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Items: 25

1.

Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species.

Zhu T, Wang L, You FM, Rodriguez JC, Deal KR, Chen L, Li J, Chakraborty S, Balan B, Jiang CZ, Brown PJ, Leslie CA, Aradhya MK, Dandekar AM, McGuire PE, Kluepfel D, Dvorak J, Luo MC.

Hortic Res. 2019 Mar 25;6:55. doi: 10.1038/s41438-019-0139-1. eCollection 2019.

2.

Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps.

Zhu T, Wang L, Rodriguez JC, Deal KR, Avni R, Distelfeld A, McGuire PE, Dvorak J, Luo MC.

G3 (Bethesda). 2019 Mar 7;9(3):619-624. doi: 10.1534/g3.118.200902.

3.

Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B.

Dvorak J, Wang L, Zhu T, Jorgensen CM, Luo MC, Deal KR, Gu YQ, Gill BS, Distelfeld A, Devos KM, Qi P, McGuire PE.

Theor Appl Genet. 2018 Nov;131(11):2451-2462. doi: 10.1007/s00122-018-3165-8. Epub 2018 Aug 23.

4.

Analysis of Brachypodium genomes with genome-wide optical maps.

Zhu T, Hu Z, Rodriguez JC, Deal KR, Dvorak J, Vogel JP, Liu Z, Luo MC.

Genome. 2018 Aug;61(8):559-565. doi: 10.1139/gen-2018-0013. Epub 2018 Jun 8.

PMID:
29883550
5.

Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size.

Dvorak J, Wang L, Zhu T, Jorgensen CM, Deal KR, Dai X, Dawson MW, Müller HG, Luo MC, Ramasamy RK, Dehghani H, Gu YQ, Gill BS, Distelfeld A, Devos KM, Qi P, You FM, Gulick PJ, McGuire PE.

Plant J. 2018 Aug;95(3):487-503. doi: 10.1111/tpj.13964. Epub 2018 Jun 17.

PMID:
29770515
6.

Introgression of the Aegilops speltoides Su1-Ph1 Suppressor into Wheat.

Li H, Deal KR, Luo MC, Ji W, Distelfeld A, Dvorak J.

Front Plant Sci. 2017 Dec 20;8:2163. doi: 10.3389/fpls.2017.02163. eCollection 2017.

7.

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J.

Nature. 2017 Nov 23;551(7681):498-502. doi: 10.1038/nature24486. Epub 2017 Nov 15.

PMID:
29143815
8.

Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes.

Xie J, Huo N, Zhou S, Wang Y, Guo G, Deal KR, Ouyang S, Liang Y, Wang Z, Xiao L, Zhu T, Hu T, Tiwari V, Zhang J, Li H, Ni Z, Yao Y, Peng H, Zhang S, Anderson OD, McGuire PE, Dvorak J, Luo MC, Liu Z, Gu YQ, Sun Q.

J Genet Genomics. 2017 Jan 20;44(1):51-61. doi: 10.1016/j.jgg.2016.09.005. Epub 2016 Oct 5.

PMID:
27765484
9.

Optical Nano-mapping and Analysis of Plant Genomes.

Luo MC, Deal KR, Murray A, Zhu T, Hastie AR, Stedman W, Sadowski H, Saghbini M.

Methods Mol Biol. 2016;1429:103-17. doi: 10.1007/978-1-4939-3622-9_9.

PMID:
27511170
10.

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.

Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, Jorgensen CM, Zhang Y, McGuire PE, Pasternak S, Stein JC, Ware D, Kramer M, McCombie WR, Kianian SF, Martis MM, Mayer KF, Sehgal SK, Li W, Gill BS, Bevan MW, Simková H, Dolezel J, Weining S, Lazo GR, Anderson OD, Dvorak J.

Proc Natl Acad Sci U S A. 2013 May 7;110(19):7940-5. doi: 10.1073/pnas.1219082110. Epub 2013 Apr 22.

11.

Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome.

Hastie AR, Dong L, Smith A, Finklestein J, Lam ET, Huo N, Cao H, Kwok PY, Deal KR, Dvorak J, Luo MC, Gu Y, Xiao M.

PLoS One. 2013;8(2):e55864. doi: 10.1371/journal.pone.0055864. Epub 2013 Feb 6.

12.

Insular organization of gene space in grass genomes.

Gottlieb A, Müller HG, Massa AN, Wanjugi H, Deal KR, You FM, Xu X, Gu YQ, Luo MC, Anderson OD, Chan AP, Rabinowicz P, Devos KM, Dvorak J.

PLoS One. 2013;8(1):e54101. doi: 10.1371/journal.pone.0054101. Epub 2013 Jan 11.

13.

Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms.

You FM, Deal KR, Wang J, Britton MT, Fass JN, Lin D, Dandekar AM, Leslie CA, Aradhya M, Luo MC, Dvorak J.

BMC Genomics. 2012 Jul 31;13:354. doi: 10.1186/1471-2164-13-354.

14.

The origin of spelt and free-threshing hexaploid wheat.

Dvorak J, Deal KR, Luo MC, You FM, von Borstel K, Dehghani H.

J Hered. 2012 May-Jun;103(3):426-41. doi: 10.1093/jhered/esr152. Epub 2012 Feb 29.

PMID:
22378960
15.

Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes.

Massa AN, Wanjugi H, Deal KR, O'Brien K, You FM, Maiti R, Chan AP, Gu YQ, Luo MC, Anderson OD, Rabinowicz PD, Dvorak J, Devos KM.

Mol Biol Evol. 2011 Sep;28(9):2537-47. doi: 10.1093/molbev/msr080. Epub 2011 Apr 6.

16.

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence.

You FM, Huo N, Deal KR, Gu YQ, Luo MC, McGuire PE, Dvorak J, Anderson OD.

BMC Genomics. 2011 Jan 25;12:59. doi: 10.1186/1471-2164-12-59.

17.

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes.

Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Deal KR, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo H, Huo N, Lazo GR, Luo MC, Ma YQ, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J.

BMC Genomics. 2010 Dec 14;11:702. doi: 10.1186/1471-2164-11-702.

18.

A new implementation of high-throughput five-dimensional clone pooling strategy for BAC library screening.

You FM, Luo MC, Xu K, Deal KR, Anderson OD, Dvorak J.

BMC Genomics. 2010 Dec 6;11:692. doi: 10.1186/1471-2164-11-692.

19.

Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS.

Fleury D, Luo MC, Dvorak J, Ramsay L, Gill BS, Anderson OD, You FM, Shoaei Z, Deal KR, Langridge P.

BMC Genomics. 2010 Jun 17;11:382. doi: 10.1186/1471-2164-11-382.

20.

Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae.

Luo MC, Deal KR, Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo HY, Huo N, Lazo G, Ma Y, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J.

Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15780-5. doi: 10.1073/pnas.0908195106. Epub 2009 Aug 26.

21.
22.

Discovery and mapping of wheat Ph1 suppressors.

Dvorak J, Deal KR, Luo MC.

Genetics. 2006 Sep;174(1):17-27. Epub 2006 May 15.

23.
24.

Comparative genetic maps reveal extreme crossover localization in the Aegilops speltoides chromosomes.

Luo MC, Deal KR, Yang ZL, Dvorak J.

Theor Appl Genet. 2005 Oct;111(6):1098-106. Epub 2005 Oct 11.

PMID:
16088396
25.

Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum L.).

Zhang D, Choi DW, Wanamaker S, Fenton RD, Chin A, Malatrasi M, Turuspekov Y, Walia H, Akhunov ED, Kianian P, Otto C, Simons K, Deal KR, Echenique V, Stamova B, Ross K, Butler GE, Strader L, Verhey SD, Johnson R, Altenbach S, Kothari K, Tanaka C, Shah MM, Laudencia-Chingcuanco D, Han P, Miller RE, Crossman CC, Chao S, Lazo GR, Klueva N, Gustafson JP, Kianian SF, Dubcovsky J, Walker-Simmons MK, Gill KS, Dvorák J, Anderson OD, Sorrells ME, McGuire PE, Qualset CO, Nguyen HT, Close TJ.

Genetics. 2004 Oct;168(2):595-608.

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