2018 Pubs - DOE Joint Genome Institute

Aguilar-Pontes, M. V. et al. (2018) The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi. Studies in mycology 91, 61-78. 10.1016/j.simyco.2018.10.001
Ahrendt, S. R. et al. (2018) Leveraging single-cell genomics to expand the fungal tree of life. Nat Microbiol . 10.1038/s41564-018-0261-0
Anantharaman, K. et al. (2018) Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J . 10.1038/s41396-018-0078-0
Arnesen, J. A. et al. (2018) Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases. G3 (Bethesda) 8(10), 3311-3319. 10.1534/g3.118.200656
Azad, A. et al. (2018) HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks. Nucleic Acids Res 46(6), e33. 10.1093/nar/gkx1313
Bachy, C. et al. (2018) Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions. Environ Microbiol 20(8), 2898-2912. 10.1111/1462-2920.14273
Bahri, B. A. et al. (2018) Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.). BMC Evol Biol 18(1), 91. 10.1186/s12862-018-1193-2
Bakermans, C. et al. (2018) Adaptations to marine versus terrestrial low temperature environments as revealed by comparative genomic analyses of the genus Psychrobacter. FEMS Microbiol Ecol 94(7). 10.1093/femsec/fiy102
Balasundaram, S. V. et al. (2018) The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings. ISME J 12(3), 791-801. 10.1038/s41396-017-0006-8
Bell, E. et al. (2018) Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater. Front Microbiol 9, 2129. 10.3389/fmicb.2018.02129
Beller, H. R. et al. (2018) Discovery of enzymes for toluene synthesis from anoxic microbial communities. Nat Chem Biol . 10.1038/s41589-018-0017-4
Benocci, T. et al. (2018) Enzymatic Adaptation of Podospora anserina to Different Plant Biomass Provides Leads to Optimized Commercial Enzyme Cocktails. Biotechnol J , e1800185. 10.1002/biot.201800185
Bernhardsgrutter, I. et al. (2018) The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite. Nat Chem Biol 14(12), 1127-1132. 10.1038/s41589-018-0153-x
Bhatnagar, J. M. et al. (2018) Litter chemistry influences decomposition through activity of specific microbial functional guilds. Ecological Monographs 88(3), 429-444. 10.1002/ecm.1303/full
Biswas, R. et al. (2018) Complete Genome Sequence of Thermoanaerobacterium sp. Strain RBIITD, a Butyrate- and Butanol-Producing Thermophile. Genome Announc 6(2). 10.1128/genomeA.01411-17
Borton, M. A. et al. (2018) Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales. Proc Natl Acad Sci U S A 115(28), E6585-E6594. 10.1073/pnas.1800155115
Borton, Mikayla A. et al. (2018) Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale. Environmental Microbiology 20(12), 4596-4611. 10.1111/1462-2920.14467
Bourgeois, Y. et al. (2018) Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon. Plant Journal 96(2), 438-451. 10.1111/tpj.14042
Bryan, A. C. et al. (2018) A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein. G3 (Bethesda) . 10.1534/g3.118.200188
Butler, J. B. et al. (2018) Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus. Heredity (Edinb) . 10.1038/s41437-018-0058-1
Camiolo, S. et al. (2018) An analysis of codon bias in six red yeast species. Yeast . 10.1002/yea.3359
Cantillo, Angela et al. (2018) Genome Sequences of Actinobacteria from Extreme Environments in Colombia. Microbiology Resource Announcements 7(22), e01384-18. 10.1128/MRA.01384-18
Cardenas, E. et al. (2018) Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones. Sci Rep 8(1), 3142. 10.1038/s41598-018-21197-0
Carella, P. et al. (2018) Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage. Proc Natl Acad Sci U S A 115(16), E3846-E3855. 10.1073/pnas.1717900115
Carro, L. et al. (2018) Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep 8(1), 525. 10.1038/s41598-017-17392-0
Chadha, S. et al. (2018) Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships. Fungal Biol Biotechnol 5, 12. 10.1186/s40694-018-0056-3
Chafee, M. et al. (2018) Recurrent patterns of microdiversity in a temperate coastal marine environment. ISME J 12(1), 237-252. 10.1038/ismej.2017.165
Chang, J. J. et al. (2018) Biomimetic strategy for constructing Clostridium thermocellum cellulosomal operons in Bacillus subtilis. Biotechnol Biofuels 11, 157. 10.1186/s13068-018-1151-7
Chang, Ying et al. (2018) Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. New Phytologist 0(0). 10.1111/nph.15613
Chen, E. C. H. et al. (2018) High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. New Phytol . 10.1111/nph.14989
Cheng, H. et al. (2018) The Biota Project: A Case Study of a Multimedia, Grassroots Approach to Scientific Communication for Engaging Diverse Audiences. Integr Comp Biol 58(6), 1294-1303. 10.1093/icb/icy091
Chernikova, T. N. et al. (2018) Draft Genome Sequence of Monaibacterium marinum C7(T), Isolated from Seawater from the Menai Straits, Wales, United Kingdom. Genome Announc 6(5). 10.1128/genomeA.01444-17
Chiang, E. et al. (2018) Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats. PLoS One 13(3), e0195112. 10.1371/journal.pone.0195112
Coates, R. C. et al. (2018) An integrated workflow for phenazine-modifying enzyme characterization. J Ind Microbiol Biotechnol . 10.1007/s10295-018-2025-5
Coradetti, S. T. et al. (2018) Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. Elife 7. 10.7554/eLife.32110
Cox, R. S. et al. (2018) Synthetic Biology Open Language (SBOL) Version 2.2.0. J Integr Bioinform 15(1). 10.1515/jib-2018-0001
Crits-Christoph, A. et al. (2018) Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature 558(7710), 440-444. 10.1038/s41586-018-0207-y
Dalcin Martins, P. et al. (2018) Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems. Microbiome 6(1), 138. 10.1186/s40168-018-0522-4
Daly, P. et al. (2018) Dichomitus squalens partially tailors its molecular responses to the composition of solid wood. Environ Microbiol . 10.1111/1462-2920.14416
Daly, P. et al. (2018) Dichomitus squalens partially tailors its molecular responses to the composition of solid wood. Environ Microbiol 20(11), 4141-4156. 10.1111/1462-2920.14416
de Freitas Pereira, M. et al. (2018) Secretome Analysis from the Ectomycorrhizal Ascomycete Cenococcum geophilum. Front Microbiol 9, 141. 10.3389/fmicb.2018.00141
Dippel, A. B. et al. (2018) Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP. ACS Chem Biol . 10.1021/acschembio.7b01019
Druzhinina, I. S. et al. (2018) Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLoS Genet 14(4), e1007322. 10.1371/journal.pgen.1007322
Duerkop, B. A. et al. (2018) Murine colitis reveals a disease-associated bacteriophage community. Nat Microbiol . 10.1038/s41564-018-0210-y
Dunivin, T. K. et al. (2018) Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil. FEMS Microbiol Ecol 94(3). 10.1093/femsec/fiy016
Dyksma, S. et al. (2018) Evidence for H2 consumption by uncultured Desulfobacterales in coastal sediments. Environ Microbiol 20(2), 450-461. 10.1111/1462-2920.13880
Eichorst, S. A. et al. (2018) Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. Environ Microbiol 20(3), 1041-1063. 10.1111/1462-2920.14043
Emerson, J. B. et al. (2018) Host-linked soil viral ecology along a permafrost thaw gradient. Nat Microbiol 3(8), 870-880. 10.1038/s41564-018-0190-y
Emery, M. et al. (2018) Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. PLoS Genet 14(3), e1007267. 10.1371/journal.pgen.1007267
Emri, T. et al. (2018) Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance. Studies in mycology 91, 23-36. 10.1016/j.simyco.2018.10.003
Eng, T. et al. (2018) Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC. Microb Cell Fact 17(1), 159. 10.1186/s12934-018-1006-8
Espinola, F. et al. (2018) Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. Microb Ecol 75(1), 123-139. 10.1007/s00248-017-1028-5
Estrada-de Los Santos, P. et al. (2018) Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae. Genes (Basel) 9(8). 10.3390/genes9080389
Evans, J. et al. (2018) Extensive Genetic Diversity is Present within North American Switchgrass Germplasm. Plant Genome 11(1). 10.3835/plantgenome2017.06.0055
Filiault, D. L. et al. (2018) The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. Elife 7. 10.7554/eLife.36426
Fischer, M. S. et al. (2018) Regulation of Cell-to-Cell Communication and Cell Wall Integrity by a Network of MAP Kinase Pathways and Transcription Factors in Neurospora crassa. Genetics 209(2), 489-506. 10.1534/genetics.118.300904
Fleming, E. J. et al. (2018) Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Appl Environ Microbiol . 10.1128/AEM.02239-17
Ganesh, S. et al. (2018) Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria. ISME J . 10.1038/s41396-018-0223-9
Ganesh, S. et al. (2018) Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria. Isme Journal 12(11), 2706-2722. 10.1038/s41396-018-0223-9
Gao, J. et al. (2018) Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions. J Vis Exp (134). 10.3791/57170
Garcia, S. L. et al. (2018) Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria. mSphere 3(3). 10.1128/mSphere.00202-18
Garsmeur, O. et al. (2018) A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nat Commun 9(1), 2638. 10.1038/s41467-018-05051-5
Gluck-Thaler, E. et al. (2018) Specialized plant biochemistry drives gene clustering in fungi. ISME J 12(7), 1694-1705. 10.1038/s41396-018-0075-3
Gould, B. A. et al. (2018) Population genomics and climate adaptation of a C4 perennial grass, Panicum hallii (Poaceae). BMC Genomics 19(1), 792. 10.1186/s12864-018-5179-7
Grum-Grzhimaylo, A. A. et al. (2018) The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet. Mol Ecol . 10.1111/mec.14912
Gryganskyi, A. P. et al. (2018) Phylogenetic and Phylogenomic Definition of Rhizopus Species. G3 (Bethesda) 8(6), 2007-2018. 10.1534/g3.118.200235
Guo, J. et al. (2018) Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation. Nat Microbiol 3(7), 781-790. 10.1038/s41564-018-0178-7
Handakumbura, P. P. et al. (2018) SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae. Plant J 96(3), 532-545. 10.1111/tpj.14047
Harrington, L. B. et al. (2018) Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science . 10.1126/science.aav4294
Hausmann, B. et al. (2018) Peatland Acidobacteria with a dissimilatory sulfur metabolism. ISME J . 10.1038/s41396-018-0077-1
Hesse, C. et al. (2018) Genome-based evolutionary history of Pseudomonas spp. Environ Microbiol . 10.1111/1462-2920.14130
Higgins, D. A. et al. (2018) Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast. Genetics 210(1), 219-234. 10.1534/genetics.118.301161
Hon, S. et al. (2018) Expressing the Thermoanaerobacterium saccharolyticum pforA in engineered Clostridium thermocellum improves ethanol production. Biotechnol Biofuels 11, 242. 10.1186/s13068-018-1245-2
Hori, C. et al. (2018) Multi-omic analyses of extensively decayed Pinus contorta reveal expression of diverse array of lignocellulose degrading enzymes. Appl Environ Microbiol . 10.1128/AEM.01133-18
Huang, Y. T. et al. (2018) Genome-based analysis of virulence determinants of a Serratia marcescens strain from soft tissues following a snake bite. Future Microbiol 13, 331-343. 10.2217/fmb-2017-0202
Huang, Y. T. et al. (2018) Draft genome sequence of carbapenem-resistant Shewanella algae strain AC isolated from small abalone (Haliotis diversicolor). J Glob Antimicrob Resist 14, 65-67. 10.1016/j.jgar.2018.06.005
Jansson, C. et al. (2018) Climate-smart crops with enhanced photosynthesis. J Exp Bot 69(16), 3801-3809. 10.1093/jxb/ery213
Jarett, J. K. et al. (2018) Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis. Microbiome 6(1), 161. 10.1186/s40168-018-0539-8
Jay, Z. J. et al. (2018) Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats. Nat Microbiol 3(6), 732-740. 10.1038/s41564-018-0163-1
Jayakody, L. N. et al. (2018) Thermochemical wastewater valorization via enhanced microbial toxicity tolerance. Energy & Environmental Science 11(6), 1625-1638. 10.1039/c8ee00460a
Kappelmann, L. et al. (2018) Polysaccharide utilization loci of North Sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans. ISME J . 10.1038/s41396-018-0242-6
Khdhiri, M. et al. (2018) Meta-omics survey of [NiFe]-hydrogenase genes fails to capture drastic variations in H-2-oxidation activity measured in three soils exposed to H-2. Soil Biology & Biochemistry 125, 239-243. 10.1016/j.soilbio.2018.07.020
Kijpornyongpan, T. et al. (2018) Broad genomic sampling reveals a smut pathogenic ancestry of the fungal clade Ustilaginomycotina. Mol Biol Evol . 10.1093/molbev/msy072
Kimbrel, J. A. et al. (2018) Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. Front Microbiol 9, 1492. 10.3389/fmicb.2018.01492
Kjaerbolling, I. et al. (2018) Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. Proc Natl Acad Sci U S A 115(4), E753-E761. 10.1073/pnas.1715954115
Kleiner, M. et al. (2018) Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. Proc Natl Acad Sci U S A 115(24), E5576-E5584. 10.1073/pnas.1722325115
Kliver, S. et al. (2018) Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. Genes (Basel) 9(4). 10.3390/genes9040185
Knapp, D. G. et al. (2018) Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi. Sci Rep 8(1), 6321. 10.1038/s41598-018-24686-4
Kolinko, S. et al. (2018) A bacterial pioneer produces cellulase complexes that persist through community succession. Nat Microbiol 3(1), 99-107. 10.1038/s41564-017-0052-z
Krassowski, T. et al. (2018) Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nat Commun 9(1), 1887. 10.1038/s41467-018-04374-7
Kroeger, M. E. et al. (2018) New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes. Front Microbiol 9, 1635. 10.3389/fmicb.2018.01635
Kuang, M. C. et al. (2018) Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution. Mol Biol Evol . 10.1093/molbev/msy102
Lang, D. et al. (2018) The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. Plant J 93(3), 515-533. 10.1111/tpj.13801
Lee, J. Z. et al. (2018) Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat. PLoS One 13(9), e0202792. 10.1371/journal.pone.0202792
Lee, L. L. et al. (2018) Genus-wide assessment of lignocellulose utilization in the extremely thermophilic Caldicellulosiruptor by genomic, pan-genomic and metagenomic analysis. Appl Environ Microbiol . 10.1128/AEM.02694-17
Levy, A. et al. (2018) Genomic features of bacterial adaptation to plants. Nat Genet 50(1), 138-150. 10.1038/s41588-017-0012-9
Levy, A. et al. (2018) Elucidating Bacterial Gene Functions in the Plant Microbiome. Cell Host Microbe 24(4), 475-485. 10.1016/j.chom.2018.09.005
Lewin, H. A. et al. (2018) Earth BioGenome Project: Sequencing life for the future of life. Proc Natl Acad Sci U S A 115(17), 4325-4333. 10.1073/pnas.1720115115
Li, G. et al. (2018) Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification. BMC Biotechnol 18(1), 54. 10.1186/s12896-018-0464-8
Li, Y. et al. (2018) Proteome and phospholipid alteration reveal metabolic network of Bacillus thuringiensis under triclosan stress. Sci Total Environ 615, 508-516. 10.1016/j.scitotenv.2017.10.004
Lin, H. et al. (2018) Combining Hadoop with MPI to Solve Metagenomics Problems that are both Data- and Compute-intensive. International Journal of Parallel Programming 46(4), 762-775. 10.1007/s10766-017-0524-z
Linz, A. M. et al. (2018) Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. Peerj 6, 24. 10.7717/peerj.6075
Looney, B. P. et al. (2018) Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates. New Phytol 218(1), 54-65. 10.1111/nph.15001
Lopez, D. et al. (2018) Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors. Front Microbiol 9, 276. 10.3389/fmicb.2018.00276
Lopez, G. et al. (2018) Description of Alicyclobacillus montanus sp. nov., a mixotrophic bacterium isolated from acidic hot springs. Int J Syst Evol Microbiol . 10.1099/ijsem.0.002718
Lovell, John T. et al. (2018) The genomic landscape of molecular responses to natural drought stress in Panicum hallii. Nature Communications 9(1), 5213. 10.1038/s41467-018-07669-x
Mackelprang, R. et al. (2018) Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States. Front Microbiol 9, 1775. 10.3389/fmicb.2018.01775
Mafu, S. et al. (2018) Discovery, Biosynthesis and Stress-Related Accumulation of Dolabradiene-Derived Defenses in Maize. Plant Physiol 176(4), 2677-2690. 10.1104/pp.17.01351
Makela, M. R. et al. (2018) Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga. Genome Announc 6(14). 10.1128/genomeA.01414-17
Mäkelä, M. R. et al. (2018) Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli. Studies in mycology 91, 79-99. 10.1016/j.simyco.2018.09.001
Marks, Peter C. et al. (2018) MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources. Database 2018, bay087-bay087. 10.1093/database/bay087
Martino, E. et al. (2018) Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. New Phytol 217(3), 1213-1229. 10.1111/nph.14974
Meier-Kolthoff, J. P. et al. (2018) Investigation of recombination-intense viral groups and their genes in the Earth’s virome. Sci Rep 8(1), 11496. 10.1038/s41598-018-29272-2
Meredith, K. Laura et al. (2018) Coupled Biological and Abiotic Mechanisms Driving Carbonyl Sulfide Production in Soils. Soil Systems 2(3). 10.3390/soilsystems2030037
Meredith, L. K. et al. (2018) Soil exchange rates of COS and CO(18)O differ with the diversity of microbial communities and their carbonic anhydrase enzymes. ISME J . 10.1038/s41396-018-0270-2
Milano, E. R. et al. (2018) Quantitative trait loci for cell wall composition traits measured using near-infrared spectroscopy in the model C4 perennial grass Panicum hallii. Biotechnol Biofuels 11, 25. 10.1186/s13068-018-1033-z
Milano, E. R. et al. (2018) Quantitative trait loci for cell wall composition traits measured using near-infrared spectroscopy in the model C4 perennial grass Panicum hallii. Biotechnol Biofuels 11, 25. 10.1186/s13068-018-1033-z
Miyauchi, S. et al. (2018) Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass. Biotechnol Biofuels 11, 201. 10.1186/s13068-018-1198-5
Monroe, J. G. et al. (2018) Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. Elife 7. 10.7554/eLife.41038
Muchero, W. et al. (2018) Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant-pathogen interactions in a tree. Proc Natl Acad Sci U S A 115(45), 11573-11578. 10.1073/pnas.1804428115
Murat, C. et al. (2018) Draft Genome Sequence of Tuber borchii Vittad., a Whitish Edible Truffle. Genome Announc 6(25). 10.1128/genomeA.00537-18
Murat, C. et al. (2018) Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle. Nature Ecology & Evolution 2(12), 1956-1965. 10.1038/s41559-018-0710-4
Murphy, K. M. et al. (2018) Functional Characterization of Two Class II Diterpene Synthases Indicates Additional Specialized Diterpenoid Pathways in Maize (Zea mays). Front Plant Sci 9, 1542. 10.3389/fpls.2018.01542
Narrowe, A. B. et al. (2018) Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids. Genome Biol Evol 10(9), 2380-2393. 10.1093/gbe/evy154
Nash, M. V. et al. (2018) Metagenomic insights into diazotrophic communities across Arctic glacier forefields. FEMS Microbiol Ecol . 10.1093/femsec/fiy114
Neumann, A. P. et al. (2018) The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential. mSphere 3(6). 10.1128/mSphere.00593-18
Nouioui, I. et al. (2018) Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 9, 2007. 10.3389/fmicb.2018.02007
Palluk, S. et al. (2018) De novo DNA synthesis using polymerase-nucleotide conjugates. Nat Biotechnol 36(7), 645-650. 10.1038/nbt.4173
Paver, S. F. et al. (2018) Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems. mSystems 3(6). 10.1128/mSystems.00232-18
Pavlopoulos, G. A. et al. (2018) Bipartite graphs in systems biology and medicine: a survey of methods and applications. Gigascience 7(4), 1-31. 10.1093/gigascience/giy014
Pawlowska, T. E. et al. (2018) Biology of Fungi and Their Bacterial Endosymbionts. Annu Rev Phytopathol 56, 289-309. 10.1146/annurev-phyto-080417-045914
Pelot, K. A. et al. (2018) Functional Diversity of Diterpene Synthases in the Biofuel Crop Switchgrass. Plant Physiol 178(1), 54-71. 10.1104/pp.18.00590
Perera, D. et al. (2018) Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis. Gene 663, 165-177. 10.1016/j.gene.2018.04.024
Perroud, P. F. et al. (2018) The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data. Plant J 95(1), 168-182. 10.1111/tpj.13940
Pitt, A. et al. (2018) Polynucleobacter meluiroseus sp. nov., a bacterium isolated from a lake located in the mountains of the Mediterranean island of Corsica. Int J Syst Evol Microbiol 68(6), 1975-1985. 10.1099/ijsem.0.002777
Pold, G. et al. (2018) Genome Sequence of Verrucomicrobium sp. Strain GAS474, a Novel Bacterium Isolated from Soil. Genome Announc 6(4). 10.1128/genomeA.01451-17
Pold, G. et al. (2018) Draft Genome Sequences of Three Strains of a Novel Rhizobiales Species Isolated from Forest Soil. Genome Announc 6(5). 10.1128/genomeA.01452-17
Pomraning, Kyle R. et al. (2018) Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica. mSphere 3(6), e00541-18. 10.1128/mSphere.00541-18
Porcar, M. et al. (2018) Microbial Ecology on Solar Panels in Berkeley, CA, United States. Front Microbiol 9, 3043. 10.3389/fmicb.2018.03043
Praet, J. et al. (2018) Large-scale cultivation of the bumblebee gut microbiota reveals an underestimated bacterial species diversity capable of pathogen inhibition. Environ Microbiol 20(1), 214-227. 10.1111/1462-2920.13973
Price, M. N. et al. (2018) Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 557(7706), 503-509. 10.1038/s41586-018-0124-0
Probst, A. J. et al. (2018) Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat Microbiol 3(3), 328-336. 10.1038/s41564-017-0098-y
Probst, A. J. et al. (2018) Homologous Recombination and Transposon Propagation Shape the Population Structure of an Organism from the Deep Subsurface with Minimal Metabolism. Genome Biol Evol 10(4), 1115-1119. 10.1093/gbe/evy067
Props, R. et al. (2018) Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels. Environ Microbiol 20(2), 521-534. 10.1111/1462-2920.13953
Raudabaugh, D. B. et al. (2018) Coniella lustricola, a new species from submerged detritus. Mycological Progress 17(1-2), 191-203. 10.1007/s11557-017-1337-6
Rodriguez, R. Lm et al. (2018) How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?. Appl Environ Microbiol 84(6). 10.1128/AEM.00014-18
Roux, S. et al. (2018) A viral reckoning: viruses emerge as essential manipulators of global ecosystems. Environ Microbiol Rep . 10.1111/1758-2229.12700
Roux, Simon et al. (2018) Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature Biotechnology 37, 29. 10.1038/nbt.4306 https://www.nature.com/articles/nbt.4306#supplementary-information
Sade, N. et al. (2018) Salt tolerance of two perennial grass Brachypodium sylvaticum accessions. Plant Mol Biol 96(3), 305-314. 10.1007/s11103-017-0696-3
Sasse, Joelle et al. (2018) Multi-lab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass. New Phytologist 0. 10.1111/nph.15662
Schmid, M. W. et al. (2018) Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha. Genome Biol 19(1), 9. 10.1186/s13059-017-1383-z
Scholthof, K. G. et al. (2018) Brachypodium: A Monocot Grass Model Genus for Plant Biology. Plant Cell 30(8), 1673-1694. 10.1105/tpc.18.00083
Schulz, F. et al. (2018) Hidden diversity of soil giant viruses. Nature Communications 9, 9. 10.1038/s41467-018-07335-2
Schwessinger, B. et al. (2018) A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity. MBio 9(1). 10.1128/mBio.02275-17
Scott, K. M. et al. (2018) Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments. Environ Microbiol . 10.1111/1462-2920.14090
Seaver, S. M. D. et al. (2018) PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency. Plant J 95(6), 1102-1113. 10.1111/tpj.14003
Seshadri, R. et al. (2018) Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nat Biotechnol . 10.1038/nbt.4110
Sieber, C. M. K. et al. (2018) Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol 3(7), 836-843. 10.1038/s41564-018-0171-1
Singer, Esther et al. (2018) Plant compartment and genetic variation drive microbiome composition in switchgrass roots. Environmental Microbiology Reports . 10.1111/1758-2229.12727
Skraban, J. et al. (2018) Draft genome sequence of Chryseobacterium limigenitum SUR2(T) (LMG 28734(T)) isolated from dehydrated sludge. Braz J Microbiol 49(1), 5-6. 10.1016/j.bjm.2017.03.009
Smith, G. J. et al. (2018) Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland. MBio 9(6). 10.1128/mBio.00815-18
Solomon, K. V. et al. (2018) Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts. Fungal Genet Biol 121, 1-9. 10.1016/j.fgb.2018.09.004
Solomon, K. V. et al. (2018) Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts. Fungal Genetics and Biology 121, 1-9. 10.1016/j.fgb.2018.09.004
Spindel, J. E. et al. (2018) Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought. BMC Genomics 19(1), 679. 10.1186/s12864-018-5055-5
Spriggs, A. et al. (2018) Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp). Gates Open Res 2, 7. 10.12688/gatesopenres.12777.1
Spriggs, A. et al. (2018) Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp). Gates Open Res 2, 7. 10.12688/gatesopenres.12777.1
Stein, J. C. et al. (2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet 50(2), 285-296. 10.1038/s41588-018-0040-0
Stiller, J. W. et al. (2018) Evolution and expression of core SWI/SNF genes in red algae. J Phycol 54(6), 879-887. 10.1111/jpy.12795
Stolze, Y. et al. (2018) Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants. Microb Biotechnol 11(4), 667-679. 10.1111/1751-7915.12982
Stough, J. M. A. et al. (2018) Diversity of Active Viral Infections within the Sphagnum Microbiome. Appl Environ Microbiol 84(23). 10.1128/AEM.01124-18
Stritt, C. et al. (2018) Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon. Genome Biol Evol 10(1), 304-318. 10.1093/gbe/evx276
Tas, N. et al. (2018) Landscape topography structures the soil microbiome in arctic polygonal tundra. Nat Commun 9(1), 777. 10.1038/s41467-018-03089-z
Theobald, S. et al. (2018) Uncovering secondary metabolite evolution and biosynthesis using gene cluster networks and genetic dereplication. Scientific Reports 8, 12. 10.1038/s41598-018-36561-3
Tran, P. et al. (2018) Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered Lakes. Environ Microbiol 20(7), 2568-2584. 10.1111/1462-2920.14283
Trubl, G. et al. (2018) Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing. Msystems 3(5), 21. 10.1128/mSystems.00076-18
Tschitschko, B. et al. (2018) Genomic variation and biogeography of Antarctic haloarchaea. Microbiome 6(1), 113. 10.1186/s40168-018-0495-3
Tsesmetzis, N. et al. (2018) Microbial community analysis of three hydrocarbon reservoir cores provides valuable insights for the assessment of reservoir souring potential. International Biodeterioration & Biodegradation 126, 177-188. 10.1016/j.ibiod.2016.09.002
Tuskan, G. A. et al. (2018) Hardwood Tree Genomics: Unlocking Woody Plant Biology. Frontiers in Plant Science 9, 9. 10.3389/fpls.2018.01799
Urquhart, A. S. et al. (2018) Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales). Frontiers in Microbiology 9(3058), 21. 10.3389/fmicb.2018.03058
van der Schuren, A. et al. (2018) Broad spectrum developmental role of Brachypodium AUX1. New Phytol . 10.1111/nph.15332
Varriale, S. et al. (2018) Talaromyces borbonicus, sp. nov., a novel fungus from biodegraded Arundo donax with potential abilities in lignocellulose conversion. Mycologia 110(2), 316-324. 10.1080/00275514.2018.1456835
Vavourakis, C. D. et al. (2018) A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. Microbiome 6(1), 168. 10.1186/s40168-018-0548-7
Vesth, T. C. et al. (2018) Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. Nat Genet . 10.1038/s41588-018-0246-1
Vigneron, A. et al. (2018) Beyond the tip of the iceberg; a new view of the diversity of sulfite- and sulfate-reducing microorganisms. ISME J . 10.1038/s41396-018-0155-4
Vogeli, B. et al. (2018) Combining Promiscuous Acyl-CoA Oxidase and Enoyl-CoA Carboxylase/Reductases for Atypical Polyketide Extender Unit Biosynthesis. Cell Chem Biol 25(7), 833-839 e4. 10.1016/j.chembiol.2018.04.009
Walters, W. A. et al. (2018) Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proc Natl Acad Sci U S A 115(28), 7368-7373. 10.1073/pnas.1800918115
Wang, W. et al. (2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557(7703), 43-49. 10.1038/s41586-018-0063-9
Warshan, D. et al. (2018) Genomic changes associated with the evolutionary transitions of Nostoc to a plant symbiont. Mol Biol Evol . 10.1093/molbev/msy029
Wehking, J. et al. (2018) Community composition and seasonal changes of archaea in coarse and fine air particulate matter. Biogeosciences 15(13), 4205-4214. 10.5194/bg-15-4205-2018
Weiss, C. V. et al. (2018) Genetic dissection of interspecific differences in yeast thermotolerance. Nat Genet 50(11), 1501-1504. 10.1038/s41588-018-0243-4
West, P. T. et al. (2018) Genome-reconstruction for eukaryotes from complex natural microbial communities. Genome Res 28(4), 569-580. 10.1101/gr.228429.117
Weston, D. J. et al. (2018) The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project. New Phytol 217(1), 16-25. 10.1111/nph.14860
Woodcroft, B. J. et al. (2018) Genome-centric view of carbon processing in thawing permafrost. Nature 560(7716), 49-54. 10.1038/s41586-018-0338-1
Woyke, Tanja et al. (2018) Entities inside one another – a matryoshka doll in biology?. Environmental Microbiology Reports 0(0). 10.1111/1758-2229.12716
Wu, B. et al. (2018) Substrate-Specific Differential Gene Expression and RNA editing in the Brown Rot Fungus Fomitopsis pinicola. Appl Environ Microbiol 84(16). 10.1128/AEM.00991-18
Wu, B. et al. (2018) Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies. Genome Biol Evol 10(12), 3250-3261. 10.1093/gbe/evy246
Wu, G. A. et al. (2018) Genomics of the origin and evolution of Citrus. Nature 554(7692), 311-316. 10.1038/nature25447
Wyman, S. K. et al. (2018) A most wanted list of conserved microbial protein families with no known domains. Plos One 13(10). 10.1371/journal.pone.0205749
Xie, L. et al. (2018) Methylglucosylation of aromatic amino and phenolic moieties of drug-like biosynthons by combinatorial biosynthesis. Proc Natl Acad Sci U S A 115(22), E4980-E4989. 10.1073/pnas.1716046115
Xie, Meng et al. (2018) A 5-enolpyruvylshikimate 3-phosphate synthase functions as a transcriptional repressor in Populus. The Plant Cell . 10.1105/tpc.18.00168
Yang, J. et al. (2018) Brassinosteroids Modulate Meristem Fate and Differentiation of Unique Inflorescence Morphology in Setaria viridis. Plant Cell 30(1), 48-66. 10.1105/tpc.17.00816
Yang, S. et al. (2018) Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032. Biotechnol Biofuels 11, 125. 10.1186/s13068-018-1116-x
Yang, X. et al. (2018) Amplification and adaptation of centromeric repeats in polyploid switchgrass species. New Phytol . 10.1111/nph.15098
Yao, Q. et al. (2018) Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil. Nat Ecol Evol 2(3), 499-509. 10.1038/s41559-017-0463-5
Yao, Q. et al. (2018) Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil. Nat Ecol Evol 2(3), 499-509. 10.1038/s41559-017-0463-5
Zhalnina, K. et al. (2018) Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol 3(4), 470-480. 10.1038/s41564-018-0129-3
Zhalnina, K. et al. (2018) Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol 3(4), 470-480. 10.1038/s41564-018-0129-3
Zhang, J. et al. (2018) Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus. New Phytol . 10.1111/nph.15297
Zhang, J. et al. (2018) Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus. New Phytol 220(2), 502-516. 10.1111/nph.15297
Zhou, E. M. et al. (2018) Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California. Extremophiles 22(6), 983-991. 10.1007/s00792-018-1055-2
Zhou, E. M. et al. (2018) Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California. Extremophiles 22(6), 983-991. 10.1007/s00792-018-1055-2
Zhou, R. et al. (2018) Characterization of a large sex determination region in Salix purpurea L. (Salicaceae). Mol Genet Genomics . 10.1007/s00438-018-1473-y
Zhou, R. et al. (2018) Characterization of a large sex determination region in Salix purpurea L. (Salicaceae). Mol Genet Genomics 293(6), 1437-1452. 10.1007/s00438-018-1473-y
Zhu, T. et al. (2018) Analysis of Brachypodium genomes with genome-wide optical maps. Genome . 10.1139/gen-2018-0013
Zhu, Y. et al. (2018) Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples. Int J Mass Spectrom 427, 4-10. 10.1016/j.ijms.2017.08.016
Zuo, C. et al. (2018) Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. Biotechnol Biofuels 11, 170. 10.1186/s13068-018-1167-z