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.
Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics
E.A. McDaniel et al. "Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics" Environmental Microbiology 6, 4 (2021) [DOI: 10.1128/mSystems.00474-21]
Here, we performed time series genome-resolved metatranscriptomics to explore gene expression patterns of coexisting Accumulibacter clades in the same bioreactor ecosystem. Our work provides an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.
Hanseniaspora smithiae sp. nov., a novel apiculate yeast species from Patagonian forests that lacks the typical genomic domestication signatures for fermentative environments
N. Čadež et al. "Hanseniaspora smithiae sp. nov., a novel apiculate yeast species from Patagonian forests that lacks the typical genomic domestication signatures for fermentative environments" Frontiers in Microbiology (2021) [DOI: 10.3389/fmicb.2021.679894]
During a survey of Nothofagus trees and their parasitic fungi in Andean Patagonia (Argentina), genetically distinct strains of Hanseniaspora were obtained from the sugar-containing stromata of parasitic Cyttaria spp.
Contributions of environmental and maternal transmission to the assembly of leaf fungal endophyte communities
L.P. Bell-Dereske and S.E. Evans "Contributions of environmental and maternal transmission to the assembly of leaf fungal endophyte communities" Proceedings of the Royal Society B 288, 1956 (2021) [DOI: 10.1098/rspb.2021.0621]
We used amplicon sequencing to track switchgrass (Panicum virgatum) LFEs in a greenhouse and field experiment as communities assembled from seed endophytes and rain fungi (integration of wet and dry aerial dispersal) in germinating seeds, seedlings, and adult plants.
Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories
D. Robinson et al. "Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories" eLife (2021) [DOI: 10.7554/eLife.70564]
Here, we measured fitness costs of over 4000 overexpressed genes in 15 Saccharomyces cerevisiae strains representing different lineages, to explore natural variation in tolerating gene overexpression (OE).
Relevance of the unfolded protein response to spaceflight-induced transcriptional reprogramming in Arabidopsis
E. Angelos et al. “Relevance of the unfolded protein response to spaceflight-induced transcriptional reprogramming in Arabidopsis” Astrobiology 21, 3 (2021) [DOI: 10.1089/ast.2020.2313]
To contribute to the understanding of how plants respond to spaceflight stress, we examined the significance of the unfolded protein response (UPR), a conserved signaling cascade that responds to a number of unfavorable environmental stresses, in the model plant Arabidopsis thaliana.
QTL x environment interactions underlie ionome divergence in switchgrass
L. Zhang et al. "QTL x environment interactions underlie ionome divergence in switchgrass" G3 Genes|Genomes|Genetics (2021) [DOI:10.1093/g3journal/jkab144]
We grew 725 clonally replicated genotypes of a large full sib family from a four-way linkage mapping population, created from deeply diverged upland and lowland switchgrass ecotypes, at three common gardens.
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.