2024
(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
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(2024) The complex polyploid genome architecture of sugarcane.
Nature , 1-7.
10.1038/s41586-024-07231-4
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(2024) Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives.
Plants 13(5), 691.
10.3390/plants13050691
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(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
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(2024) Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment.
Nature Plants 10(2), 240-255.
10.1038/s41477-023-01608-5
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(2024) Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species.
Molecular Ecology 33(4), e17261.
10.1111/mec.17261
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(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
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(2024) Major impacts of widespread structural variation on sorghum..
Genome Research 34(2), 286-299.
10.1101/gr.278396.123
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2023
(2023) Metabolomic, photoprotective, and photosynthetic acclimatory responses to post‐flowering drought in sorghum.
Plant Direct 7(11), e545.
10.1002/pld3.545
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(2023) Metabolomic, photoprotective, and photosynthetic acclimatory responses to post‐flowering drought in sorghum.
Plant Direct 7(11), e545.
10.1002/pld3.545
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(2023) Metabolomic, photoprotective, and photosynthetic acclimatory responses to post‐flowering drought in sorghum.
Plant Direct 7(11), e545.
10.1002/pld3.545
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(2023) Evolutionary Analyses of Gene Expression Divergence in Panicum hallii: Exploring Constitutive and Plastic Responses Using Reciprocal Transplants.
Molecular Biology and Evolution 40(10), msad210.
10.1093/molbev/msad210
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(2023) The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus.
Plant Biotechnology Journal .
10.1111/pbi.14199
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(2023) The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus.
Plant Biotechnology Journal .
10.1111/pbi.14199
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(2023) The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus.
Plant Biotechnology Journal .
10.1111/pbi.14199
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(2023) Epicuticular wax accumulation and regulation of wax pathway gene expression during bioenergy Sorghum stem development.
Frontiers in Plant Science 14, 1227859.
10.3389/fpls.2023.1227859
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(2023) Epicuticular wax accumulation and regulation of wax pathway gene expression during bioenergy Sorghum stem development.
Frontiers in Plant Science 14, 1227859.
10.3389/fpls.2023.1227859
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(2023) Epicuticular wax accumulation and regulation of wax pathway gene expression during bioenergy Sorghum stem development.
Frontiers in Plant Science 14, 1227859.
10.3389/fpls.2023.1227859
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(2023) Multiplex Editing of the Nucleoredoxin1 Tandem Array in Poplar: From Small Indels to Translocations and Complex Inversions.
The CRISPR Journal .
10.1089/crispr.2022.0096
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(2023) The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses.
Current Biology 33(23), 5199-5207.e4.
10.1016/j.cub.2023.10.009
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(2023) The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses.
Current Biology 33(23), 5199-5207.e4.
10.1016/j.cub.2023.10.009
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(2023) The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses.
Current Biology 33(23), 5199-5207.e4.
10.1016/j.cub.2023.10.009
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(2023) Predicted structural proteome of Sphagnum divinum and proteome-scale annotation.
Bioinformatics 39(8), btad511.
10.1093/bioinformatics/btad511
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(2023) Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet.
Nature Communications 14(1), 3694.
10.1038/s41467-023-38915-6
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(2023) Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range.
Current Biology 33(10), 1926-1938.e6.
10.1016/j.cub.2023.03.078
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(2023) Mixed-Linkage Glucan Is the Main Carbohydrate Source and Starch Is an Alternative Source during Brachypodium Grain Germination.
International Journal of Molecular Sciences 24(7), 6821.
10.3390/ijms24076821
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(2023) Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics.
Nature Plants 9(2), 238-254.
10.1038/s41477-022-01333-5
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(2023) Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias.
Molecular Biology and Evolution 40(12), msad251.
10.1093/molbev/msad251
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(2023) Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias.
Molecular Biology and Evolution 40(12), msad251.
10.1093/molbev/msad251
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(2023) Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias.
Molecular Biology and Evolution 40(12), msad251.
10.1093/molbev/msad251
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(2023) A large sequenced mutant library – valuable reverse genetic resource that covers 98% of sorghum genes.
The Plant Journal .
10.1111/tpj.16582
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(2023) A large sequenced mutant library – valuable reverse genetic resource that covers 98% of sorghum genes.
The Plant Journal .
10.1111/tpj.16582
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(2023) A large sequenced mutant library – valuable reverse genetic resource that covers 98% of sorghum genes.
The Plant Journal .
10.1111/tpj.16582
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(2023) Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant.
Genome Biology and Evolution 15(9), evad167.
10.1093/gbe/evad167
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(2023) Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant.
Genome Biology and Evolution 15(9), evad167.
10.1093/gbe/evad167
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(2023) Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant.
Genome Biology and Evolution 15(9), evad167.
10.1093/gbe/evad167
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(2023) Quantitative genetic-by-soil microbiome interactions in a perennial grass affect functional traits.
Proceedings of the Royal Society B 290(1991), 20221350.
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(2023) Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa.
Plant Phenomics 5, 0072.
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(2023) The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum.
G3: Genes, Genomes, Genetics 14(1), jkad245.
10.1093/g3journal/jkad245
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(2023) The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum.
G3: Genes, Genomes, Genetics 14(1), jkad245.
10.1093/g3journal/jkad245
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(2023) The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum.
G3: Genes, Genomes, Genetics 14(1), jkad245.
10.1093/g3journal/jkad245
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(2023) A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.).
The Plant Genome , e20319.
10.1002/tpg2.20319
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(2023) Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists.
Microbiology Spectrum 11(2), e04247-22.
10.1128/spectrum.04247-22
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(2023) Regulation of hair cell and stomatal size by a hair cell-specific peroxidase in the grass Brachypodium distachyo n.
Current Biology 33(9), 1844-1854.e6.
10.1016/j.cub.2023.03.089
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(2023) Plant myo-inositol transport influences bacterial colonization phenotypes.
Current Biology 33(15), 3111-3124.e5.
10.1016/j.cub.2023.06.057
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(2023) The diatom Fragilariopsis cylindrus: A model alga to understand cold‐adapted life.
Journal of Phycology 59(2), 301-306.
10.1111/jpy.13325
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(2023) Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss)..
Annals of Botany .
10.1093/aob/mcad104
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(2023) Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases.
Frontiers in Plant Science 14, 1210146.
10.3389/fpls.2023.1210146
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(2023) Genome to gut: crop engineering for human microbiomes.
Nature Reviews Microbiology 21(3), 132-132.
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(2023) Transposon signatures of allopolyploid genome evolution.
Nature Communications 14(1), 3180.
10.1038/s41467-023-38560-z
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(2023) JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom.
Nucleic Acids Research 51(16), 8383-8401.
10.1093/nar/gkad616
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(2023) Genomic prediction of switchgrass winter survivorship across diverse lowland populations.
G3: Genes, Genomes, Genetics 13(3), jkad014.
10.1093/g3journal/jkad014
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(2023) Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii.
Plant Physiology 192(3), 2374-2393.
10.1093/plphys/kiad209
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(2023) PHYTOCHROME C regulation of photoperiodic flowering via PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon.
PLOS Genetics 19(5), e1010706.
10.1371/journal.pgen.1010706
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(2023) Expression quantitative trait loci mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus.
New Phytologist 239(6), 2248-2264.
10.1111/nph.19126
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(2023) Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina).
Nature Plants 9(8), 1207-1220.
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(2023) Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus..
Plant Physiology .
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(2023) Secreted Effector Proteins of the Poplar Leaf Spot and Stem Canker Pathogen Sphaerulina musiva Manipulate Plant Immunity and Contribute to Virulence in Diverse Ways..
Molecular Plant-Microbe Interactions .
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(2023) Haplotype‐resolved genome assembly of Populus tremula × P. alba reveals aspen‐specific megabase satellite DNA.
The Plant Journal .
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(2023) Single-cell profiling of Arabidopsis leaves to Pseudomonas syringae infection.
Cell Reports 42(7), 112676.
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2022
(2022) High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa.
G3: Genes, Genomes, Genetics 13(1), jkac269.
10.1093/g3journal/jkac269
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(2022) Do Genetic Drift and Gene Flow Affect the Geographic Distribution of Female Plants in Gynodioecious Lobelia siphilitica?.
Plants 11(6), 825.
10.3390/plants11060825
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(2022) Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA.
Plant Physiology 189(2), 516-526.
10.1093/plphys/kiac128
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(2022) The western redcedar genome reveals low genetic diversity in a self-compatible conifer.
Genome Research 32(10), gr.276358.121.
10.1101/gr.276358.121
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(2022) EARLY FLOWERING 3 and Photoperiod Sensing in Brachypodium distachyon.
Frontiers in Plant Science 12, 769194.
10.3389/fpls.2021.769194
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(2022) Chromosome evolution and the genetic basis of agronomically important traits in greater yam.
Nature Communications 13(1), 2001.
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(2022) Representing sex chromosomes in genome assemblies.
Cell Genomics 2(5), 100132.
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(2022) Habitat‐adapted microbial communities mediate Sphagnum peatmoss resilience to warming.
New Phytologist 234(6), 2111-2125.
10.1111/nph.18072
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(2022) The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory.
The Plant Cell 35(2), 644-672.
10.1093/plcell/koac347
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(2022) Thermal Stress Has Minimal Effects on Bacterial Communities of Thermotolerant Symbiodinium Cultures.
Frontiers in Ecology and Evolution 10, 764086.
10.3389/fevo.2022.764086
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(2022) Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.
Life Science Alliance 6(3), e202201833.
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(2022) Toward a data infrastructure for the Plant Cell Atlas..
Plant Physiology 191(1), 35-46.
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(2022) Thousands of small, novel genes predicted in global phage genomes.
Cell Reports 39(12), 110984.
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(2022) Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression.
Molecular Ecology 32(10), 2674-2687.
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(2022) Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities.
Nature Communications 13(1), 3867.
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(2022) Brachypodium: 20 years as a grass biology model system; the way forward?.
Trends in Plant Science 27(10), 1002-1016.
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(2022) Comparative genomics analysis of drought response between obligate CAM and C3 photosynthesis plants.
Journal of Plant Physiology 277, 153791.
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(2022) DNA Sequence Analysis of an Inversion Hot Spot in Lobeliaceae Plastomes.
Plants 11(21), 2863.
10.3390/plants11212863
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(2022) N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon.
Journal of Experimental Botany 73(15), 5306-5321.
10.1093/jxb/erac184
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(2022) Agave REVEILLE1 regulates the onset and release of seasonal dormancy in Populus.
Plant Physiology 191(3), 1492-1504.
10.1093/plphys/kiac588
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(2022) Silencing of Dicer‐like protein 2a restores the resistance phenotype in the rice mutant, sxi4 (suppressor of Xa21‐mediated immunity 4).
The Plant Journal 110(3), 646-657.
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(2022) GENESPACE tracks regions of interest and gene copy number variation across multiple genomes.
eLife 11, e78526.
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(2022) The first complete human genome.
Nature 606(7914), 468-469.
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(2022) Dynamic genome evolution in a model fern.
Nature Plants 8(9), 1038-1051.
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(2022) The Transcription Factor Roc1 Is a Key Regulator of Cellulose Degradation in the Wood-Decaying Mushroom Schizophyllum commune.
mBio 13(3), e00628-22.
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(2022) High‐throughput identification of novel heat tolerance genes via genome‐wide pooled mutant screens in the model green alga Chlamydomonas reinhardtii.
Plant Cell & Environment 46(3), 865-888.
10.1111/pce.14507
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(2022) KARRIKIN INSENSITIVE2 regulates leaf development, root system architecture and arbuscular‐mycorrhizal symbiosis in Brachypodium distachyon.
The Plant Journal 109(6), 1559-1574.
10.1111/tpj.15651
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(2022) Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification.
Theoretical and Applied Genetics 135(4), 1279-1292.
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(2022) Critical Assessment of Metagenome Interpretation: the second round of challenges.
Nature Methods 19(4), 429-440.
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(2022) Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population.
Genetics 221(2), iyac063-.
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(2022) The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange.
Science Advances 8(6), eabj4633.
10.1126/sciadv.abj4633
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(2022) A generalist–specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range.
Proceedings of the National Academy of Sciences of the United States of America 119(15), e2118879119.
10.1073/pnas.2118879119
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(2022) Re-evaluating the Systematics of Dendrolycopodium Using Restriction-Site Associated DNA-Sequencing.
Frontiers in Plant Science 13, 912080.
10.3389/fpls.2022.912080
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(2022) A sorghum genome-wide association study (GWAS) identifies a WRKY transcription factor as a candidate gene underlying sugarcane aphid (Melanaphis sacchari) resistance.
Planta 255(2), 37.
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(2022) Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids.
The Plant Journal 109(6), 1535-1558.
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(2022) Patterns of pan‐genome occupancy and gene coexpression under water‐deficit in Brachypodium distachyon.
Molecular Ecology 31(20), 5285-5306.
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(2022) Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium.
Genetics 223(2), iyac146.
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(2022) A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.
Developmental Cell 57(4), 543-560.e9.
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(2022) The western redcedar genome reveals low genetic diversity in a self-compatible conifer.
Genome Research 32(10), gr.276358.121.
10.1101/gr.276358.121
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(2022) Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta).
New Phytologist 236(4), 1497-1511.
10.1111/nph.18429
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(2022) The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle.
The Plant Journal 112(2), 352-368.
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(2022) Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass.
Nature Communications 13(1), 7731.
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(2022) Host genotype controls ecological change in the leaf fungal microbiome.
PLOS Biology 20(8), e3001681.
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(2022) A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass.
Molecular Biology and Evolution 39(10), msac203.
10.1093/molbev/msac203
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(2022) The CC–NB–LRR protein BSR1 from Brachypodium confers resistance to Barley stripe mosaic virus in gramineous plants by recognising TGB1 movement protein.
New Phytologist 236(6), 2233-2248.
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(2022) Bioenergy sorghum stem growth regulation: intercalary meristem localization, development, and gene regulatory network analysis.
The Plant Journal 112(2), 476-492.
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2021
(2021) Genomic variation within the maize stiff-stalk heterotic germplasm pool.
Plant Genome .
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(2021) Phosphate Availability Modulates Root Exudate Composition and Rhizosphere Microbial Community in a Teosinte and a Modern Maize Cultivar.
Phytobiomes Journal .
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(2021) Gene-rich UV sex chromosomes harbor conserved regulators of sexual development.
Science Advances 7(27).
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(2021) Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology 16(4), 1074-1085.
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(2021) Plant single-cell solutions for energy and the environment.
Communications Biology 4(1).
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(2021) Gamete expression of TALE class HD genes activates the diploid sporophyte program in Marchantia polymorpha.
eLife 10, e57088.
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(2021) The contributions from the progenitor genomes of the mesopolyploid brassiceae are evolutionarily distinct but functionally compatible.
Genome Research 31(5), 799-810.
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(2021) Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae.
Journal of Integrative Plant Biology n/a(n/a).
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(2021) Pests, diseases, and aridity have shaped the genome of Corymbia citriodora.
Communications Biology 4(1).
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(2021) Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat.
Frontiers in Plant Science 12.
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(2021) Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, Yucca gloriosa (Asparagaceae).
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(2021) Integrative genomics reveals paths to sex dimorphism in Salix purpurea L.
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(2021) Vision, challenges and opportunities for a plant cell atlas.
eLife 10.
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(2021) Bioenergy sorghum’s deep roots: A key to sustainable biomass production on annual cropland.
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(2021) Plant Pan-Genomics Comes of Age.
Annual Review of Plant Biology 72, 411-435.
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(2021) Genetic dissection of natural variation in oilseed traits of camelina by whole-genome resequencing and QTL mapping.
Plant Genome .
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(2021) Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.
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(2021) Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding.
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(2021) Current status and impending progress for cassava structural genomics.
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(2021) Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass) [version 1; peer review: 1 approved].
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(2021) Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus.
Molecular Biology and Evolution .
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(2021) Cytochrome P450-catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass (Panicum virgatum L.).
Plant Journal .
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(2021) Three founding ancestral genomes involved in the origin of sugarcane.
Annals of Botany 127(6), 827-840.
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(2021) Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting.
Proceedings of the National Academy of Sciences of the United States of America 118(29).
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(2021) BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon.
BMC Plant Biology 21(1).
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(2021) Cell Wall Compositions of Sorghum bicolor Leaves and Roots Remain Relatively Constant Under Drought Conditions.
Frontiers in Plant Science 12, 747225.
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(2021) Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome.
Phytobiomes Journal 5(2).
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(2021) Diversification of mandarin citrus by hybrid speciation and apomixis.
Nature Communications 12.
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(2021) The Ancient Salicoid Genome Duplication Event: A Platform for Reconstruction of De Novo Gene Evolution in Populus trichocarpa.
Genome Biology and Evolution 13(9).
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(2021) Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers.
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2020
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(2020) Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean.
Genetics 215(1), 267-284.
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(2020) A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci.
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(2020) Genome biology of the paleotetraploid perennial biomass crop Miscanthus.
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2019
(2019) High-density linkage map reveals QTL underlying growth traits in AP13xVS16 biparental population of switchgrass.
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(2019) The genome sequence of segmental allotetraploid peanut Arachis hypogaea.
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(2019) A New Method to Correct for Habitat Filtering in Microbial Correlation Networks.
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(2019) Genome sequence of the model rice variety KitaakeX.
BMC Genomics 20(1), 905.
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(2019) The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass.
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(2019) Mediation of plant-mycorrhizal interaction by a lectin receptor-like kinase.
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(2018) Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage.
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(2018) Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp).
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