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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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News & Publications
Home › News & Publications › Publications › 2005 Publications

2005 Publications

Alexandrino, J. et al. (2005) Strong selection against hybrids at a hybrid zone in the Ensatina ring species complex and its evolutionary implications. Evolution 59(6), 1334-1347.
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Boore, J. L. et al. (2005) Sequencing and comparing whole mitochondrial genomes of animals. Molecular Evolution: Producing the Biochemical Data, Part B 395, 311-348. Doi 10.1016/S0076-6879(05)95019-2
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Dehal, P. et al. (2005) Two rounds of whole genome duplication in the ancestral vertebrate. Plos Biology 3(10), 1700-1708. ARTN e314 DOI 10.1371/journal.pbio.0030314
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Foster, J. et al. (2005) The Wolbachia genome of Brugia malayi: Endosymbiont evolution within a human pathogenic nematode. Plos Biology 3(4), 599-614. ARTN e121 DOI 10.1371/journal.pbio.0030121
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Francino, M. P. et al. (2005) An adaptive radiation model for the origin of new gene functions. Nature Genetics 37(6), 573-577. Doi 10.1038/Ng1579
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Gatesy, J. et al. (2005) Hidden likelihood support in genomic data: Can forty-five wrongs make a right?. Systematic Biology 54(3), 483-492. Doi 10.1080/10635150590945368
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Jansen, R. K. et al. (2005) Methods for obtaining and analyzing whole chloroplast genome sequences. Molecular Evolution: Producing the Biochemical Data, Part B 395, 348-384. Doi 10.1016/S0076-6879(05)95020-9
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Keys, D. N. et al. (2005) A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis. Proceedings of the National Academy of Sciences of the United States of America 102(3), 679-683. Doi 10.1073/Pnas.0408952102
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Leebens-Mack, J. et al. (2005) Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one's way out of the felsenstein zone. Molecular Biology and Evolution 22(10), 1948-1963. Doi 10.1093/Molbev/Msi191
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Macey, J. R. et al. (2005) Plethodontid salamander mitochondrial genomics: A parsimony evaluation of character conflict and implications for historical biogeography. Cladistics 21(2), 194-202. Doi 10.1111/J.1096-0031.2005.00054.X
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Macey, J. R. et al. (2005) The complete mitochondrial genome of a gecko and the phylogenetic position of the Middle Eastern Teratoscincus keyserlingii. Molecular Phylogenetics and Evolution 36(1), 188-193. Doi 10.1016/J.Ympev.2005.03.025
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Medina, M. et al. (2005) Genomes, phylogeny, and evolutionary systems biology. Proceedings of the National Academy of Sciences of the United States of America 102, 6630-6635. Doi 10.1073/Pnas.0501984102
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Medina, M. et al. (2005) Phylogeny of sea hares in the Aplysia clade based on mitochondrial DNA sequence data. Bulletin of Marine Science 76(3), 691-698.
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Mueller, R. L. et al. (2005) Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Molecular Biology and Evolution 22(10), 2104-2112. Doi 10.1093/Molbev/Msi204
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Noonan, J. P. et al. (2005) Genomic sequencing of Pleistocene cave bears. Science 309(5734), 597-9. 10.1126/science.1113485
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Parham, J. F. et al. (2005) A reassessment of the referral of sea turtle skulls to the genus Osteopygis (Late Cretaceous, New Jersey, USA). Journal of Vertebrate Paleontology 25(1), 71-77. Doi 10.1671/0272-4634(2005)025[0071:Arotro]2.0.Co;2
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Place, A. R. et al. (2005) Genetic markers in blue crabs (Callinectes sapidus) II. Complete mitochondrial genome sequence and characterization of genetic variation. Journal of Experimental Marine Biology and Ecology 319(1-2), 15-27. Doi 10.1016/J.Jembe.2004.03.024
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Richards, S. et al. (2005) Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Research 15(1), 1-18. Doi 10.1101/Gr.3059305
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Rojas, A. et al. (2005) Gata4 expression in lateral mesoderm is downstream of BMP4 and is activated directly by Forkhead and GATA transcription factors through a distal enhancer element. Development 132(15), 3405-3417. Doi 10.1242/Dev.01913
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Tringe, S. G. et al. (2005) Comparative metagenomics of microbial communities. Science 308(5721), 554-557. Doi 10.1126/Science.1107851
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Vrdoljak, G. et al. (2005) Characterization of a diesel sludge microbial consortia for bioremediation. Scanning 27(1), 8-14.
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Weng, L. et al. (2005) Lack of MEF2A mutations in coronary artery disease. Journal of Clinical Investigation 115(4), 1016-1020. Doi 10.1172/Jci24186
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Wolf, P. G. et al. (2005) The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene 350(2), 117-128. Doi 10.1016/J.Gene.2005.01.018
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