchell J., Eldredge G., Scholl T., Miller R.M., Bhatnagar S., Adey N., Rubano T., Tusneem N., Robinson R., Feldhaus J., Macalma T., Oliphant A., and Briggs S. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296 5565 (2002) 92-100
5. Levy S., Sutton G., Ng P.C., Feuk L., Halpern A.L., Walenz B.P., Axelrod N., Huang J., Kirkness E.F., Denisov G., Lin Y., MacDonald J.R., Wing A., Pang C., Shago M., Stockwell T.B., Tsiamouri A., Bafna V., Bansal V., Kravitz S.A., Busam D.A., Beeson K.Y., McIntosh T.C., Remington K.A., Abril J.F., Gill J., Borman J., Rogers Y.-H., Frazier M.E., Scherer S.W., Strausberg R.L., and Venter J.C. The diploid genome sequence of an individual human. PLOS Biol. 5 10 (2007) e254
6. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L., Jarvie T.P., Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., and Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 7057 (2005) 376-380
7. Pindo M., Vezzulli S., Coppola G., Cartwright D., Zharkikh A., Velasco R., and Troggio M. SNP High throughput screening in grapevine using the SNPlexTM genotyping system. BMC Plant Biol. 8 (2008) 12
8. Sanger F., Nicklen S., and Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 74 12 (1977) 5463-5467
9. Sea Urchin Genome Sequencing Consortium: Sodergren, E., Weinstock, G.M., Davidson, E.H., Cameron, R.A., Gibbs, R.A., Angerer, R.C., Angerer, L. M., Arnone, M.I., Burgess, D.R., Burke, R.D., Coffman, J.A., Dean, M., Elphick, M.R., Ettensohn, C.A., Foltz, K.R., Hamdoun, A., Hynes, R.O., Klein, W.H., Marzluff, W., McClay, D.R., Morris, R.L., Mushegian, A., Rast, J.P., Smith, L.C., Thorndyke, M.C., Vacquier, V.D., Wessel, G.M., Wray, G., Zhang, L., Elsik, C.G., Ermolaeva, O., Hlavina, W., Hofmann, G., Kitts, P., Landrum, M.J., Mackey, A.J., Maglott, D., Panopoulou, G., Poustka, A.J., Pruitt, K., Sapojnikov, V., Song, X., Souvorov, A., Solovyev, V., Wei, Z., Whittaker, C.A., Worley, K., Durbin, K.J., Shen, Y., Fedrigo, O., Garfield, D., Haygood, R., Primus, A., Satija, R., Severson, T., Gonzalez-Garay, M.L., Jackson, A.R., Milosavljevic, A., Tong, M., Killian, C.E., Livingston, B.T., Wilt, F.H., Adams, N., Belle, R., Carbonneau, S., Cheung, R., Cormier, P., Cosson, B., Croce, J., Fernandez-Guerra, A., Geneviere, A.M., Goel, M., Kelkar, H., Morales, J., Mulner-Lorillon, O., Robertson, A.J., Goldstone, J.V., Cole, B., Epel, D., Gold, B., Hahn, M.E., Howard-Ashby, M., Scally, M., Stegeman, J.J., Allgood, E.L., Cool, J., Judkins, K.M., McCafferty, S.S., Musante, A.M., Obar, R.A., Rawson, A.P., Rossetti, B.J., Gibbons, I.R., Hoffman, M.P., Leone, A., Istrail, S., Materna, S.C., Samanta, M.P., Stolc, V., Tongprasit, W., Tu, Q., Bergeron, K.F., Brandhorst, B.P., Whittle, J., Berney, K., Bottjer, D.J., Calestani, C., Peterson, K., Chow, E., Yuan, Q.A., Elhaik, E., Graur, D., Reese, J.T., Bosdet, I., Heesun, S., Marra, M.A., Schein, J., Anderson, M. K., Brockton, V., Buckley, K. M., Cohen, A. H., Fugmann, S. D., Hibino, T., Loza-Coll, M., Majeske, A.J., Messier, C., Nair, S.V., Pancer, Z., Terwilliger, D.P., Agca, C., Arboleda, E., Chen, N., Churcher, A.M., Hallbook, F., Humphrey, G.W., Idris, M.M., Kiyama, T., Liang, S., Mellott, D., Mu, X., Murray, G., Olinski, R.P., Raible, F., Rowe, M., Taylor, J.S., Tessmar-Raible, K., Wang, D., Wilson, K.H., Yaguchi, S., Gaasterland, T., Galindo, B.E., Gunaratne, H. J., Juliano, C., Kinukawa, M., Moy, G.W., Neill, A.T., Nomura, M., Raisch, M., Reade, A., Roux, M.M., Song, J.L., Su, Y.H., Townley, I.K., Voronina, E., Wong, J.L., Amore, G., Branno, M., Brown, E.R., Cavalieri, V., Duboc, V., Duloquin, L., Flytzanis, C., Gache, C., Lapraz, F., Lepage, T., Locascio, A., Martinez, P., Matassi, G., Matranga, V., Range, R., Rizzo, F., Rottinger, E., Beane, W., Bradham, C., Byrum, C., Glenn, T., Hussain, S., Manning, G., Miranda, E., Thomason, R., Walton, K., Wikramanayke, A., Wu, S.Y., Xu, R., Brown, C.T., Chen, L., Gray, R.F., Lee, P.Y., Nam, J., Oliveri, P., Smith, J., Muzny, D., Bell, S., Chacko, J., Cree, A., Curry, S., Davis, C., Dinh, H., Dugan-Rocha, S., Fowler, J., Gill, R., Hamilton, C., Hernandez, J., Hines, S., Hume, J., Jackson, L., Jolivet, A., Kovar, C., Lee, S., Lewis, L., Miner, G., Morgan, M., Nazareth, L.V., Okwuonu, G., Parker, D., Pu, L.L., Thorn, R., Wright, R., 2006. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314(5801), 941-952.
10. Small K.S., Brudno M., Hill M.M., and Sidow A. A haplome alignment and reference sequence of the highly polymorphic Ciona Savignyi genome. Genome Biol. 8 (2007) R41
11. Troggio M., Malacarne G., Coppola G., Segala C., Cartwright D.A., Pindo M., Mank R., Morgante M., Grando M.S., and Velasco R. A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs. Genetics 176 (2007) 2637-2650
12. Tuskan G.A., DiFazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., Schein J., Sterck L., Aerts A., Bhalerao R.R., Bhalerao R.P., Blaudez D., Boerjan W., Brun A., Brunner A., Busov V., Campbell M., Carlson J., Chalot M., Chapman J., Chen G.-L., Cooper D., Coutinho P.M., Couturier J., Covert S., Cronk Q., Cunningham R., Davis J., Degroeve S., Dejardin A., de Pamphilis C., Detter J., Dirks B., Dubchak I., Duplessis S., Ehlting J., Ellis B., Gendler K., Goodstein D., Gribskov M., Grimwood J., Groover A., Gunter L., Hamberger B., Heinze B., Helariutta Y., Henrissat B., Holligan D., Holt R., Huang W., Islam-Faridi N., Jones S., Jones-Rhoades M., Jorgensen R., Joshi C., Kangasjarvi J., Karlsson J., Kelleher C., Kirkpatrick R., Kirst M., Kohler A., Kalluri U., Larimer F., Leebens-Mack J., Leple J.-C., Locascio P., Lou Y., Lucas S., Martin F., Montanini B., Napoli C., Nelson D.R., Nelson C., Nieminen K., Nilsson O., Pereda V., Peter G., Philippe R., Pilate G., Poliakov A., Razumovskaya J., Richardson P., Rinaldi C., Ritland K., Rouze P., Ryaboy D., Schmutz J., Schrader J., Segerman B., Shin H., Siddiqui A., Sterky F., Terry A., Tsai C.-J., Uberbacher E., Unneberg P., Vahala J., Wall K., Wessler S., Yang G., Yin T., Douglas C., Marra M., Sandberg G., Van de Peer Y., and Rokhsar D. The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). Science 313 5793 (2006) 1596-1604
13. Velasco R., Zharkikh A., Troggio M., Cartwright D.A., Cestaro A., Pruss D., Pindo M., FitzGerald L.M., Vezzulli S., Reid J., Malacarne G., Iliev D., Coppola G., Wardell B., Micheletti D., Macalma T.M., Facci M., Mitchell J.T., Perazzolli M., Eldredge G., Gatto P., Oyzerski R., Moretto M., Gutin N., Stefanini M., Chen Y., Segala C., Davenport C., Demattè L., Mraz A., Battilana J., Stormo K., Costa F., Tao Q., Si-Ammour A., Harkins T., Lackey A., Perbost C., Taillon B., Stella A., Solovyev V., Fawcett J.A., Sterck L., Vandepoele K., Grando M.S., Toppo S., Moser C., Lanchbury J., Bogden R., Skolnick M., Sgaramella V., Bhatnagar S.K., Fontana P., Gutin A., Van de Peer Y., Salamini F., and Viola R.A. High quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2 12 (2007) e1326