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Items: 1 to 50 of 184

1.

Progress in single-access information systems for wheat and rice crop improvement.

Scheben A, Chan CK, Mansueto L, Mauleon R, Larmande P, Alexandrov N, Wing RA, McNally KL, Quesneville H, Edwards D.

Brief Bioinform. 2018 Apr 5. doi: 10.1093/bib/bby016. [Epub ahead of print]

PMID:
29659709
2.

Genome and evolution of the shade-requiring medicinal herb Panax ginseng.

Kim NH, Jayakodi M, Lee SC, Choi BS, Jang W, Lee J, Kim HH, Waminal NE, Lakshmanan M, Van Nguyen B, Lee YS, Park HS, Koo HJ, Park JY, Perumal S, Joh HJ, Lee H, Kim J, Kim IS, Kim K, Koduru L, Kang KB, Sung SH, Yu Y, Park DS, Choi D, Seo E, Kim S, Kim YC, Hyun DY, Park YI, Kim C, Lee TH, Kim HU, Soh MS, Lee Y, In JG, Kim HS, Kim YM, Yang DC, Wing RA, Lee DY, Paterson AH, Yang TJ.

Plant Biotechnol J. 2018 Mar 31. doi: 10.1111/pbi.12926. [Epub ahead of print]

3.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.

Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, Rosa Farias DD, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA.

Nat Genet. 2018 Feb;50(2):285-296. doi: 10.1038/s41588-018-0040-0. Epub 2018 Jan 22.

PMID:
29358651
4.

The asparagus genome sheds light on the origin and evolution of a young Y chromosome.

Harkess A, Zhou J, Xu C, Bowers JE, Van der Hulst R, Ayyampalayam S, Mercati F, Riccardi P, McKain MR, Kakrana A, Tang H, Ray J, Groenendijk J, Arikit S, Mathioni SM, Nakano M, Shan H, Telgmann-Rauber A, Kanno A, Yue Z, Chen H, Li W, Chen Y, Xu X, Zhang Y, Luo S, Chen H, Gao J, Mao Z, Pires JC, Luo M, Kudrna D, Wing RA, Meyers BC, Yi K, Kong H, Lavrijsen P, Sunseri F, Falavigna A, Ye Y, Leebens-Mack JH, Chen G.

Nat Commun. 2017 Nov 2;8(1):1279. doi: 10.1038/s41467-017-01064-8.

5.

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti.

Copetti D, Búrquez A, Bustamante E, Charboneau JLM, Childs KL, Eguiarte LE, Lee S, Liu TL, McMahon MM, Whiteman NK, Wing RA, Wojciechowski MF, Sanderson MJ.

Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):12003-12008. doi: 10.1073/pnas.1706367114. Epub 2017 Oct 23.

PMID:
29078296
6.

A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication.

Wu W, Liu X, Wang M, Meyer RS, Luo X, Ndjiondjop MN, Tan L, Zhang J, Wu J, Cai H, Sun C, Wang X, Wing RA, Zhu Z.

Nat Plants. 2017 May 8;3:17064. doi: 10.1038/nplants.2017.64.

PMID:
28481332
7.

Aflatoxin-free transgenic maize using host-induced gene silencing.

Thakare D, Zhang J, Wing RA, Cotty PJ, Schmidt MA.

Sci Adv. 2017 Mar 10;3(3):e1602382. doi: 10.1126/sciadv.1602382. eCollection 2017 Mar.

8.

Evolutionary analysis of the SUB1 locus across the Oryza genomes.

Dos Santos RS, Farias DDR, Pegoraro C, Rombaldi CV, Fukao T, Wing RA, de Oliveira AC.

Rice (N Y). 2017 Dec;10(1):4. doi: 10.1186/s12284-016-0140-3. Epub 2017 Feb 7.

9.

The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice.

Choi JY, Platts AE, Fuller DQ, Hsing YI, Wing RA, Purugganan MD.

Mol Biol Evol. 2017 Apr 1;34(4):969-979. doi: 10.1093/molbev/msx049.

10.

Rice SNP-seek database update: new SNPs, indels, and queries.

Mansueto L, Fuentes RR, Borja FN, Detras J, Abriol-Santos JM, Chebotarov D, Sanciangco M, Palis K, Copetti D, Poliakov A, Dubchak I, Solovyev V, Wing RA, Hamilton RS, Mauleon R, McNally KL, Alexandrov N.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1075-D1081. doi: 10.1093/nar/gkw1135. Epub 2016 Nov 29.

11.

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice.

Brozynska M, Copetti D, Furtado A, Wing RA, Crayn D, Fox G, Ishikawa R, Henry RJ.

Plant Biotechnol J. 2017 Jun;15(6):765-774. doi: 10.1111/pbi.12674. Epub 2017 Jan 23.

12.

Tracing ancestor rice of Suriname Maroons back to its African origin.

van Andel TR, Meyer RS, Aflitos SA, Carney JA, Veltman MA, Copetti D, Flowers JM, Havinga RM, Maat H, Purugganan MD, Wing RA, Schranz ME.

Nat Plants. 2016 Oct 3;2:16149. doi: 10.1038/nplants.2016.149.

PMID:
27694825
13.

The Dark Side of the Genome: Revealing the Native Transposable Element/Repeat Content of Eukaryotic Genomes.

Copetti D, Wing RA.

Mol Plant. 2016 Dec 5;9(12):1664-1666. doi: 10.1016/j.molp.2016.09.006. Epub 2016 Sep 28. No abstract available.

14.

Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data.

Zhang J, Chen LL, Sun S, Kudrna D, Copetti D, Li W, Mu T, Jiao WB, Xing F, Lee S, Talag J, Song JM, Du B, Xie W, Luo M, Maldonado CE, Goicoechea JL, Xiong L, Wu C, Xing Y, Zhou DX, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Hurtado BE, Danowitz A, Wing RA, Zhang Q.

Sci Data. 2016 Sep 13;3:160076. doi: 10.1038/sdata.2016.76.

15.

DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses.

Wicker T, Yu Y, Haberer G, Mayer KF, Marri PR, Rounsley S, Chen M, Zuccolo A, Panaud O, Wing RA, Roffler S.

Nat Commun. 2016 Sep 7;7:12790. doi: 10.1038/ncomms12790.

16.

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.

Zhang J, Chen LL, Xing F, Kudrna DA, Yao W, Copetti D, Mu T, Li W, Song JM, Xie W, Lee S, Talag J, Shao L, An Y, Zhang CL, Ouyang Y, Sun S, Jiao WB, Lv F, Du B, Luo M, Maldonado CE, Goicoechea JL, Xiong L, Wu C, Xing Y, Zhou DX, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Zhou ZW, Hurtado BE, Danowitz A, Wing RA, Zhang Q.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):E5163-71. doi: 10.1073/pnas.1611012113. Epub 2016 Aug 17.

17.

Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences.

Zhang J, Kudrna D, Mu T, Li W, Copetti D, Yu Y, Goicoechea JL, Lei Y, Wing RA.

Bioinformatics. 2016 Oct 15;32(20):3058-3064. Epub 2016 Jun 17.

18.

Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha.

Ray S, Bose LK, Ray J, Ngangkham U, Katara JL, Samantaray S, Behera L, Anumalla M, Singh ON, Chen M, Wing RA, Mohapatra T.

Mol Genet Genomics. 2016 Aug;291(4):1783-94. doi: 10.1007/s00438-016-1214-z. Epub 2016 Jun 14.

PMID:
27299359
19.

DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements.

Wang J, Yu Y, Tao F, Zhang J, Copetti D, Kudrna D, Talag J, Lee S, Wing RA, Fan C.

Genome Biol. 2016 May 6;17(1):92. doi: 10.1186/s13059-016-0954-8.

20.

The impact and origin of copy number variations in the Oryza species.

Bai Z, Chen J, Liao Y, Wang M, Liu R, Ge S, Wing RA, Chen M.

BMC Genomics. 2016 Mar 29;17:261. doi: 10.1186/s12864-016-2589-2.

21.

Evolution of plant genome architecture.

Wendel JF, Jackson SA, Meyers BC, Wing RA.

Genome Biol. 2016 Mar 1;17:37. doi: 10.1186/s13059-016-0908-1. Review.

22.

Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement.

De Vega JJ, Ayling S, Hegarty M, Kudrna D, Goicoechea JL, Ergon Å, Rognli OA, Jones C, Swain M, Geurts R, Lang C, Mayer KF, Rössner S, Yates S, Webb KJ, Donnison IS, Oldroyd GE, Wing RA, Caccamo M, Powell W, Abberton MT, Skøt L.

Sci Rep. 2015 Nov 30;5:17394. doi: 10.1038/srep17394.

23.

Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species.

Kim K, Lee SC, Lee J, Yu Y, Yang K, Choi BS, Koh HJ, Waminal NE, Choi HI, Kim NH, Jang W, Park HS, Lee J, Lee HO, Joh HJ, Lee HJ, Park JY, Perumal S, Jayakodi M, Lee YS, Kim B, Copetti D, Kim S, Kim S, Lim KB, Kim YD, Lee J, Cho KS, Park BS, Wing RA, Yang TJ.

Sci Rep. 2015 Oct 28;5:15655. doi: 10.1038/srep15655.

24.

Harvesting rice's dispensable genome.

Wing RA.

Genome Biol. 2015 Oct 1;16:217. doi: 10.1186/s13059-015-0787-x.

25.

Recurrent sequence exchange between homeologous grass chromosomes.

Wicker T, Wing RA, Schubert I.

Plant J. 2015 Nov;84(4):747-59. doi: 10.1111/tpj.13040.

26.

Genome and Comparative Transcriptomics of African Wild Rice Oryza longistaminata Provide Insights into Molecular Mechanism of Rhizomatousness and Self-Incompatibility.

Zhang Y, Zhang S, Liu H, Fu B, Li L, Xie M, Song Y, Li X, Cai J, Wan W, Kui L, Huang H, Lyu J, Dong Y, Wang W, Huang L, Zhang J, Yang Q, Shan Q, Li Q, Huang W, Tao D, Wang M, Chen M, Yu Y, Wing RA, Wang W, Hu F.

Mol Plant. 2015 Nov 2;8(11):1683-6. doi: 10.1016/j.molp.2015.08.006. Epub 2015 Sep 7. No abstract available.

27.

RiTE database: a resource database for genus-wide rice genomics and evolutionary biology.

Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Maldonado L CE, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de Oliveira A, Han B, Henry R, Hsing YI, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA.

BMC Genomics. 2015 Jul 22;16:538. doi: 10.1186/s12864-015-1762-3.

28.

Transposons play an important role in the evolution and diversification of centromeres among closely related species.

Gao D, Jiang N, Wing RA, Jiang J, Jackson SA.

Front Plant Sci. 2015 Apr 7;6:216. doi: 10.3389/fpls.2015.00216. eCollection 2015.

29.

Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution.

Geering AD, Maumus F, Copetti D, Choisne N, Zwickl DJ, Zytnicki M, McTaggart AR, Scalabrin S, Vezzulli S, Wing RA, Quesneville H, Teycheney PY.

Nat Commun. 2014 Nov 10;5:5269. doi: 10.1038/ncomms6269.

30.

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication.

Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KF, Rounsley S, Wing RA.

Nat Genet. 2014 Sep;46(9):982-8. doi: 10.1038/ng.3044. Epub 2014 Jul 27.

PMID:
25064006
31.

A reference genome for common bean and genome-wide analysis of dual domestications.

Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MM, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA.

Nat Genet. 2014 Jul;46(7):707-13. doi: 10.1038/ng.3008. Epub 2014 Jun 8.

32.

Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data.

Wang J, Wing RA.

Acta Crystallogr D Biol Crystallogr. 2014 May;70(Pt 5):1491-7. doi: 10.1107/S1399004714005318. Epub 2014 Apr 30.

33.

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

Zwickl DJ, Stein JC, Wing RA, Ware D, Sanderson MJ.

Syst Biol. 2014 Sep;63(5):645-59. doi: 10.1093/sysbio/syu027. Epub 2014 Apr 9.

PMID:
24721692
34.

Global genomic diversity of Oryza sativa varieties revealed by comparative physical mapping.

Wang X, Kudrna DA, Pan Y, Wang H, Liu L, Lin H, Zhang J, Song X, Goicoechea JL, Wing RA, Zhang Q, Luo M.

Genetics. 2014 Apr;196(4):937-49. doi: 10.1534/genetics.113.159970. Epub 2014 Jan 14.

35.

Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.

Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB.

Science. 2013 Dec 20;342(6165):1516-7. doi: 10.1126/science.1241130.

PMID:
24357320
36.

Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93-11 and evaluation of the two rice reference sequence assemblies.

Pan Y, Deng Y, Lin H, Kudrna DA, Wing RA, Li L, Zhang Q, Luo M.

Plant J. 2014 Mar;77(5):795-805. doi: 10.1111/tpj.12412. Epub 2014 Feb 3.

37.

Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion.

Jacquemin J, Ammiraju JS, Haberer G, Billheimer DD, Yu Y, Liu LC, Rivera LF, Mayer K, Chen M, Wing RA.

Mol Plant. 2014 Apr;7(4):642-56. doi: 10.1093/mp/sst149. Epub 2013 Nov 8.

38.

Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives.

Wang C, Shi X, Liu L, Li H, Ammiraju JS, Kudrna DA, Xiong W, Wang H, Dai Z, Zheng Y, Lai J, Jin W, Messing J, Bennetzen JL, Wing RA, Luo M.

Genetics. 2013 Nov;195(3):723-37. doi: 10.1534/genetics.113.157115. Epub 2013 Sep 13. Erratum in: Genetics. 2014 Jan;196(1):365.

39.

Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave.

Ortiz M, Legatzki A, Neilson JW, Fryslie B, Nelson WM, Wing RA, Soderlund CA, Pryor BM, Maier RM.

ISME J. 2014 Feb;8(2):478-91. doi: 10.1038/ismej.2013.159. Epub 2013 Sep 12.

40.

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. 2013 Aug 15;500(7462):335-9. doi: 10.1038/nature12309. Epub 2013 Jul 24.

41.

Evolution of a complex locus for terpene biosynthesis in solanum.

Matsuba Y, Nguyen TT, Wiegert K, Falara V, Gonzales-Vigil E, Leong B, Schäfer P, Kudrna D, Wing RA, Bolger AM, Usadel B, Tissier A, Fernie AR, Barry CS, Pichersky E.

Plant Cell. 2013 Jun;25(6):2022-36. doi: 10.1105/tpc.113.111013. Epub 2013 Jun 11.

42.

High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences.

Zhang C, Wang J, Marowsky NC, Long M, Wing RA, Fan C.

Genome Biol Evol. 2013;5(5):1038-48. doi: 10.1093/gbe/evt071.

43.

The Reference Genome of the Halophytic Plant Eutrema salsugineum.

Yang R, Jarvis DE, Chen H, Beilstein MA, Grimwood J, Jenkins J, Shu S, Prochnik S, Xin M, Ma C, Schmutz J, Wing RA, Mitchell-Olds T, Schumaker KS, Wang X.

Front Plant Sci. 2013 Mar 21;4:46. doi: 10.3389/fpls.2013.00046. eCollection 2013.

44.

The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question.

Jacquemin J, Bhatia D, Singh K, Wing RA.

Curr Opin Plant Biol. 2013 May;16(2):147-56. doi: 10.1016/j.pbi.2013.02.014. Epub 2013 Mar 19.

PMID:
23518283
45.

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.

Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C, Chen C, Zhang W, Sun S, Liao Y, Zhang X, Yang L, Song C, Wang M, Shi J, Liu G, Liu J, Zhou H, Zhou W, Yu Q, An N, Chen Y, Cai Q, Wang B, Liu B, Min J, Huang Y, Wu H, Li Z, Zhang Y, Yin Y, Song W, Jiang J, Jackson SA, Wing RA, Wang J, Chen M.

Nat Commun. 2013;4:1595. doi: 10.1038/ncomms2596.

46.

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.

Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):5241-6. doi: 10.1073/pnas.1220766110. Epub 2013 Mar 11.

47.

Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids.

Koo HJ, McDowell ET, Ma X, Greer KA, Kapteyn J, Xie Z, Descour A, Kim H, Yu Y, Kudrna D, Wing RA, Soderlund CA, Gang DR.

BMC Plant Biol. 2013 Feb 15;13:27. doi: 10.1186/1471-2229-13-27.

48.

Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ.

Ortiz M, Neilson JW, Nelson WM, Legatzki A, Byrne A, Yu Y, Wing RA, Soderlund CA, Pryor BM, Pierson LS 3rd, Maier RM.

Microb Ecol. 2013 Feb;65(2):371-83. doi: 10.1007/s00248-012-0143-6. Epub 2012 Dec 9.

PMID:
23224253
49.

Comparative sequence analysis of the Ghd7 orthologous regions revealed movement of Ghd7 in the grass genomes.

Yang L, Liu T, Li B, Sui Y, Chen J, Shi J, Wing RA, Chen M.

PLoS One. 2012;7(11):e50236. doi: 10.1371/journal.pone.0050236. Epub 2012 Nov 21.

50.

The hexameric helicase DnaB adopts a nonplanar conformation during translocation.

Itsathitphaisarn O, Wing RA, Eliason WK, Wang J, Steitz TA.

Cell. 2012 Oct 12;151(2):267-77. doi: 10.1016/j.cell.2012.09.014. Epub 2012 Sep 27.

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