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19 Article(s) on File
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Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3
Zwickl DJ,
Stein JC,
Wing RA,
Ware D,
Sanderson MJ

Systematic biology
  63 (5): 645-59; Sep 2014   Nlm
[Abstract]
[DOI] [Full Text]

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds
Singh R,
Ong-Abdullah M,
Low ET,
Manaf MA,
Rosli R,
Nookiah R,
Ooi LC,
Ooi SE,
Chan KL,
Halim MA,
Azizi N,
Nagappan J,
Bacher B,
Lakey N,
Smith SW,
He D,
Hogan M,
Budiman MA,
Lee EK,
Desalle R,
Kudrna D,
Goicoechea JL,
Wing RA,
Wilson RK,
Fulton RS,
Ordway JM,
Martienssen RA,
Sambanthamurthi R

Nature
  500 (7462): 335-339; Aug 15 2013   NLM
[Abstract]
[DOI] [Full Text]

Aluminum tolerance in maize is associated with higher MATE1 gene copy number
Maron LG,
Guimarães CT,
Kirst M,
Albert PS,
Birchler JA,
Bradbury PJ,
Buckler ES,
Coluccio AE,
Danilova TV,
Kudrna D,
Magalhaes JV,
Piñeros MA,
Schatz MC,
Wing RA,
Kochian LV

Proceedings of the National Academy of Sciences of the United States of America
  110 (13): 5241-5246; Mar 26 2013  
[Abstract]
[DOI] [Full Text]

The tomato genome sequence provides insights into fleshy fruit evolution
Sato S,
Tabata S,
Hirakawa H,
Asamizu E,
Shirasawa K,
Isobe S,
Kaneko T,
Nakamura Y,
Shibata D,
Aoki K,
Egholm M,
Knight J,
Bogden R,
Li CB,
Shuang Y,
Xu X,
Pan SK,
Cheng SF,
Liu X,
Ren YY,
Wang J,
Albiero A,
Dal Pero F,
Todesco S,
Van Eck J,
Buels RM,
Bombarely A,
Gosselin JR,
Huang MY,
Leto JA,
Menda N,
Strickler S,
Mao LY,
Gao S,
Tecle IY,
York T,
Zheng Y,
Vrebalov JT,
Lee J,
Zhong SL,
Mueller LA,
Stiekema WJ,
Ribeca P,
Alioto T,
Yang WC,
Huang SW,
Du YC,
Zhang ZH,
Gao JC,
Guo YM,
Wang XX,
Li Y,
He J,
Li CY,
Cheng ZK,
Zuo JR,
Ren JF,
Zhao JH,
Yan LH,
Jiang HL,
Wang B,
Li HS,
Li ZJ,
Fu FY,
Chen BT,
Han B,
Feng Q,
Fan DL,
Wang Y,
Ling HQ,
Xue YB,
Ware D,
McCombie WR,
Lippman ZB,
Chia JM,
Jiang K,
Pasternak S,
Gelley L,
Kramer M,
Anderson LK,
Chang SB,
Royer SM,
Shearer LA,
Stack SM,
Rose JK,
Xu YM,
Eannetta N,
Matas AJ,
McQuinn R,
Tanksley SD,
Camara F,
Guigo R,
Rombauts S,
Fawcett J,
Van de Peer Y,
Zamir D,
Liang CB,
Spannagl M,
Gundlach H,
Bruggmann R,
Mayer K,
Jia ZQ,
Zhang JH,
Ye ZB,
Bishop GJ,
Butcher S,
Lopez-Cobollo R,
Buchan D,
Filippis I,
Abbott J,
Dixit R,
Singh M,
Singh A,
Pal JK,
Pandit A,
Singh PK,
Mahato AK,
Dogra V,
Gaikwad K,
Sharma TR,
Mohapatra T,
Singh NK,
Causse M,
Rothan C,
Schiex T,
Noirot C,
Bellec A,
Klopp C,
Delalande C,
Berges H,
Mariette J,
Frasse P,
Vautrin S,
Zouine M,
Latche A,
Rousseau C,
Regad F,
Pech JC,
Philippot M,
Bouzayen M,
Pericard P,
Osorio S,
del Carmen AF,
Monforte A,
Granell A,
Fernandez-Munoz R,
Conte M,
Lichtenstein G,
Carrari F,
De Bellis G,
Fuligni F,
Peano C,
Grandillo S,
Termolino P,
Pietrella M,
Fantini E,
Falcone G,
Fiore A,
Giuliano G,
Lopez L,
Facella P,
Perrotta G,
Daddiego L,
Bryan G,
Orozco M,
Pastor X,
Torrents D,
van Schriek K,
Feron RM,
van Oeveren J,
de Heer P,
daPonte L,
Jacobs-Oomen S,
Cariaso M,
Prins M,
van Eijk MJ,
Janssen A,
van Haaren MJ,
Jo SH,
Kim J,
Kwon SY,
Kim S,
Koo DH,
Lee S,
Hur CG,
Clouser C,
Rico A,
Hallab A,
Gebhardt C,
Klee K,
Jocker A,
Warfsmann J,
Gobel U,
Kawamura S,
Yano K,
Sherman JD,
Fukuoka H,
Negoro S,
Bhutty S,
Chowdhury P,
Chattopadhyay D,
Datema E,
Smit S,
Schijlen EW,
van de Belt J,
van Haarst JC,
Peters SA,
van Staveren MJ,
Henkens MH,
Mooyman PJ,
Hesselink T,
van Ham R,
Jiang GY,
Droege M,
Choi D,
Kang BC,
Kim BD,
Park M,
Yeom SI,
Lee YH,
Choi YD,
Li GC,
Gao JW,
Liu YS,
Huang SX,
Fernandez-Pedrosa V,
Collado C,
Zuniga S,
Wang GP,
Cade R,
Dietrich RA,
Rogers J,
Knapp S,
Fei ZJ,
White RA,
Thannhauser TW,
Giovannoni JJ,
Botella MA,
Gilbert L,
Gonzalez R,
Goicoechea JL,
Yu Y,
Kudrna D,
Collura K,
Wissotski M,
Wing R,
Schoof H,
Meyers BC,
Gurazada AB,
Green PJ,
Mathur S,
Vyas S,
Solanke AU,
Kumar R,
Gupta V,
Sharma AK,
Khurana P,
Khurana JP,
Tyagi AK,
Dalmay T,
Mohorianu I,
Walts B,
Chamala S,
Barbazuk WB,
Li JP,
Guo H,
Lee TH,
Wang YP,
Zhang D,
Paterson AH,
Wang XY,
Tang HB,
Barone A,
Chiusano ML,
Ercolano MR,
DAgostino N,
Di Filippo M,
Traini A,
Sanseverino W,
Frusciante L,
Seymour GB,
Elharam M,
Fu Y,
Hua A,
Kenton S,
Lewis J,
Lin SP,
Najar F,
Lai HS,
Qin BF,
Qu CM,
Shi RH,
White D,
White J,
Xing YB,
Yang KQ,
Yi J,
Yao ZY,
Zhou LP,
Roe BA,
Vezzi A,
DAngelo M,
Zimbello R,
Schiavon R,
Caniato E,
Rigobello C,
Campagna D,
Vitulo N,
Valle G,
Nelson DR,
De Paoli E,
Szinay D,
de Jong HH,
Bai YL,
Visser RG,
Lankhorst RM,
Beasley H,
McLaren K,
Nicholson C,
Riddle C,
Gianese G

Nature
  485 (7400): 635-641; May 2012  
[Abstract]
[DOI] [Full Text]

The genome of Theobroma cacao
Argout X,
Salse J,
Aury JM,
Guiltinan MJ,
Droc G,
Gouzy J,
Allegre M,
Chaparro C,
Legavre T,
Maximova SN,
Abrouk M,
Murat F,
Fouet O,
Poulain J,
Ruiz M,
Roguet Y,
Rodier-Goud M,
Barbosa-Neto JF,
Sabot F,
Kudrna D,
Ammiraju JS,
Schuster SC,
Carlson JE,
Sallet E,
Schiex T,
Dievart A,
Kramer MR,
Gelley L,
Shi Z,
Bérard A,
Viot C,
Boccara M,
Risterucci AM,
Guignon V,
Sabau X,
Axtell MJ,
Ma Z,
Zhang Y,
Brown S,
Bourge M,
Golser W,
Song X,
Clement D,
Rivallan R,
Tahi M,
Akaza JM,
Pitollat B,
Gramacho K,
DHont A,
Brunel D,
Infante D,
Kebe I,
Costet P,
Wing R,
McCombie WR,
Guiderdoni E,
Quetier F,
Panaud O,
Wincker P,
Bocs S,
Lanaud C

Nature Genetics
  43 (2): 101-108; 2011   Elsevier Scopus
[Abstract]
[DOI]

Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents
Gill N,
SanMiguel P,
Dhillon BD,
Abernathy B,
Kim H,
Stein LD,
Ware DH,
Wing R,
Jackson SA

Rice
  (0): 1-19; 2010  
[Abstract]
[DOI] [Full Text]

The Oryza BAC resource: A genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives
Ammiraju JS,
Song X,
Luo M,
Sisneros N,
Angelova A,
Kudrna D,
Kim H,
Yu Y,
Goicoechea JL,
Lorieux M,
Kurata N,
Brar D,
Ware DH,
Jackson S,
Wing RA

Breeding Science
  60 (5): 536-543; 2010   Elsevier
[Abstract]
[DOI]

Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae)
Cranston KA,
Hurwitz BL,
Sanderson MJ,
Ware DH,
Wing RA,
Stein LD

Systematic Botany
  35 (3): 512-523; 2010  
[Abstract]
[DOI] [Full Text]

Rice structural variation: A comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza
Hurwitz BL,
Kudrna D,
Yu Y,
Sebastian A,
Zuccolo A,
Jackson SA,
Ware DH,
Wing RA,
Stein LD

Plant Journal
  63 (6): 990-1003; 2010  
[Abstract]
[DOI] [Full Text] [PDF]

The B73 Maize Genome: Complexity, Diversity, and Dynamics
Schnable PS,
Ware DH,
Fulton RS,
Stein JC,
Wei FS,
Pasternak S,
Liang CZ,
Zhang JW,
Fulton L,
Graves TA,
Minx P,
Reily AD,
Courtney L,
Kruchowski SS,
Tomlinson C,
Strong C,
Delehaunty K,
Fronick C,
Courtney B,
Rock SM,
Belter E,
Du FY,
Kim K,
Abbott RM,
Cotton M,
Levy A,
Marchetto P,
Ochoa K,
Jackson SM,
Gillam B,
Chen WZ,
Yan L,
Higginbotham J,
Cardenas M,
Waligorski J,
Applebaum E,
Phelps L,
Falcone J,
Kanchi K,
Thane T,
Scimone A,
Thane N,
Henke J,
Wang T,
Ruppert J,
Shah N,
Rotter K,
Hodges J,
Ingenthron E,
Cordes M,
Kohlberg S,
Sgro J,
Delgado B,
Mead K,
Chinwalla A,
Leonard S,
Crouse K,
Collura K,
Kudrna D,
Currie J,
He RF,
Angelova A,
Rajasekar S,
Mueller T,
Lomeli R,
Scara G,
Ko A,
Delaney K,
Wissotski M,
Lopez G,
Campos D,
Braidotti M,
Ashley E,
Golser W,
Kim H,
Lee S,
Lin JK,
Dujmic Z,
Kim W,
Talag J,
Zuccolo A,
Fan C,
Sebastian A,
Kramer MR,
Spiegel L,
Nascimento L,
Zutavern T,
Miller B,
Ambroise C,
Muller S,
Spooner W,
Narechania A,
Ren LY,
Wei S,
Kumari S,
Faga BP,
Levy MJ,
McMahan L,
Van Buren P,
Vaughn MW,
Ying K,
Yeh CT,
Emrich SJ,
Jia Y,
Kalyanaraman A,
Hsia AP,
Barbazuk WB,
Baucom RS,
Brutnell TP,
Carpita NC,
Chaparro C,
Chia JM,
Deragon JM,
Estill JC,
Fu Y,
Jeddeloh JA,
Han YJ,
Lee H,
Li PH,
Lisch DR,
Liu SZ,
Liu ZJ,
Nagel DH,
McCann MC,
SanMiguel P,
Myers AM,
Nettleton D,
Nguyen J,
Penning BW,
Ponnala L,
Schneider KL,
Schwartz DC,
Sharma A,
Soderlund C,
Springer NM,
Sun Q,
Wang H,
Waterman M,
Westerman R,
Wolfgruber TK,
Yang LX,
Yu Y,
Zhang LF,
Zhou SG,
Zhu Q,
Bennetzen JL,
Dawe RK,
Jiang JM,
Jiang N,
Presting GG,
Wessler SR,
Aluru S,
Martienssen RA,
Clifton SW,
McCombie WR,
Wing RA,
Wilson RK

Science
  326 (5956): 1112-1115; Nov 20 2009  
[Abstract]
[DOI] [Full Text] [PDF]

Detailed analysis of a contiguous 22-Mb region of the maize genome
Wei F,
Stein JC,
Liang C,
Zhang J,
Fulton RS,
Baucom RS,
De Paoli E,
Zhou S,
Yang L,
Han Y,
Pasternak S,
Narechania A,
Zhang L,
Yeh CT,
Ying K,
Nagel DH,
Collura K,
Kudrna D,
Currie J,
Lin J,
Kim H,
Angelova A,
Scara G,
Wissotski M,
Golser W,
Courtney L,
Kruchowski S,
Graves TA,
Rock SM,
Adams S,
Fulton LA,
Fronick C,
Courtney W,
Kramer M,
Spiegel L,
Nascimento L,
Kalyanaraman A,
Chaparro C,
Deragon JM,
Miguel PS,
Jiang N,
Wessler SR,
Green PJ,
Yu Y,
Schwartz DC,
Meyers BC,
Bennetzen JL,
Martienssen RA,
McCombie WR,
Aluru S,
Clifton SW,
Schnable PS,
Ware D,
Wilson RK,
Wing RA

PLoS genetics
  5 (11): e1000728; Nov 2009  
[Abstract]
[DOI] [Full Text]

The physical and genetic framework of the maize b73 genome
Wei F,
Zhang J,
Zhou S,
He R,
Schaeffer M,
Collura K,
Kudrna D,
Faga BP,
Wissotski M,
Golser W,
Rock SM,
Graves TA,
Fulton RS,
Coe E,
Schnable PS,
Schwartz DC,
Ware DH,
Clifton SW,
Wilson RK,
Wing RA

PLoS Genet
  5 (11): e1000715; Nov 2009   PMCID: PMC2774505
[Abstract]
[DOI] [Full Text] [PDF]

A single molecule scaffold for the maize genome
Zhou S,
Wei F,
Nguyen J,
Bechner M,
Potamousis K,
Goldstein S,
Pape L,
Mehan MR,
Churas C,
Pasternak S,
Forrest DK,
Wise R,
Ware DH,
Wing RA,
Waterman MS,
Livny M,
Schwartz DC

PLoS Genet
  5 (11): e1000711; Nov 2009   PMCID: PMC2774507
[Abstract]
[DOI] [Full Text] [PDF]

Species Trees from Highly Incongruent Gene Trees in Rice
Cranston KA,
Hurwitz BL,
Ware DH,
Stein LD,
Wing RA

Systematic Biology
  58 (5): 489-500; Oct 2009  
[Abstract]
[Full Text]

Construction, alignment and analysis of 12 framework physical maps that represent the 10 genome types of the genus Oryza
Kim HR,
Hurwitz BL,
Yu Y,
Collura K,
Gill N,
SanMiguel P,
Mullikin JC,
Maher C,
Nelson W,
Wissotski M,
Braidotti M,
Kudrna D,
Goigochia JL,
Stein LD,
Ware DH,
Jackson S,
Soderlund C,
Wing R

Genome Biology
  9 (2): R45; Feb 27 2008   PMCID: PMC2374706
[Abstract]
[DOI] [Full Text] [PDF]

The rice annotation project database (RAP-DB): 2008 update
Tanaka T,
Antonio BA,
Kikuchi S,
Matsumoto T,
Nagamura Y,
Numa H,
Sakai H,
Wu J,
Itoh T,
Sasaki T,
Aono R,
Fujii Y,
Habara T,
Harada E,
Kanno M,
Kawahara Y,
Kawashima H,
Kubooka H,
Matsuya A,
Nakaoka H,
Saichi N,
Sanbonmatsu R,
Sato Y,
Shinso Y,
Suzuki M,
Takeda JI,
Tanino M,
Todokoro F,
Yamaguchi K,
Yamamoto N,
Yamasaki C,
Imanishi T,
Okido T,
Tada M,
Ikeo K,
Tateno Y,
Gojobori T,
Lin YC,
Wei FJ,
Hsing YI,
Zhao Q,
Han B,
Kramer MR,
McCombie RW,
Lonsdale D,
ODonovan CC,
Whitfield EJ,
Apweiler R,
Koyanagi KO,
Khurana JP,
Raghuvanshi S,
Singh NK,
Tyagi AK,
Haberer G,
Fujisawa M,
Hosokawa S,
Ito Y,
Ikawa H,
Shibata M,
Yamamoto M,
Bruskiewich RM,
Hoen DR,
Bureau TE,
Namiki N,
Ohyanagi H,
Sakai Y,
Nobushima S,
Sakata K,
Barrero RA,
Souvorov A,
Smith-White B,
Tatusova T,
An S,
An G,
Oota S,
Fuks G,
Messing J,
Christie KR,
Lieberherr D,
Kim H,
Zuccolo A,
Wing RA,
Nobuta K,
Green PJ,
Lu C,
Meyers BC,
Chaparro C,
Piegu B,
Panaud O

Nucleic Acids Research
  36 (0): D1028-D1033; Jan 2008   PMCID: PMC2238920
[Abstract]
[DOI] [Full Text] [PDF]

The Oryza Map Alignment Project: The golden path to unlocking the genetic potential of wild rice species
Wing RA,
Ammiraju JS,
Luo MZ,
Kim H,
Yu YS,
Kudrna D,
Goicoechea JL,
Wang WM,
Nelson W,
Rao K,
Brar D,
Mackill DJ,
Han B,
Soderlund C,
Stein L,
SanMiguel P,
Jackson S

Plant Molecular Biology
  59 (1): 53-62; Sep 2005  
[Abstract]
[Full Text]

The map-based sequence of the rice genome
Matsumoto T,
Wu JZ,
Kanamori H,
Katayose Y,
Fujisawa M,
Namiki N,
Mizuno H,
Yamamoto K,
Antonio BA,
Baba T,
Sakata K,
Nagamura Y,
Aoki H,
Arikawa K,
Arita K,
Bito T,
Chiden Y,
Fujitsuka N,
Fukunaka R,
Hamada M,
Harada C,
Hayashi A,
Hijishita S,
Honda M,
Hosokawa S,
Ichikawa Y,
Idonuma A,
Iijima M,
Ikeda M,
Ikeno M,
Ito K,
Ito S,
Ito T,
Ito Y,
Iwabuchi A,
Kamiya K,
Karasawa W,
Kurita K,
Katagiri S,
Kikuta A,
Kobayashi H,
Kobayashi N,
Machita K,
Maehara T,
Masukawa M,
Mizubayashi T,
Mukai Y,
Nagasaki H,
Nagata Y,
Naito S,
Nakashima M,
Nakama Y,
Nakamichi Y,
Nakamura M,
Meguro A,
Negishi M,
Ohta I,
Ohta T,
Okamoto M,
Ono N,
Saji S,
Sakaguchi M,
Sakai K,
Shibata M,
Shimokawa T,
Song JY,
Takazaki Y,
Terasawa K,
Tsugane M,
Tsuji K,
Ueda S,
Waki K,
Yamagata H,
Yamamoto M,
Yamamoto S,
Yamane H,
Yoshiki S,
Yoshihara R,
Yukawa K,
Zhong HS,
Yano M,
Sasaki T,
Yuan QP,
Shu OT,
Liu J,
Jones KM,
Gansberger K,
Moffat K,
Hill J,
Bera J,
Fadrosh D,
Jin SH,
Johri S,
Kim M,
Overton L,
Reardon M,
Tsitrin T,
Vuong H,
Weaver B,
Ciecko A,
Tallon L,
Jackson J,
Pai G,
Van Aken S,
Utterback T,
Reidmuller S,
Feldblyum T,
Hsiao J,
Zismann V,
Iobst S,
de Vazeille AR,
Buell CR,
Ying K,
Li Y,
Lu TT,
Huang YC,
Zhao Q,
Feng Q,
Zhang L,
Zhu JJ,
Weng QJ,
Mu J,
Lu YQ,
Fan DL,
Liu YL,
Guan JP,
Zhang YJ,
Yu SL,
Liu XH,
Zhang Y,
Hong GF,
Han B,
Choisne N,
Demange N,
Orjeda G,
Samain S,
Cattolico L,
Pelletier E,
Couloux A,
Segurens B,
Wincker P,
DHont A,
Scarpelli C,
Weissenbach J,
Salanoubat M,
Quetier F,
Yu Y,
Kim HR,
Rambo T,
Currie J,
Collura K,
Luo MZ,
Yang TJ,
Ammiraju JS,
Engler F,
Soderlund C,
Wing RA,
Palmer LE,
de la Bastide M,
Spiegel L,
Nascimento L,
Zutavern T,
OShaughnessy A,
Dike S,
Dedhia N,
Preston R,