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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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News & Publications
Home › News & Publications › Publications › 2007 Publications

2007 Publications

Adamska, M. et al. (2007) The evolutionary origin of hedgehog proteins. Curr Biol 17(19), R836-7. 10.1016/j.cub.2007.08.010
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Ahituv, N. et al. (2007) Deletion of ultraconserved elements yields viable mice. Plos Biology 5(9), 1906-1911. ARTN e234 DOI 10.1371/journal.pbio.0050234
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Allen, E. E. et al. (2007) Genome dynamics in a natural archaeal population. Proc Natl Acad Sci U S A 104(6), 1883-8. 10.1073/pnas.0604851104
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Alonso, C. et al. (2007) High local and global diversity of Flavobacteria in marine plankton. Environ Microbiol 9(5), 1253-66. 10.1111/j.1462-2920.2007.01244.x
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Anderson, S. J. et al. (2007) Phenotypic and genetic variation among soybean rust isolates. Phytopathology 97(7), S4-S4.
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Arp, D. J. et al. (2007) The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annual Review of Microbiology 61, 503-528. DOI 10.1146/annurev.micro.61.080706.093449
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Auerbach, R. K. et al. (2007) Yersinia pestis Evolution on a Small Timescale: Comparison of Whole Genome Sequences from North America. Plos One 2(8). ARTN e770 DOI 10.1371/journal.pone.0000770
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Bailey, Joseph M. et al. (2007) Confederate guerrilla : the Civil War memoir of Joseph M. Bailey. The Civil War in the West , xix, 148 p..
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Barns, S. M. et al. (2007) Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 73(9), 3113-6. 10.1128/AEM.02012-06
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Beckstrom-Sternberg, S. M. et al. (2007) Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS One 2(9), e947. 10.1371/journal.pone.0000947
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Challacombe, J. F. et al. (2007) The complete genome sequence of Bacillus thuringiensis Al Hakam. J Bacteriol 189(9), 3680-1. 10.1128/JB.00241-07
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Chistoserdova, L. et al. (2007) Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. J Bacteriol 189(11), 4020-7. 10.1128/JB.00045-07
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Dalevi, D. et al. (2007) Automated group assignment in large phylogenetic trees using GRUNT: GRouping, ungrouping, naming tool. Bmc Bioinformatics 8. Artn 402 Doi 10.1186/1471-2105-8-402
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Field, D. et al. (2007) The positive role of the ecological community in the genomic revolution. Microb Ecol 53(3), 507-11. 10.1007/s00248-007-9206-5
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Fong, J. J. et al. (2007) A genetic survey of heavily exploited, endangered turtles: caveats on the conservation value of trade animals. Animal Conservation 10(4), 452-460. DOI 10.1111/j.1469-1795.2007.00131.x
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Fujita, M. K. et al. (2007) Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; squamata, gekkonidae). Molecular Biology and Evolution 24(12), 2775-2786. DOI 10.1093/molbev/msm212
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Giraud, E. et al. (2007) Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science 316(5829), 1307-12. 10.1126/science.1139548
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Gordon, L. et al. (2007) Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. Genome Res 17(11), 1603-13. 10.1101/gr.6775107
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Gowda, M. et al. (2007) Interrogation of the RNA species in Magnaporthe grisea. Phytopathology 97(7), S42-S42.
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Grossman, A. R. et al. (2007) Novel metabolism in Chlamydomonas through the lens of genomics. Current Opinion in Plant Biology 10(2), 190-198. Doi 10.1016/J.Pbi.2007.01.012
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Gu, S. Y. et al. (2007) TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics 23(6), 764-766. Doi 10.1093/Bioinformatics/Btl643
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Horner-Devine, M. C. et al. (2007) A comparison of taxon co-occurrence patterns for macro- and microorganisms. Ecology 88(6), 1345-1353. Doi 10.1890/06-0286
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Housman, D. C. et al. (2007) Heterogeneity of soil nutrients and subsurface biota in a dryland ecosystem. Soil Biology & Biochemistry 39(8), 2138-2149. Doi 10.1016/J.Soilbio.2007.03.015
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Hristova, K. R. et al. (2007) Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Applied and Environmental Microbiology 73(22), 7347-7357. Doi 10.1128/Aem.01604-07
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Hugenholtz, P. et al. (2007) Riding giants. Environmental Microbiology 9(1), 5-5. Doi 10.1111/J.1462-2920.2006.01222_4.X
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Hugenholtz, P. et al. (2007) Increasing focus on environmental biotechnology in the face of pressing environmental challenges. Current Opinion in Biotechnology 18(3), 235-236. Doi 10.1016/J.Copbio.2007.05.004
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Jansen, R. K. et al. (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences of the United States of America 104(49), 19369-19374. DOI 10.1073/pnas.0709121104
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Jeffries, T. W. et al. (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotechnol 25(3), 319-26. 10.1038/nbt1290
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Johnson, S. L. et al. (2007) Export of nitrogenous compounds due to incomplete cycling within biological soil crusts of arid lands. Environmental Microbiology 9(3), 680-689. Doi 10.1111/J.1462-2920.2006.01187.X
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Kalluri, U. C. et al. (2007) Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. Bmc Plant Biology 7. Artn 59Doi 10.1186/1471-2229-7-59
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Kamburov, A. et al. (2007) Denoising inferred functional association networks obtained by gene fusion analysis. Bmc Genomics 8. Artn 460 Doi 10.1186/1471-2164-8-460
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Kane, S. R. et al. (2007) Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. J Bacteriol 189(5), 1931-45. 10.1128/JB.01259-06
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Kane, S. R. et al. (2007) Whole-genorne analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. Journal of Bacteriology 189(5), 1931-1945. Doi 10.1128/Jb.01259-06
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Kazakov, A. E. et al. (2007) RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Research 35, D407-D412. Doi 10.1093/Nar/Gkl865
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Kelleher, C. T. et al. (2007) A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant Journal 50(6), 1063-1078. Doi 10.1111/J.1365-313x.2007.03112.X
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Larroux, C. et al. (2007) The NK homeobox gene cluster predates the origin of Hox genes. Current Biology 17(8), 706-710. Doi 10.1016/J.Cub.2007.03.008
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Leonardi, R. et al. (2007) Localization and regulation of mouse pantothenate kinase 2. FEBS Lett 581(24), 4639-44. 10.1016/j.febslet.2007.08.056
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Lo, I. et al. (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446(7135), 537-541. Doi 10.1038/Nature05624
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Lykidis, A. et al. (2007) Comparative genomics and evolution of eukaryotic phospholipid biosynthesis. Progress in Lipid Research 46(3-4), 171-199. Doi 10.1016/J.Plipres.2007.03.003
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Lykidis, A. et al. (2007) Genomics and evolution of eukaryotic phospholipid biosynthesis. Faseb Journal 21(6), A976-A976.
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Lykidis, A. et al. (2007) Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. Journal of Bacteriology 189(6), 2477-2486. Doi 10.1128/Jb.01899-06
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Makarova, K. S. et al. (2007) Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS One 2(9), e955. 10.1371/journal.pone.0000955
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Marcy, Y. et al. (2007) Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences of the United States of America 104(29), 11889-11894. Doi 10.1073/Pnas.0704662104
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Markowitz, V. M. et al. (2007) Microbial genome data resources. Curr Opin Biotechnol 18(3), 267-72. 10.1016/j.copbio.2007.04.005
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Markowitz, V. M. et al. (2007) Comparative genome analysis in the integrated microbial genomes (IMG) system. Methods Mol Biol 395, 35-56.
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Martin, F. N. et al. (2007) Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P-sojae. Current Genetics 51(5), 285-296. Doi 10.1007/S00294-007-0121-6
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Mavromatis, K. et al. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods 4(6), 495-500. Doi 10.1038/Nmeth1043
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McHardy, A. C. et al. (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods 4(1), 63-72. Doi 10.1038/Nmeth976
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McMahon, K. D. et al. (2007) Integrating ecology into biotechnology. Current Opinion in Biotechnology 18(3), 287-292. Doi 10.1016/J.Copbio.2007.04.007
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McNeal, J. R. et al. (2007) Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). Bmc Biology 5. Artn 55 Doi 10.1186/1741-7007-5-55
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McNeal, J. R. et al. (2007) Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. Bmc Plant Biology 7. Artn 57 Doi 10.1186/1471-2229-7-57
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Meier, S. et al. (2007) Continuous molecular evolution of protein-domain structures by single amino acid changes. Current Biology 17(2), 173-178. Doi 10.1016/J.Cub.2006.10.063
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Merchant, S. et al. (2007) Establishing potential chloroplast function through phylogenomics. Photosynthesis Research 91(2-3), 271-272.
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Merchant, S. S. et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318(5848), 245-251. Doi 10.1126/Science.1143609
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Minovitsky, S. et al. (2007) Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. Bmc Genomics 8. Artn 378 Doi 10.1186/1471-2164-8-378
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Montsant, A. et al. (2007) Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana. Journal of Phycology 43(3), 585-604. Doi 10.1111/J.1529-8817.2007.00342.X
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Moran, M. A. et al. (2007) Ecological genomics of marine roseobacters. Applied and Environmental Microbiology 73(14), 4559-4569. Doi 10.1128/Aem.02580-06
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Newton, I. L. G. et al. (2007) The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315(5814), 998-1000. Doi 10.1126/Science.1138438
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Normand, P. et al. (2007) Genome characteristics of facultatively symbiotic Frankia sp strains reflect host range and host plant biogeography. Genome Research 17(1), 7-15. Doi 10.1101/Gr.5798407
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Oudot-Le Secq, M. P. et al. (2007) Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage. Molecular Genetics and Genomics 277(4), 427-439. Doi 10.1007/S00438-006-0199-4
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Palenik, B. et al. (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proceedings of the National Academy of Sciences of the United States of America 104(18), 7705-7710. Doi 10.1073/Pnas.0611046104
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Pel, H. J. et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25(2), 221-31. 10.1038/nbt1282
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Putnam, N. H. et al. (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317(5834), 86-94. 10.1126/science.1139158
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Raubeson, L. A. et al. (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. Bmc Genomics 8. Artn 174 Doi 10.1186/1471-2164-8-174
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Romeo, S. et al. (2007) Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nature Genetics 39(4), 513-516. Doi 10.1038/Ng1984
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Smith, T. J. et al. (2007) Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PLoS One 2(12), e1271. 10.1371/journal.pone.0001271
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Smith, T. J. et al. (2007) Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PLoS One 2(12), e1271. 10.1371/journal.pone.0001271
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Sorek, R. et al. (2007) The birth of new exons: mechanisms and evolutionary consequences. RNA 13(10), 1603-8. 10.1261/rna.682507
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Sorek, R. et al. (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318(5855), 1449-52. 10.1126/science.1147112
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Stein, L. Y. et al. (2007) Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ Microbiol 9(12), 2993-3007. 10.1111/j.1462-2920.2007.01409.x
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Tanaka, S. et al. (2007) Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803. Acta Crystallogr D Biol Crystallogr 63(Pt 10), 1109-12. 10.1107/S090744490704228X
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Tang, Y. J. et al. (2007) Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid. Appl Environ Microbiol 73(12), 3859-64. 10.1128/AEM.02986-06
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Timme, R. E. et al. (2007) A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am J Bot 94(3), 302-12. 10.3732/ajb.94.3.302
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Tuanyok, A. et al. (2007) A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. Journal of Bacteriology 189(24), 9044-9049. Doi 10.1128/Jb.01264-07
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Tuanyok, A. et al. (2007) A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. Journal of Bacteriology 189(24), 9044-9049. Doi 10.1128/Jb.01264-07
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Udwary, D. W. et al. (2007) Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proceedings of the National Academy of Sciences of the United States of America 104(25), 10376-10381. Doi 10.1073/Pnas.0700962104
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Vannini, C. et al. (2007) Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria). Environmental Microbiology 9(2), 347-359. Doi 10.1111/J.1462-2920.2006.01144.X
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Visel, A. et al. (2007) Enhancer identification through comparative genomics. Seminars in Cell & Developmental Biology 18(1), 140-152. Doi 10.1016/J.Semcdb.2006.12.014
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von Mering, C. et al. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315(5815), 1126-1130. Doi 10.1126/Science.1133420
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Warnecke, F. et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450(7169), 560-U17. Doi 10.1038/Nature06269
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Warnecke, F. et al. (2007) Building on basic metagenomics with complementary technologies. Genome Biol 8(12), 231. 10.1186/gb-2007-8-12-231
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Warnecke, F. et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450(7169), 560-U17. Doi 10.1038/Nature06269
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Wong, R. et al. (2007) The story told by 100 shotgun sequenced microbial genomes - Why the clonability for genomes are different.. Plasmid 57(2), 239-239.
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Xie, G. et al. (2007) Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Applied and Environmental Microbiology 73(11), 3536-3546. Doi 10.1128/Aem.00225-07
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Yamada, T. et al. (2007) Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. Isme Journal 1(3), 246-255. Doi 10.1038/Ismej.2007.28
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Yeager, C. M. et al. (2007) Three distinct clades of cultured heterocystous cyanobacteria constitute the dominant N-2-fixing members of biological soil crusts of the Colorado Plateau, USA. Fems Microbiology Ecology 60(1), 85-97. Doi 10.1111/J.1574-6941.2006.00265.X
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