Jeffrey L Bennetzen

Jeffrey L Bennetzen

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Jeffrey L Bennetzen

Jeffrey L Bennetzen

Publications by authors named "Jeffrey L Bennetzen"

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Draft Genome Sequence of a Serratia marcescens Strain Isolated from the Pitcher Fluids of a Pitcher Plant.

Microbiol Resour Announc 2020 Jan 9;9(2). Epub 2020 Jan 9.

Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA

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http://dx.doi.org/10.1128/MRA.01216-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6952653PMC
January 2020

Genome Sequence Analysis of sp. C6, Found in the Pitcher Fluids of .

Microbiol Resour Announc 2020 Jan 16;9(3). Epub 2020 Jan 16.

Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA

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http://dx.doi.org/10.1128/MRA.01214-19DOI Listing
January 2020

Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis.

BMC Genomics 2019 Jul 31;20(1):624. Epub 2019 Jul 31.

State Key Laboratory of Tea Plant Biology and Utilization/International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, West 130 Changjiang Road, Hefei, 230036, Anhui, People's Republic of China.

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5988-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6670155PMC
July 2019

Genome sequence of Malania oleifera, a tree with great value for nervonic acid production.

Gigascience 2019 02;8(2)

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.

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https://academic.oup.com/gigascience/advance-article/doi/10.
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http://dx.doi.org/10.1093/gigascience/giy164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377399PMC
February 2019

Circular RNA architecture and differentiation during leaf bud to young leaf development in tea (Camellia sinensis).

Planta 2018 Dec 20;248(6):1417-1429. Epub 2018 Aug 20.

State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.

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http://link.springer.com/10.1007/s00425-018-2983-x
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http://dx.doi.org/10.1007/s00425-018-2983-xDOI Listing
December 2018

Birth and Death of LTR-Retrotransposons in .

Genetics 2018 11 29;210(3):1039-1051. Epub 2018 Aug 29.

Department of Statistics, University of California, Davis, California 95616.

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http://dx.doi.org/10.1534/genetics.118.301198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218219PMC
November 2018

Analysis of retrotransposon abundance, diversity and distribution in holocentric Eleocharis (Cyperaceae) genomes.

Ann Bot 2018 08;122(2):279-290

Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Center for Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil.

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http://dx.doi.org/10.1093/aob/mcy066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6070107PMC
August 2018

Species-Associated Differences in the Below-Ground Microbiomes of Wild and Domesticated .

Front Plant Sci 2018 21;9:1183. Epub 2018 Aug 21.

Department of Genetics, University of Georgia, Athens, GA, United States.

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http://dx.doi.org/10.3389/fpls.2018.01183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6111228PMC
August 2018

Discovery of Lineage-Specific Genome Change in Rice Through Analysis of Resequencing Data.

Genetics 2018 06 19;209(2):617-626. Epub 2018 Apr 19.

Department of Genetics, University of Georgia, Athens, Georgia 30602

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http://dx.doi.org/10.1534/genetics.118.300848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5972431PMC
June 2018

Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana.

BMC Genomics 2018 Jun 27;19(1):500. Epub 2018 Jun 27.

Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, People's Republic of China.

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http://dx.doi.org/10.1186/s12864-018-4878-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6020451PMC
June 2018

Distinguishing friends, foes, and freeloaders in giant genomes.

Curr Opin Genet Dev 2018 04 12;49:49-55. Epub 2018 Mar 12.

Department of Genetics, University of Georgia, Athens, GA 30602, United States.

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http://dx.doi.org/10.1016/j.gde.2018.02.013DOI Listing
April 2018

The Hardy Rubber Tree Genome Provides Insights into the Evolution of Polyisoprene Biosynthesis.

Mol Plant 2018 03 9;11(3):429-442. Epub 2017 Dec 9.

Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China. Electronic address:

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http://dx.doi.org/10.1016/j.molp.2017.11.014DOI Listing
March 2018

Relationships between Gene Structure and Genome Instability in Flowering Plants.

Mol Plant 2018 03 17;11(3):407-413. Epub 2018 Feb 17.

State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China; Department of Genetics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1016/j.molp.2018.02.003DOI Listing
March 2018

Integrating transcriptome and microRNA analysis identifies genes and microRNAs for AHO-induced systemic acquired resistance in N. tabacum.

Sci Rep 2017 10 2;7(1):12504. Epub 2017 Oct 2.

Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, P. R. China.

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http://dx.doi.org/10.1038/s41598-017-12249-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624873PMC
October 2017

Developmental programmed cell death during asymmetric microsporogenesis in holocentric species of Rhynchospora (Cyperaceae).

J Exp Bot 2016 10 4;67(18):5391-5401. Epub 2016 Aug 4.

Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Center of Biological Sciences, State University of Londrina, Londrina 86057-970, Paraná, Brazil

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049389PMC
http://dx.doi.org/10.1093/jxb/erw300DOI Listing
October 2016

Teff, an Orphan Cereal in the Chloridoideae, Provides Insights into the Evolution of Storage Proteins in Grasses.

Genome Biol Evol 2016 06 13;8(6):1712-21. Epub 2016 Jun 13.

Waksman Institute of Microbiology, Rutgers University.

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http://dx.doi.org/10.1093/gbe/evw117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4943188PMC
June 2016

Grass genome structure and evolution.

Genome Dyn 2008 ;4:41-56

Waksman Institute of Microbiology, Rutgers University, Piscataway, N.J.; USA.

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https://www.karger.com/Article/FullText/126005
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http://dx.doi.org/10.1159/000126005DOI Listing
April 2016

Brachypodium distachyon and Setaria viridis: Model Genetic Systems for the Grasses.

Annu Rev Plant Biol 2015 22;66:465-85. Epub 2015 Jan 22.

Donald Danforth Plant Science Center, St. Louis, Missouri 63132; email:

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http://dx.doi.org/10.1146/annurev-arplant-042811-105528DOI Listing
December 2015

Adaptive evolution of signaling partners.

Mol Biol Evol 2015 Apr 6;32(4):998-1007. Epub 2015 Jan 6.

Department of Biology, University of North Carolina, Chapel Hill Department of Pharmacology, University of North Carolina, Chapel Hill

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http://dx.doi.org/10.1093/molbev/msu404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379405PMC
April 2015

Current status and prospects for the study of Nicotiana genomics, genetics, and nicotine biosynthesis genes.

Mol Genet Genomics 2015 Feb 13;290(1):11-21. Epub 2015 Jan 13.

Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, People's Republic of China,

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http://link.springer.com/content/pdf/10.1007/s00438-015-0989
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http://link.springer.com/10.1007/s00438-015-0989-7
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http://dx.doi.org/10.1007/s00438-015-0989-7DOI Listing
February 2015

Recurrent loss of specific introns during angiosperm evolution.

PLoS Genet 2014 Dec 4;10(12):e1004843. Epub 2014 Dec 4.

Department of Genetics, University of Georgia, Athens, Georgia, United States of America; Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Kunming, Yunnan, P.R. China.

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http://dx.doi.org/10.1371/journal.pgen.1004843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256211PMC
December 2014

Rapid diversification of five Oryza AA genomes associated with rice adaptation.

Proc Natl Acad Sci U S A 2014 Nov 3;111(46):E4954-62. Epub 2014 Nov 3.

Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;

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http://dx.doi.org/10.1073/pnas.1418307111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246335PMC
November 2014

Variation in allelic expression associated with a recombination hotspot in Zea mays.

Plant J 2014 Aug 9;79(3):375-84. Epub 2014 Jul 9.

Department of Biology, West Virginia University, Morgantown, WV, 26506, USA; Department of Genetics, The University of Georgia, Athens, GA, 30602, USA.

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http://dx.doi.org/10.1111/tpj.12537DOI Listing
August 2014

The contributions of transposable elements to the structure, function, and evolution of plant genomes.

Annu Rev Plant Biol 2014 21;65:505-30. Epub 2014 Feb 21.

Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.

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http://www.annualreviews.org/doi/10.1146/annurev-arplant-050
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http://dx.doi.org/10.1146/annurev-arplant-050213-035811DOI Listing
July 2014

Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair.

Proc Natl Acad Sci U S A 2014 May 23;111(18):6684-9. Epub 2014 Apr 23.

Department of Genetics, University of Georgia, Athens, GA 30602.

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http://dx.doi.org/10.1073/pnas.1321854111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4020087PMC
May 2014

Isolation and bioinformatic analysis of a novel transposable element, ISCbe4, from the hyperthermophilic bacterium, Caldicellulosiruptor bescii.

J Ind Microbiol Biotechnol 2013 Dec 1;40(12):1443-8. Epub 2013 Oct 1.

Department of Genetics, University of Georgia, Athens, GA, 30602, USA.

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http://link.springer.com/10.1007/s10295-013-1345-8
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http://dx.doi.org/10.1007/s10295-013-1345-8DOI Listing
December 2013

Isolation and diversity analysis of resistance gene homologues from switchgrass.

G3 (Bethesda) 2013 Jun 21;3(6):1031-42. Epub 2013 Jun 21.

Department of Genetics, The University of Georgia, Athens, Georgia 30602, USA.

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http://dx.doi.org/10.1534/g3.112.005447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689800PMC
June 2013

Permanent genetic resources added to molecular ecology resources database 1 October 2012-30 November 2012.

Mol Ecol Resour 2013 Mar 25;13(2):341-3. Epub 2013 Jan 25.

Molecular Ecology Resources Editorial Office, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.

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http://doi.wiley.com/10.1111/1755-0998.12061
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http://dx.doi.org/10.1111/1755-0998.12061DOI Listing
March 2013

Centromere retention and loss during the descent of maize from a tetraploid ancestor.

Proc Natl Acad Sci U S A 2012 Dec 29;109(51):21004-9. Epub 2012 Nov 29.

Department of Genetics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1073/pnas.1218668109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529015PMC
December 2012

G protein activation without a GEF in the plant kingdom.

PLoS Genet 2012 Jun 28;8(6):e1002756. Epub 2012 Jun 28.

Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1002756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386157PMC
June 2012

Dynamic gene copy number variation in collinear regions of grass genomes.

Mol Biol Evol 2012 Feb 14;29(2):861-71. Epub 2011 Oct 14.

Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, New Jersey, USA.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msr261DOI Listing
February 2012

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.

Authors:
Jo Ann Banks Tomoaki Nishiyama Mitsuyasu Hasebe John L Bowman Michael Gribskov Claude dePamphilis Victor A Albert Naoki Aono Tsuyoshi Aoyama Barbara A Ambrose Neil W Ashton Michael J Axtell Elizabeth Barker Michael S Barker Jeffrey L Bennetzen Nicholas D Bonawitz Clint Chapple Chaoyang Cheng Luiz Gustavo Guedes Correa Michael Dacre Jeremy DeBarry Ingo Dreyer Marek Elias Eric M Engstrom Mark Estelle Liang Feng Cédric Finet Sandra K Floyd Wolf B Frommer Tomomichi Fujita Lydia Gramzow Michael Gutensohn Jesper Harholt Mitsuru Hattori Alexander Heyl Tadayoshi Hirai Yuji Hiwatashi Masaki Ishikawa Mineko Iwata Kenneth G Karol Barbara Koehler Uener Kolukisaoglu Minoru Kubo Tetsuya Kurata Sylvie Lalonde Kejie Li Ying Li Amy Litt Eric Lyons Gerard Manning Takeshi Maruyama Todd P Michael Koji Mikami Saori Miyazaki Shin-ichi Morinaga Takashi Murata Bernd Mueller-Roeber David R Nelson Mari Obara Yasuko Oguri Richard G Olmstead Naoko Onodera Bent Larsen Petersen Birgit Pils Michael Prigge Stefan A Rensing Diego Mauricio Riaño-Pachón Alison W Roberts Yoshikatsu Sato Henrik Vibe Scheller Burkhard Schulz Christian Schulz Eugene V Shakirov Nakako Shibagaki Naoki Shinohara Dorothy E Shippen Iben Sørensen Ryo Sotooka Nagisa Sugimoto Mamoru Sugita Naomi Sumikawa Milos Tanurdzic Günter Theissen Peter Ulvskov Sachiko Wakazuki Jing-Ke Weng William W G T Willats Daniel Wipf Paul G Wolf Lixing Yang Andreas D Zimmer Qihui Zhu Therese Mitros Uffe Hellsten Dominique Loqué Robert Otillar Asaf Salamov Jeremy Schmutz Harris Shapiro Erika Lindquist Susan Lucas Daniel Rokhsar Igor V Grigoriev

Science 2011 May 5;332(6032):960-3. Epub 2011 May 5.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.

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http://sites.psu.edu/axtell/wp-content/uploads/sites/21458/2
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http://www.sciencemag.org/cgi/doi/10.1126/science.1203810
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http://dx.doi.org/10.1126/science.1203810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166216PMC
May 2011

Transposable element origins of epigenetic gene regulation.

Curr Opin Plant Biol 2011 Apr 4;14(2):156-61. Epub 2011 Apr 4.

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.pbi.2011.01.003DOI Listing
April 2011

Epigenetics of the epigenome.

Curr Opin Plant Biol 2011 Apr 12;14(2):113-5. Epub 2011 Apr 12.

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http://dx.doi.org/10.1016/j.pbi.2011.03.015DOI Listing
April 2011

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 April 2010 - 31 May 2010.

Authors:
K Andree Jan Axtner M J Bagley E J Barlow T J C Beebee Jeffrey L Bennetzen Eldredge Bermingham M C Boisselier-Dubayle Christine A Bozarth Christopher P Brooks R P Brown Gaetano Catanese S Cavers Ivania Ceron-Souza Solomon T C Chak M N Chan P Charles-Dominique C Y Chen J D Chen Leah Chinchilla D DA Silva S Dafreville F Daunt H Delatte T Dorge N Duncan J D Durand D Duvernell Matt Estep Sigang Fan R Fattahi Oscar Flores Villela Yokking Fong H Fréville Victoria Funes C Gallardo-Escarate K N Ganeshaiah M R Ghaffari C Girod B J Gomez-Moliner Gracia P Gonzalez-Porter A Gosa F Govers F Guérin Diarah Guindo Frank Hailer P A Haye Kim A Hoelmer S Hofmann Yan Hong Chaoqun Hu S W Huang L Humeau Carlos Infante S A Jackson E Jacobsen A Jowkar M Kafi M J Kermani Hyojoong Kim Kyung Seok Kim Min-Young Kim W Knibb Ousmane A Koita H Korpelainen J Lambourdiere Eloisa Lasso R Leblois Hang Lee Seunghwan Lee F C C Leung Kenneth M Y Leung Chunhong Li Y Li Dietmar Lieckfeldt M Lizana W J Loughry Peng Luo M J Madeira P Mahmoodi Jesús E Maldonado M Mardi O Mendes G Miehe Peter Muth D Nacci L Naveen Kumar Wai-Chuen Ng T Pailler Heiko K Parzies Laura Perez M Pfunder M Pietiläinen S M Pirseyedi D Porta J Porta J M Porta S Quilici F P Rakotoarivelo B T Ramesha G Ravikanth B Riéra A M Risterucci D A Roberts S Samadi V Sarasola-Puente E Sarrazin C Sarthou Anke Schmidt N I Segovia K N Shen C Simiand Muhammad Hidayat Bin Sman T Solhoy Simone Sommer R C Sumangala Ramona Taubert T Tejangkura A Telford A Testa C Tollon-Cordet W N Tzeng R Uma Shaanker T A J Van Der Lee Thomas A VAN Mourik R Vasudeva T C Wai R L Wang Mark E Welch Eva Weltzien A Whitehead Anastasia Woodard Jianjun Xia M Zeinolabedini Lvping Zhang

Mol Ecol Resour 2010 Nov;10(6):1098-105

IRTA Sant Carles de la Rapita. Ctra Poble Nou Km5.5, 43540 Sant Carles de la Rapita, Spain.

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http://doi.wiley.com/10.1111/j.1755-0998.2010.02898.x
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http://dx.doi.org/10.1111/j.1755-0998.2010.02898.xDOI Listing
November 2010

Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza.

Plant J 2010 Aug 6;63(3):430-42. Epub 2010 May 6.

Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USABiodiversity Synthesis Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USADepartment of Genetics, University of Georgia, Athens, GA 30602-7223, USAState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, ChinaDepartment of Agronomy, Purdue University, West Lafayette, IN 47907-2054, USADepartment of Horticulture, Michigan State University, East Lansing, MI 48823, USA.

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http://dx.doi.org/10.1111/j.1365-313X.2010.04251.xDOI Listing
August 2010

On the tetraploid origin of the maize genome.

Comp Funct Genomics 2004 ;5(3):281-4

Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA.

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http://dx.doi.org/10.1002/cfg.395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447450PMC
June 2010

An examination of targeted gene neighborhoods in strawberry.

BMC Plant Biol 2010 May 4;10:81. Epub 2010 May 4.

Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA.

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http://dx.doi.org/10.1186/1471-2229-10-81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890015PMC
May 2010

Distribution, diversity, evolution, and survival of Helitrons in the maize genome.

Proc Natl Acad Sci U S A 2009 Nov 19;106(47):19922-7. Epub 2009 Nov 19.

Department of Genetics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1073/pnas.0908008106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785268PMC
November 2009

The B73 maize genome: complexity, diversity, and dynamics.

Authors:
Patrick S Schnable Doreen Ware Robert S Fulton Joshua C Stein Fusheng Wei Shiran Pasternak Chengzhi Liang Jianwei Zhang Lucinda Fulton Tina A Graves Patrick Minx Amy Denise Reily Laura Courtney Scott S Kruchowski Chad Tomlinson Cindy Strong Kim Delehaunty Catrina Fronick Bill Courtney Susan M Rock Eddie Belter Feiyu Du Kyung Kim Rachel M Abbott Marc Cotton Andy Levy Pamela Marchetto Kerri Ochoa Stephanie M Jackson Barbara Gillam Weizu Chen Le Yan Jamey Higginbotham Marco Cardenas Jason Waligorski Elizabeth Applebaum Lindsey Phelps Jason Falcone Krishna Kanchi Thynn Thane Adam Scimone Nay Thane Jessica Henke Tom Wang Jessica Ruppert Neha Shah Kelsi Rotter Jennifer Hodges Elizabeth Ingenthron Matt Cordes Sara Kohlberg Jennifer Sgro Brandon Delgado Kelly Mead Asif Chinwalla Shawn Leonard Kevin Crouse Kristi Collura Dave Kudrna Jennifer Currie Ruifeng He Angelina Angelova Shanmugam Rajasekar Teri Mueller Rene Lomeli Gabriel Scara Ara Ko Krista Delaney Marina Wissotski Georgina Lopez David Campos Michele Braidotti Elizabeth Ashley Wolfgang Golser HyeRan Kim Seunghee Lee Jinke Lin Zeljko Dujmic Woojin Kim Jayson Talag Andrea Zuccolo Chuanzhu Fan Aswathy Sebastian Melissa Kramer Lori Spiegel Lidia Nascimento Theresa Zutavern Beth Miller Claude Ambroise Stephanie Muller Will Spooner Apurva Narechania Liya Ren Sharon Wei Sunita Kumari Ben Faga Michael J Levy Linda McMahan Peter Van Buren Matthew W Vaughn Kai Ying Cheng-Ting Yeh Scott J Emrich Yi Jia Ananth Kalyanaraman An-Ping Hsia W Brad Barbazuk Regina S Baucom Thomas P Brutnell Nicholas C Carpita Cristian Chaparro Jer-Ming Chia Jean-Marc Deragon James C Estill Yan Fu Jeffrey A Jeddeloh Yujun Han Hyeran Lee Pinghua Li Damon R Lisch Sanzhen Liu Zhijie Liu Dawn Holligan Nagel Maureen C McCann Phillip SanMiguel Alan M Myers Dan Nettleton John Nguyen Bryan W Penning Lalit Ponnala Kevin L Schneider David C Schwartz Anupma Sharma Carol Soderlund Nathan M Springer Qi Sun Hao Wang Michael Waterman Richard Westerman Thomas K Wolfgruber Lixing Yang Yeisoo Yu Lifang Zhang Shiguo Zhou Qihui Zhu Jeffrey L Bennetzen R Kelly Dawe Jiming Jiang Ning Jiang Gernot G Presting Susan R Wessler Srinivas Aluru Robert A Martienssen Sandra W Clifton W Richard McCombie Rod A Wing Richard K Wilson

Science 2009 Nov;326(5956):1112-5

Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.

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http://www.dawelab.org/wp-content/uploads/2011/03/schnable-2
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http://www.sciencemag.org/cgi/doi/10.1126/science.1178534
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http://dx.doi.org/10.1126/science.1178534DOI Listing
November 2009

Structure-based discovery and description of plant and animal Helitrons.

Proc Natl Acad Sci U S A 2009 Aug 21;106(31):12832-7. Epub 2009 Jul 21.

Department of Genetics, University of Georgia, Athens, GA 30602, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0905563106
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http://dx.doi.org/10.1073/pnas.0905563106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2722332PMC
August 2009

The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes.

Plant Methods 2009 Jun 19;5. Epub 2009 Jun 19.

Department of Plant Biology, The University of Georgia, Athens, Georgia 30602-7271, USA.

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http://plantmethods.biomedcentral.com/articles/10.1186/1746-
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http://dx.doi.org/10.1186/1746-4811-5-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705364PMC
June 2009

Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome.

Genome Res 2009 Feb 24;19(2):243-54. Epub 2008 Nov 24.

Department of Genetics, University of Georgia, Athens, Georgia 30602-7223, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.083360.108
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http://dx.doi.org/10.1101/gr.083360.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652206PMC
February 2009

Biology and the beasts: individual investigator-driven research in the megaprojects era.

Trends Genet 2009 Feb 8;25(2):57-9. Epub 2008 Dec 8.

Department of Genetics, Davison Life Sciences Complex, University of Georgia, Athens, GA 30602-7223, USA.

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February 2009

Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes.

Proc Natl Acad Sci U S A 2009 Feb 22;106(6):2071-6. Epub 2009 Jan 22.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1073/pnas.0812798106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629783PMC
February 2009

Foxtail millet: a sequence-driven grass model system.

Plant Physiol 2009 Jan;149(1):137-41

Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078, USA.

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http://dx.doi.org/10.1104/pp.108.129627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613750PMC
January 2009

Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster.

Genome Res 2008 Dec 21;18(12):1918-23. Epub 2008 Aug 21.

Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.

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http://dx.doi.org/10.1101/gr.078766.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593579PMC
December 2008

Enchilada redux: how complete is your genome sequence?

New Phytol 2008 Jul;179(2):249-50

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July 2008

A unified classification system for eukaryotic transposable elements.

Nat Rev Genet 2007 Dec;8(12):973-82

Institute of Plant Biology, University Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland.

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http://dx.doi.org/10.1038/nrg2165DOI Listing
December 2007

Evolutionary history and positional shift of a rice centromere.

Genetics 2007 Oct 29;177(2):1217-20. Epub 2007 Jul 29.

Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA.

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http://www.genetics.org/cgi/doi/10.1534/genetics.107.078709
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034625PMC
October 2007

A GeneTrek analysis of the maize genome.

Proc Natl Acad Sci U S A 2007 Jul 5;104(28):11844-9. Epub 2007 Jul 5.

Department of Genetics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1073/pnas.0704258104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913904PMC
July 2007

Identification of stress-responsive genes in an indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings.

J Exp Bot 2007 28;58(2):253-65. Epub 2006 Nov 28.

Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad-500046, AP, India.

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http://dx.doi.org/10.1093/jxb/erl213DOI Listing
April 2007

Patterns in grass genome evolution.

Curr Opin Plant Biol 2007 Apr 8;10(2):176-81. Epub 2007 Feb 8.

Department of Genetics, University of Georgia, Athens, Georgia 30602-7223, USA.

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http://dx.doi.org/10.1016/j.pbi.2007.01.010DOI Listing
April 2007

Plant centromere organization: a dynamic structure with conserved functions.

Trends Genet 2007 Mar 1;23(3):134-9. Epub 2007 Feb 1.

Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA.

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March 2007

The genetic map of finger millet, Eleusine coracana.

Theor Appl Genet 2007 Jan 14;114(2):321-32. Epub 2006 Nov 14.

John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.

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http://dx.doi.org/10.1007/s00122-006-0435-7DOI Listing
January 2007

Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution.

Proc Natl Acad Sci U S A 2006 Nov 13;103(47):17638-43. Epub 2006 Nov 13.

Department of Genetics, University of Georgia, Athens, GA 30602-7223, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0605618103
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693799PMC
November 2006

Promoter mutations of an essential gene for pollen development result in disease resistance in rice.

Genes Dev 2006 May 28;20(10):1250-5. Epub 2006 Apr 28.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.

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http://dx.doi.org/10.1101/gad.1416306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1472899PMC
May 2006

The maize genome as a model for efficient sequence analysis of large plant genomes.

Curr Opin Plant Biol 2006 Apr 3;9(2):149-56. Epub 2006 Feb 3.

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.

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April 2006

Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice.

Proc Natl Acad Sci U S A 2006 Jan 28;103(2):383-8. Epub 2005 Dec 28.

Department of Genetics, University of Georgia, Athens, GA 30602, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1326179PMC
January 2006

Transposable elements, gene creation and genome rearrangement in flowering plants.

Curr Opin Genet Dev 2005 Dec 10;15(6):621-7. Epub 2005 Oct 10.

Department of Genetics, University of Georgia, Athens, GA 40602-7223, USA.

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December 2005

Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat.

Proc Natl Acad Sci U S A 2005 Dec 15;102(52):19243-8. Epub 2005 Dec 15.

Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1073/pnas.0509473102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1323192PMC
December 2005

Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries.

Genome Res 2005 Oct;15(10):1441-6

Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

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http://dx.doi.org/10.1101/gr.3362105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240087PMC
October 2005

DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes.

Genetics 2005 Jul 16;170(3):1209-20. Epub 2005 Apr 16.

Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.

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http://dx.doi.org/10.1534/genetics.105.040915DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1451190PMC
July 2005

Mechanisms of recent genome size variation in flowering plants.

Ann Bot 2005 Jan;95(1):127-32

Department of Genetics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1093/aob/mci008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246713PMC
January 2005

Consistent over-estimation of gene number in complex plant genomes.

Curr Opin Plant Biol 2004 Dec;7(6):732-6

Department of Genetics, University of Georgia, Athens, GA 30602, USA.

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December 2004