Publications

JGI publications for calendar year 2024 appear below, listed alphabetically by author.

Alsup, Tyler A. et al. (2024) Characterization of UbiA terpene synthases with a precursor overproduction system in Escherichia coli. . 10.1016/bs.mie.2024.02.001
More Details

Arahal, David R. et al. (2024) Judicial Opinion 129.. International Journal of Systematic and Evolutionary Microbiology 74(2). 10.1099/ijsem.0.006064
More Details

Bálint, Balázs et al. (2024) ContScout: sensitive detection and removal of contamination from annotated genomes. Nature Communications 15(1), 936. 10.1038/s41467-024-45024-5
More Details

Barros, Katharina O. et al. (2024) Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces. Biotechnology for Biofuels and Bioproducts 17(1), 20. 10.1186/s13068-024-02467-8
More Details

Ben Ayed, Amal et al. (2024) Genome sequencing of Porostereum spadiceum to study the degradation of levofloxacin. Ecotoxicology and Environmental Safety 270, 115808. 10.1016/j.ecoenv.2023.115808
More Details

Blow, Matthew J. et al. (2024) Mapping the microbiome milieu. Nature Reviews Microbiology 22(4), 190-190. 10.1038/s41579-024-01019-z
More Details

Bustos-Diaz, Edder D. et al. (2024) Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals. Microbial Genomics 10(3), 001207. 10.1099/mgen.0.001207
More Details

Champagne, Sarah E. et al. (2024) Biocatalytic Stereoselective Oxidation of 2‑Arylindoles. Journal of the American Chemical Society 146(4), 2728-2735. 10.1021/jacs.3c12393
More Details

Coleine, Claudia et al. (2024) Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability. The Science of The Total Environment 917, 170290. 10.1016/j.scitotenv.2024.170290
More Details

DeChellis, Antonio et al. (2024) Supercharging Carbohydrate Binding Module Alone Enhances Endocellulase Thermostability, Binding, and Activity on Cellulosic Biomass. ACS Sustainable Chemistry & Engineering 12(9), 3500-3516. 10.1021/acssuschemeng.3c06266
More Details

Doré, Hugo et al. (2024) Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proceedings of the National Academy of Sciences of the United States of America 121(9), e2316469121. 10.1073/pnas.2316469121
More Details

Fadum, J. M. et al. (2024) Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics. mSystems 9(2), e01059-23. 10.1128/msystems.01059-23
More Details

Feitosa-Junior, Oseias R. et al. (2024) The Exometabolome of Xylella fastidiosa in Contact with Paraburkholderia phytofirmans Supernatant Reveals Changes in Nicotinamide, Amino Acids, Biotin, and Plant Hormones. Metabolites 14(2), 82. 10.3390/metabo14020082
More Details

Grones, Carolin et al. (2024) Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics. The Plant Cell 36(4), 812-828. 10.1093/plcell/koae003
More Details

Hartman, Wyatt H. et al. (2024) Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient. mSystems 9(1), e00936-23. 10.1128/msystems.00936-23
More Details

Healey, A. L. et al. (2024) The complex polyploid genome architecture of sugarcane. Nature , 1-7. 10.1038/s41586-024-07231-4
More Details

Hiraoka, Yoko et al. (2024) Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives. Plants 13(5), 691. 10.3390/plants13050691
More Details

Howard-Varona, Cristina et al. (2024) Environment-specific virocell metabolic reprogramming. The ISME Journal: Multidisciplinary Journal of Microbial Ecology , wrae055. 10.1093/ismejo/wrae055
More Details

Kraisitudomsook, Nattapol et al. (2024) On the origin of bird’s nest fungi: Phylogenomic analyses of fungi in the Nidulariaceae (Agaricales, Basidiomycota). Molecular Phylogenetics and Evolution 193, 108010. 10.1016/j.ympev.2024.108010
More Details

Kridler, Melanie R. et al. (2024) Draft genome sequences of Arthrobacter sp. AZCC_0090 and Mycobacterium sp. AZCC_0083 isolated from oligotrophic subsurface forest soil in the Santa Catalina mountains of Southern Arizona. Microbiology Resource Announcements 13(3), e01089-23. 10.1128/mra.01089-23
More Details

Lee, Ye-Gi et al. (2024) Self-Buffering system for Cost-Effective production of lactic acid from glucose and xylose using Acid-Tolerant Issatchenkia orientalis. Bioresource Technology 399, 130641. 10.1016/j.biortech.2024.130641
More Details

Li, Cheng et al. (2024) Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes. Proceedings of the National Academy of Sciences of the United States of America 121(4), e2312607121. 10.1073/pnas.2312607121
More Details

Li, Li et al. (2024) Biosynthesis of Cytosporones in Leotiomycetous Filamentous Fungi. Journal of the American Chemical Society 146(9), 6189-6198. 10.1021/jacs.3c14066
More Details

Lumian, Jessica et al. (2024) Genomic profiles of four novel cyanobacteria MAGs from Lake Vanda, Antarctica: insights into photosynthesis, cold tolerance, and the circadian clock. Frontiers in Microbiology 14, 1330602. 10.3389/fmicb.2023.1330602
More Details

Ma, Xiao et al. (2024) Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment. Nature Plants 10(2), 240-255. 10.1038/s41477-023-01608-5
More Details

Mantel, Samuel J. et al. (2024) Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species. Molecular Ecology 33(4), e17261. 10.1111/mec.17261
More Details

Marinos, Georgios et al. (2024) Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics.. Microbiology Spectrum 12(2), e0114423. 10.1128/spectrum.01144-23
More Details

Markel, Kasey et al. (2024) Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls. Plant Physiology , kiae001. 10.1093/plphys/kiae001
More Details

Marqués‐Gálvez, José Eduardo et al. (2024) Populus MYC2 orchestrates root transcriptional reprogramming of defence pathway to impair Laccaria bicolor ectomycorrhizal development. New Phytologist 242(2), 658-674. 10.1111/nph.19609
More Details

Mathieu, Davis et al. (2024) Multilevel analysis between Physcomitrium patens and Mortierellaceae endophytes explores potential long‐standing interaction among land plants and fungi. The Plant Journal 118(2), 304-323. 10.1111/tpj.16605
More Details

Miliotis, Georgios et al. (2024) Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.. mBio 15(4), e00181-24. 10.1128/mbio.00181-24
More Details

Mills, Daniel B. et al. (2024) Constraining the oxygen requirements for modern microbial eukaryote diversity. Proceedings of the National Academy of Sciences of the United States of America 121(2), e2303754120. 10.1073/pnas.2303754120
More Details

Navarro, David et al. (2024) Draft genome sequencing and assembly of Favolaschia claudopus CIRM-BRFM 2984 isolated from oak limbs. Journal of Genomics 12, 44-46. 10.7150/jgen.92255
More Details

Nelson, Amelia R et al. (2024) Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrae047. 10.1093/ismejo/wrae047
More Details

Nguyen, Thuy M. et al. (2024) Metatranscriptomes of two biological soil crust types from the Mojave desert in response to wetting. Microbiology Resource Announcements 13(2), e01080-23. 10.1128/mra.01080-23
More Details

Nguyen, Thuy M. et al. (2024) Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert. Microbiology Resource Announcements 13(3), e00980-23. 10.1128/mra.00980-23
More Details

Pellitier, Peter T et al. (2024) Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient. ISME Communications 4(1), ycae031. 10.1093/ismeco/ycae031
More Details

Ramos, Victor M. Gonzalez et al. (2024) Transcriptional response of the white-rot fungus Dichomitus squalens to polysaccharides reveals a co-expression network of plant biomass conversion related genes. Current Research in Biotechnology 7, 100198. 10.1016/j.crbiot.2024.100198
More Details

Sebastián, Marta et al. (2024) Water aging and the quality of organic carbon sources drive niche partitioning of the active bathypelagic prokaryotic microbiome. Limnology and Oceanography 69(3), 562-575. 10.1002/lno.12505
More Details

Shen, Yihui et al. (2024) Mitochondrial ATP generation is more proteome efficient than glycolysis. Nature Chemical Biology , 1-10. 10.1038/s41589-024-01571-y
More Details

Strenkert, Daniela et al. (2024) Distinct function of Chlamydomonas CTRA-CTR transporters in Cu assimilation and intracellular mobilization. Metallomics 16(3), mfae013. 10.1093/mtomcs/mfae013
More Details

Thieme, Michael et al. (2024) Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon. PLOS Genetics 20(3), e1011200. 10.1371/journal.pgen.1011200
More Details

Tsola, S. L. et al. (2024) Methanolobus use unspecific methyltransferases to produce methane from dimethylsulphide in Baltic Sea sediments. Microbiome 12(1), 3. 10.1186/s40168-023-01720-w
More Details

Vitale, Giovanni Andrea et al. (2024) Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products. Natural Product Reports . 10.1039/d3np00050h
More Details

Wang, Yixu et al. (2024) Identification of synthetic consortia from a set of plant‐beneficial bacteria. Microbial Biotechnology 17(2), e14330. 10.1111/1751-7915.14330
More Details

Zhang, Zhihai et al. (2024) Major impacts of widespread structural variation on sorghum.. Genome Research 34(2), 286-299. 10.1101/gr.278396.123
More Details

Zhong, Zhi-Ping et al. (2024) Viral potential to modulate microbial methane metabolism varies by habitat. Nature Communications 15(1), 1857. 10.1038/s41467-024-46109-x
More Details