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.
A multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1
N.C. Oates et al. "A multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1" PNAS 118,18 (2021) [DOI:10.1073/pnas.2008888118]
Here, we describe the isolation of an exceptional lignocellulose-degrading fungus that produces new oxidase activity with no cofactor requirements.
Genome-resolved metagenomics of a photosynthetic bioreactor performing biological nutrient removal
E.A. McDaniel et al. "Genome-resolved metagenomics of a photosynthetic bioreactor performing biological nutrient removal" Microbiology Resource Announcements 10,18 (2021) [DOI:10.1128/MRA.00244-21]
We present a genome-resolved metagenomics data set consisting of 86 metagenome-assembled genome sequences from a photosynthetically operated lab-scale bioreactor simulating EBPR.
Efficient synthesis of pinoresinol, an important lignin dimeric model compound
F. Yue et al. "Efficient synthesis of pinoresinol, an important lignin dimeric model compound" Frontiers in Energy Research 9 (2021) [DOI: 10.3389/fenrg.2021.640337]
The synthetic yield and isolation efficiency of racemic pinoresinol from coniferyl alcohol by conventional radical coupling methods is sub-optimal. In this work, a facile and efficient synthetic approach was developed to synthesize pinoresinol with much higher yield.
Predictive models of genetic redundancy in Arabidopsis thaliana
S.A. Cusack et al. "Predictive models of genetic redundancy in Arabidopsis thaliana" Molecular Biology and Evolution (2021) [DOI: 10.1093/molbev/msab111]
Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plant Arabidopsis thaliana based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including posttranslational modifications, gene expression, and gene network properties.
A genome-scale phylogeny of the kingdom Fungi
L. Yuanning et al. “A genome-scale phylogeny of the kingdom Fungi” Nature Ecology 31, 8 (2020) [DOI:10.1016/j.cub.2021.01.074]
To examine poorly resolved relationships and assess progress toward a genome-scale phylogeny of the fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 species that includes representatives from most major fungal lineages.
Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples
C.E. O’Brien et al. "Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples" PLoS Pathogens 17, 3 (2021) [DOI: 10.1371/journal.ppat.1009138]
By carrying out a phylogenomic analysis of 77 isolates, we find that C. tropicalis genomes range from very homozygous to highly heterozygous. We show that the heterozygous isolates are hybrids, most likely formed by mating between different parents.
Accuracy, Bias, and Improvements in Mapping Crops and Cropland across the United States Using the USDA Cropland Data Layer
T. Lark et al. "Accuracy, bias, and improvements in mapping crops and cropland across the United States using the USDA Cropland Data Layer" Remote Sensing 15, 5 (2021) [DOI: 10.3390/rs13050968]
We used state- and land cover class-specific accuracy statistics from the USDA from 2008 to 2016 to comprehensively characterize the performance of the CDL across space and time. We estimated nationwide area-weighted accuracies for the CDL for specific crops as well as for the aggregated classes of cropland and non-cropland.
Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops
K.L. Grady et al. "Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops" Nature Communications 10, 4135 (2019) [DOI:10.1038/s41467-019-11974-4]
Here, we characterize the 16S rRNA gene diversity and seasonal assembly of bacterial and archaeal microbiomes of two perennial cellulosic feedstocks, switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus).
Quantifying and correcting for pre-assay CO2 loss in short-term carbon mineralization assays
M. Belanger et al. “Quantifying and correcting for pre-assay CO2 loss in short-term carbon mineralization assays” SOIL 11, 4295 (2020) [DOI: 10.5194/soil-2020-55]
Soils can lose carbon (C) as they dry and, if soil samples vary in moisture content at sampling, differential C loss during the pre-assay dry-down period may complicate the assay’s interpretations. We examined the impact of pre-assay CO2 loss in a long-cultivated agricultural soil at initial moisture contents of 30 %, 50 %, and 70 % water-filled pore space (WFPS).
Eudicot Nutshells: Cell-Wall Composition and Biofuel Feedstock Potential
L. Landucci et al. “Eudicot Nutshells: Cell-Wall Composition and Biofuel Feedstock Potential” ACS Sustainable Chemistry and Engineering 34, 12 (2020) [DOI: 10.1021/acs.energyfuels.0c03131]
In the context of understanding the general character of phylogenetically diverse eudicot species, we provide a chemical analysis of the lignin in the shells of commonly eaten nuts and detail the chemical composition of their lignins.
A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR
D.K. Ko et al. “A temporal hierarchy underpins the transcription factor-DNA interactome of the maize UPR” The Plant journal 105, 1 (2020) [DOI: 10.1111/tpj.15044]
We performed a large-scale systems-level analysis of the protein-DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high-throughput enhanced yeast one-hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR.
Switchgrass Rhizosphere Metabolite Chemistry Driven by Nitrogen Availability
D.N. Smercina et al. “Switchgrass rhizosphere metabolite chemistry driven by nitrogen availability” Phytobiomes 5, 1 (2020) [DOI: 10.1094/PBIOMES-09-19-0055-FI]
It is not known how or if switchgrass responds to diazotrophs or their activity. To explore this question, we assessed rhizosphere metabolite chemistry of switchgrass grown in a hydroponic system under two N levels and under inoculated or uninoculated conditions.
Cropland expansion in the United States produces marginal yields at high costs to wildlife
T. Lark et al. “Cropland expansion in the United States produces marginal yields at high costs to wildlife” Nature Communications 11, 4295 (2020) [DOI: 10.1038/s41467-020-18045-z]
Here we assess annual land use change 2008–16 and its impacts on crop yields and wildlife habitat. We find that croplands have expanded at a rate of over one million acres per year, and that 69.5% of new cropland areas produced yields below the national average, with a mean yield deficit of 6.5%.
The AGCVIII kinase Dw2 modulates cell proliferation, endomembrane trafficking, and MLG/xylan cell wall localization in elongating stem internodes of Sorghum bicolor
J. Oliver et al. “The AGCVIII kinase Dw2 modulates cell proliferation, endomembrane trafficking, and MLG/xylan cell wall localization in elongating stem internodes of Sorghum bicolor” The plant journal (2020) [DOI: 10.111/tpl.15086]
Here we provide evidence that mutation of Dw2 reduces cell proliferation in internode intercalary meristems, inhibits endocytosis, and alters the distribution of heteroxylan and mixed linkage glucan in cell walls.
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.