Jeremy Schmutz

Jeremy Schmutz

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Jeremy Schmutz

Jeremy Schmutz

Publications by authors named "Jeremy Schmutz"

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A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.

Dev Biol 2019 Aug 10;452(1):8-20. Epub 2019 Apr 10.

University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA; Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 9040495, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ydbio.2019.03.015DOI Listing
August 2019

Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium).

Theor Appl Genet 2019 Aug 6;132(8):2325-2351. Epub 2019 Jun 6.

United States Department of Agriculture, Agriculture Research Service, Forage and Range Research, Utah State University, Logan, UT, 84322, USA.

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http://dx.doi.org/10.1007/s00122-019-03357-6DOI Listing
August 2019

Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation.

Front Genet 2019 31;10:487. Epub 2019 May 31.

The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.

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http://dx.doi.org/10.3389/fgene.2019.00487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6554479PMC
May 2019

Enhancing microRNA167A expression in seed decreases the α-linolenic acid content and increases seed size in Camelina sativa.

Plant J 2019 Apr 14;98(2):346-358. Epub 2019 Feb 14.

Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.

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http://dx.doi.org/10.1111/tpj.14223DOI Listing
April 2019

Characterization of a large sex determination region in Salix purpurea L. (Salicaceae).

Mol Genet Genomics 2018 Dec 18;293(6):1437-1452. Epub 2018 Jul 18.

Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA.

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http://dx.doi.org/10.1007/s00438-018-1473-yDOI Listing
December 2018

Population genomics and climate adaptation of a C4 perennial grass, Panicum hallii (Poaceae).

BMC Genomics 2018 Nov 1;19(1):792. Epub 2018 Nov 1.

Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.

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http://dx.doi.org/10.1186/s12864-018-5179-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211516PMC
November 2018

Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.

Gene 2018 Jul 12;663:165-177. Epub 2018 Apr 12.

Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA; Department of Plant & Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2018.04.024DOI Listing
July 2018

Amplification and adaptation of centromeric repeats in polyploid switchgrass species.

New Phytol 2018 06 25;218(4):1645-1657. Epub 2018 Mar 25.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.

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http://dx.doi.org/10.1111/nph.15098DOI Listing
June 2018

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.

Genes (Basel) 2018 Mar 28;9(4). Epub 2018 Mar 28.

Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia.

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http://dx.doi.org/10.3390/genes9040185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924527PMC
March 2018

Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids.

Sci Rep 2017 11 10;7(1):15274. Epub 2017 Nov 10.

Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA.

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http://dx.doi.org/10.1038/s41598-017-14885-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681701PMC
November 2017

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.

Authors:
John L Bowman Takayuki Kohchi Katsuyuki T Yamato Jerry Jenkins Shengqiang Shu Kimitsune Ishizaki Shohei Yamaoka Ryuichi Nishihama Yasukazu Nakamura Frédéric Berger Catherine Adam Shiori Sugamata Aki Felix Althoff Takashi Araki Mario A Arteaga-Vazquez Sureshkumar Balasubrmanian Kerrie Barry Diane Bauer Christian R Boehm Liam Briginshaw Juan Caballero-Perez Bruno Catarino Feng Chen Shota Chiyoda Mansi Chovatia Kevin M Davies Mihails Delmans Taku Demura Tom Dierschke Liam Dolan Ana E Dorantes-Acosta D Magnus Eklund Stevie N Florent Eduardo Flores-Sandoval Asao Fujiyama Hideya Fukuzawa Bence Galik Daniel Grimanelli Jane Grimwood Ueli Grossniklaus Takahiro Hamada Jim Haseloff Alexander J Hetherington Asuka Higo Yuki Hirakawa Hope N Hundley Yoko Ikeda Keisuke Inoue Shin-Ichiro Inoue Sakiko Ishida Qidong Jia Mitsuru Kakita Takehiko Kanazawa Yosuke Kawai Tomokazu Kawashima Megan Kennedy Keita Kinose Toshinori Kinoshita Yuji Kohara Eri Koide Kenji Komatsu Sarah Kopischke Minoru Kubo Junko Kyozuka Ulf Lagercrantz Shih-Shun Lin Erika Lindquist Anna M Lipzen Chia-Wei Lu Efraín De Luna Robert A Martienssen Naoki Minamino Masaharu Mizutani Miya Mizutani Nobuyoshi Mochizuki Isabel Monte Rebecca Mosher Hideki Nagasaki Hirofumi Nakagami Satoshi Naramoto Kazuhiko Nishitani Misato Ohtani Takashi Okamoto Masaki Okumura Jeremy Phillips Bernardo Pollak Anke Reinders Moritz Rövekamp Ryosuke Sano Shinichiro Sawa Marc W Schmid Makoto Shirakawa Roberto Solano Alexander Spunde Noriyuki Suetsugu Sumio Sugano Akifumi Sugiyama Rui Sun Yutaka Suzuki Mizuki Takenaka Daisuke Takezawa Hirokazu Tomogane Masayuki Tsuzuki Takashi Ueda Masaaki Umeda John M Ward Yuichiro Watanabe Kazufumi Yazaki Ryusuke Yokoyama Yoshihiro Yoshitake Izumi Yotsui Sabine Zachgo Jeremy Schmutz

Cell 2017 Oct;171(2):287-304.e15

Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.

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http://dx.doi.org/10.1016/j.cell.2017.09.030DOI Listing
October 2017

Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis.

Dev Biol 2017 06 5;426(2):236-244. Epub 2016 Oct 5.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1016/j.ydbio.2016.04.014DOI Listing
June 2017

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.

New Phytol 2017 Apr 20;214(2):808-819. Epub 2017 Jan 20.

Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.

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http://dx.doi.org/10.1111/nph.14421DOI Listing
April 2017

Sparse panicle1 is required for inflorescence development in Setaria viridis and maize.

Nat Plants 2017 04 18;3:17054. Epub 2017 Apr 18.

Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, Missouri 63132, USA.

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http://dx.doi.org/10.1038/nplants.2017.54DOI Listing
April 2017

Empty Niches after Extinctions Increase Population Sizes of Modern Corals.

Curr Biol 2016 12 17;26(23):3190-3194. Epub 2016 Nov 17.

Department of Biology, The Pennsylvania State University, 208 Mueller Lab, State College, PA 16802, USA; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10(th) and Constitution Avenue, NW Washington, DC 20560-0163, USA; Smithsonian Tropical Research Institute, Smithsonian Institution, 9100 Panama City PL, Washington, DC 20521, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2016.09.039DOI Listing
December 2016

Genome evolution in the allotetraploid frog Xenopus laevis.

Nature 2016 10;538(7625):336-343

University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.

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http://dx.doi.org/10.1038/nature19840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313049PMC
October 2016

Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation.

Mol Plant 2016 07 24;9(7):1078-81. Epub 2016 Mar 24.

Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA; Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molp.2016.03.009DOI Listing
July 2016

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication.

Curr Biol 2016 06 26;26(12):1577-1584. Epub 2016 May 26.

US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5089372PMC
http://dx.doi.org/10.1016/j.cub.2016.04.038DOI Listing
June 2016

Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins.

Cell 2016 Jan 7;164(1-2):45-56. Epub 2016 Jan 7.

Howard Hughes Medical Institute; Stanford University School of Medicine, Department of Developmental Biology, 279 Campus Drive, Beckman Center B300, Stanford, CA 94305, USA. Electronic address:

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http://www.cell.com/cell/pdf/S0092-8674(15)01631-1.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S009286741501631
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http://dx.doi.org/10.1016/j.cell.2015.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4759241PMC
January 2016

Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host-microbiome interactions on understanding ecosystem function.

Plant Cell Environ 2015 Sep 7;38(9):1737-51. Epub 2014 Dec 7.

Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.

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http://dx.doi.org/10.1111/pce.12458DOI Listing
September 2015

Proteome profile of the endomembrane of developing coleoptiles from switchgrass (Panicum virgatum).

Proteomics 2015 Jul 16;15(13):2286-90. Epub 2015 Mar 16.

Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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http://dx.doi.org/10.1002/pmic.201400487DOI Listing
July 2015

The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii.

New Phytol 2015 Jan 23;205(1):402-14. Epub 2014 Sep 23.

Department of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA; Division of Science and Environmental Policy, California State University, Monterey Bay, 100 Campus Center, Seaside, CA, 93955, USA.

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http://dx.doi.org/10.1111/nph.13027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265272PMC
January 2015

Complete plastome sequences from Glycine syndetika and six additional perennial wild relatives of soybean.

G3 (Bethesda) 2014 Aug 25;4(10):2023-33. Epub 2014 Aug 25.

Cornell University, Department of Plant Biology, Ithaca, New York 14853.

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http://dx.doi.org/10.1534/g3.114.012690DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199708PMC
August 2014

Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris).

Front Plant Sci 2014 11;5:339. Epub 2014 Jul 11.

Center for Applied Genetic Technologies, University of Georgia Athens, GA, USA.

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http://dx.doi.org/10.3389/fpls.2014.00339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4093653PMC
July 2014

The genome of Eucalyptus grandis.

Nature 2014 Jun 11;510(7505):356-62. Epub 2014 Jun 11.

1] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USA.

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http://dx.doi.org/10.1038/nature13308DOI Listing
June 2014

Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L.

Front Plant Sci 2014 13;5:185. Epub 2014 May 13.

Genomics and Bioinformatics Program, North Dakota State University Fargo, ND, USA ; Department of Plant Sciences, North Dakota State University Fargo, ND, USA.

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http://dx.doi.org/10.3389/fpls.2014.00185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026720PMC
May 2014

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing.

Proc Natl Acad Sci U S A 2013 Nov 13;110(48):19478-82. Epub 2013 Nov 13.

Department of Energy Joint Genome Institute, Walnut Creek, CA 94598.

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http://dx.doi.org/10.1073/pnas.1319032110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3845195PMC
November 2013

Identification and characterization of functional centromeres of the common bean.

Plant J 2013 Oct 5;76(1):47-60. Epub 2013 Aug 5.

Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics, and Genomics, University of Georgia, Athens, GA, 30602, USA.

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http://dx.doi.org/10.1111/tpj.12269DOI Listing
October 2013

A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar.

Front Plant Sci 2013 25;4:210. Epub 2013 Jun 25.

Plant Science Research Unit, USDA-Agricultural Research Service St. Paul, MN, USA ; Department of Agronomy and Plant Genetics, University of Minnesota St. Paul, MN, USA.

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http://dx.doi.org/10.3389/fpls.2013.00210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691542PMC
June 2013