GLBRC Data Sets
Highlighted below are a variety of published studies that include data sets that might be of interest to the scientific community and have been deposited in online data repositories. Only data sets published in GLBRC-approved repositories following the FAIR Guiding Principles are highlighted. More information can be found on our guidelines page.
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass
J.T. Lovell et al. “Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass” Nature 590 (2021) [DOI: 10.1038/s41586-020-03127-1]
Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation.
Machine learning improves predictions of agricultural nitrous oxide emissions from intensively managed cropping systems
D. Saha et al. “Machine learning improves predictions of agricultural nitrous oxide (N2O) emissions from intensively managed cropping systems” Environmental Research Letters 16, 2 (2020) [DOI: 10.1088/1748-9326/abd2f3]
Here we show the promise for machine learning (ML) to significantly improve field-level flux predictions, especially when coupled with a cropping systems model to simulate unmeasured parameters.
Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss
M.A.B. Haase et al. “Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss” Genetics 217, 2 (2020) [DOI: 10.1093/genetics/iyaa012]
Here, through phylogenomic analyses, we reconstructed the evolutionary history of the yeast galactose utilization pathway and observed widespread and repeated losses of the ability to utilize galactose, which occurred concurrently with the losses of GALactose (GAL) utilization genes.
Widespread irreproducibility in phylogenetics
X. Shen et al. “Widespread irreproducibility in phylogenetics” Nature Communications 11, 6096 (2020) [DOI: 10.1038/s41467-020-20005-6]
Phylogenetic trees are essential for studying biology, but their reproducibility under identical parameter settings remains unexplored. Here, we find that 3515 (18.11%) IQ-TREE-inferred and 1813 (9.34%) RAxML-NG-inferred maximum likelihood (ML) gene trees are topologically irreproducible.
A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation
K.K. Henry et al. “A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation” PNAS 117, 47 (2020) [DOI: 10.1073/pnas.2010087117]
Bacterial promoters are often predicted by similarity to the Escherichia coli −10 and −35 consensus elements. Although these elements are highly conserved in diverse bacterial phyla, only 30 to 43% of promoters we analyzed from Rhodobacter sphaeroides and two other α-proteobacteria contained −7T.
Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota
X. Shen et al. “Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota” Science Advances 6, 45 (2020) [DOI: 10.1126/sciadv.abd0079]
By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period.
Diagnosing and predicting mixed culture fermentations with unicellular and guild-based metabolic models
M.J. Scarborough et al. “Diagnosing and predicting mixed culture fermentations with unicellular and guild-based metabolic models” mSystems 5, 5 (2020) [DOI: 10.1128/mSystems.00755-20]
Predicting behavior of self-assembled or synthetic microbiomes, however, remains a challenge. In this work, we used unicellular and guild-based metabolic models to investigate the production of medium-chain fatty acids by a mixed microbial community that is fed multiple organic substrates.
Seasonal dynamics of core fungi and bacterial networks in the switchgrass phyllosphere.
A.W. Bowsher et al. “Seasonal dynamics of core fungi and bacterial networks in the switchgrass phyllosphere” Phytobiomes journal 104 (2020) [DOI: 10.1094/PBIOMES-07-20-0051-R]
Here, we investigated seasonal dynamics of epiphytic phyllosphere fungal communities in switchgrass (Panicum virgatum L.), a focal bioenergy crop. We also leverage previously published data on switchgrass phyllosphere bacterial communities from the same experimental plants, allowing us to compare fungal and bacterial dynamics and explore interdomain network associations in the switchgrass phyllosphere.
The biosynthesis of the anti‐microbial diterpenoid leubethanol in Leucophyllum frutescens proceeds via an all‐cis prenyl intermediate
G. P. Miller et al. “The biosynthesis of the anti‐microbial diterpenoid leubethanol in Leucophyllum frutescens proceeds via an all‐cis prenyl intermediate.” The plant journal for cell and molecular biology 104 (2020) [DOI: 10.1111/tpj.14957]
Here we leverage the simple product profile and high accumulation of leubethanol in the roots of L. frutescens and compare tissue‐specific transcriptomes with existing data from Eremophila serrulata to decipher the biosynthesis of leubethanol.
Genome-wide identification of transcription start sites in two Alphaproteobacteria
K. Myers et al. “Genome-Wide Identification of Transcription Start Sites in Two Alphaproteobacteria, Rhodobacter sphaeroides and Novosphingobium aromaticivorans.” Microbiology Resource Announcements 9, 36 (2020) [DOI: 10.1128/MRA.00880-20]
Here we report the genome-wide identification of transcription start sites (TSSs) from two alphaproteobacteria grown under conditions that result in significant changes in gene expression.
GLBRC energy balance measurements
Chen Jiquan, Robertson Phil, Abraha Michael
AmeriFlux is a network of sites measuring ecosystem CO2, water, and energy fluxes in North, Central, and South America supported by the U.S. Department of Energy's Office of Biological and Environmental Research.
Synthetic hybrids of six yeast species
D. Peris, et al. “Synthetic hybrids of six yeast species.” Nature Communications (2020) 11, 2085 [DOI: 10.1038/s41467-020-15559-4]
Here we develop an iterative method of Hybrid Production (iHyPr) to combine the genomes of multiple budding yeast species, generating Saccharomyces allopolyploids of at least six species. When making synthetic hybrids, chromosomal instability and cell size increase dramatically as additional copies of the genome are added.
Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome
M.J. Scarborough et al. (2018). Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome. mSystems 3:e00221-18
Here, we integrated metagenomic, metatranscriptomic, and thermodynamic analyses to predict and characterize the metabolic network of an anaerobic microbiome producing MCFA from organic matter derived from lignocellulosic ethanol fermentation conversion residue.
Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype
G. Bonito et al. (2019). Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype. Frontiers in Microbiology 10:481.
We used bioassay common garden experiments to decouple plant genotype and soil property impacts on fungal and bacterial community structure in the Populus rhizobiome. High throughput amplification and sequencing of 16S, ITS, 28S and 18S rDNA was accomplished through 454 pyrosequencing.
Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases
E.M. Glasgow et al. (2019). Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases. Journal of Molecular Biology 431:1217–1233.
To deepen the understanding of the structural and evolutionary driving forces underlying specificity patterns in glycoside hydrolase family 5, we quantitatively screened the activity of the catalytic core domains from subfamily 4 (GH5_4) and closely related enzymes on four substrates: lichenan, xylan, mannan, and xyloglucan.
Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast
K.S. Myers et al. (2019). Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast. PLOS Genetics 15: e1008037
To understand flux rerouting, we investigated a panel of Saccharomyces cerevisiae strains with progressive improvements in anaerobic fermentation of xylose, a sugar abundant in sustainable plant biomass used for biofuel production. We combined comparative transcriptomics, proteomics, and phosphoproteomics with network analysis to understand the physiology of improved anaerobic xylose fermentation.
Eukaryotic Acquisition of a Bacterial Operon
J. Kominek et al. (2018). Eukaryotic Acquisition of a Bacterial Operon. Cell 176:1356–1366.
Here, we report the horizontal operon transfer of a siderophore biosynthesis pathway from relatives of Escherichia coli into a group of budding yeast taxa. We further show that the co-linearly arranged secondary metabolism genes are expressed, exhibit eukaryotic transcriptional features, and enable the sequestration and uptake of iron.
Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production
M. J. Scarborough et al. (2018). Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production. Biotechnology for Biofuels 11:200
Here we test the hypothesis that a bacterial community could transform the organics in stillage into valuable bioproducts. We demonstrate the ability of this microbiome to convert stillage organics into medium-chain fatty acids (MCFAs), identify the predominant community members, and perform a technoeconomic analysis of recovering MCFAs as co-products of ethanol production.
Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032
S. Yang 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. Biotechnology for Biofuels 11: 125
In this study, we determined the complete chromosome and plasmid sequences of ZM4 and its engineered xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4 chromosome sequences, the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well as a 2400-bp insertion.
Reductive Cleavage Method for Quantitation of Monolignols and Low‐Abundance Monolignol Conjugates
M. Regner et al. (2018). Reductive Cleavage Method for Quantitation of Monolignols and Low-Abundance Monolignol Conjugates ChemSusChem 11:1600-1605.
As the derivatization followed by reductive cleavage (DFRC) method is particularly effective for structurally characterizing natively acylated lignins, we used an array of synthetic β‐ether γ‐acylated model compounds to determine theoretical yields for all monolignol conjugates currently known to exist in lignin, and we synthesized a new set of deuterated analogs as internal standards for quantification using GC–MS/MS.