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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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Home › Our Science › Science Programs › Plant Program › Plant Publications

Plant Publications

All JGI Publications

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2022

Appiah-Madson, Hannah J. et al. (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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Bewg, William P. et al. (2022) Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA. Plant physiology . 10.1093/plphys/kiac128
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Bouché, Frédéric et al. (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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Carrell, Alyssa A. et al. (2022) Habitat‐adapted microbial communities mediate Sphagnum peatmoss resilience to warming. New Phytologist . 10.1111/nph.18072
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Gao, Cheng et al. (2022) Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression. Molecular Ecology . 10.1111/mec.16343
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Lamb, Austin et al. (2022) Bioenergy sorghum’s deep roots: A key to sustainable biomass production on annual cropland. GCB Bioenergy 14(2), 132-156. 10.1111/gcbb.12907
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Liu, Furong et al. (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 . 10.1111/tpj.15692
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Muleta, Kebede T. et al. (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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Shahan, Rachel et al. (2022) A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Developmental Cell 57(4), 543-560.e9. 10.1016/j.devcel.2022.01.008
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2021

Bornowski, N. et al. (2021) Genomic variation within the maize stiff-stalk heterotic germplasm pool. Plant Genome . 10.1002/tpg2.20114
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Brisson, V. et al. (2021) Phosphate Availability Modulates Root Exudate Composition and Rhizosphere Microbial Community in a Teosinte and a Modern Maize Cultivar. Phytobiomes Journal . 10.1094/pbiomes-06-21-0041-r
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Carey, S. B. et al. (2021) Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. Science Advances 7(27). 10.1126/sciadv.abh2488
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Carrell, Alyssa A. et al. (2021) Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism. The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-12. 10.1038/s41396-021-01136-0
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Cole, B. et al. (2021) Plant single-cell solutions for energy and the environment. Communications Biology 4(1). 10.1038/s42003-021-02477-4
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Dierschke, Tom et al. (2021) Gamete expression of TALE class HD genes activates the diploid sporophyte program in Marchantia polymorpha. eLife 10, e57088. 10.7554/elife.57088
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Hao, Y. et al. (2021) The contributions from the progenitor genomes of the mesopolyploid brassiceae are evolutionarily distinct but functionally compatible. Genome Research 31(5), 799-810. 10.1101/GR.270033.120
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Hawkins, Charles et al. (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). https://doi.org/10.1111/jipb.13163
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Healey, A. L. et al. (2021) Pests, diseases, and aridity have shaped the genome of Corymbia citriodora. Communications Biology 4(1). 10.1038/s42003-021-02009-0
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Henningsen, E. C. et al. (2021) Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat. Frontiers in Plant Science 12. 10.3389/fpls.2021.657796
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Heyduk, K. et al. (2021) Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, Yucca gloriosa (Asparagaceae). Frontiers in Plant Science 11, 16. 10.3389/fpls.2020.573767
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Hyden, B. et al. (2021) Integrative genomics reveals paths to sex dimorphism in Salix purpurea L. Horticulture Research 8(1). 10.1038/s41438-021-00606-y
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Jha, S. G. et al. (2021) Vision, challenges and opportunities for a plant cell atlas. eLife 10. 10.7554/eLife.66877
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Lei, L. et al. (2021) Plant Pan-Genomics Comes of Age. Annual Review of Plant Biology 72, 411-435. 10.1146/annurev-arplant-080720-105454
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Li, H. et al. (2021) Genetic dissection of natural variation in oilseed traits of camelina by whole-genome resequencing and QTL mapping. Plant Genome . 10.1002/tpg2.20110
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Lovell, J. T. et al. (2021) Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding. Nature Communications 12(1). 10.1038/s41467-021-24328-w
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Lovell, J. T. et al. (2021) Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature , 23. 10.1038/s41586-020-03127-1
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Lyons, J. B. et al. (2021) Current status and impending progress for cassava structural genomics. Plant Molecular Biology , 15. 10.1007/s11103-020-01104-w
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Ma, X et al. (2021) Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass) [version 1; peer review: 1 approved]. F1000Research 10(289). 10.12688/f1000research.38156.1
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Meleshko, Olena et al. (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 . 10.1093/molbev/msab063
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Meng, Yongjie et al. (2021) KARRIKIN INSENSITIVE2 regulates leaf development, root system architecture and arbuscular‐mycorrhizal symbiosis in Brachypodium distachyon. The Plant Journal . 10.1111/tpj.15651
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Muchlinski, A. et al. (2021) Cytochrome P450-catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass (Panicum virgatum L.). Plant Journal . 10.1111/tpj.15492
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Pompidor, N. et al. (2021) Three founding ancestral genomes involved in the origin of sugarcane. Annals of Botany 127(6), 827-840. 10.1093/aob/mcab008
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Rodrigues, J. A. et al. (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). 10.1073/pnas.2104445118
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Sakai, K. et al. (2021) BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon. BMC Plant Biology 21(1). 10.1186/s12870-021-02970-2
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Sancho, Rubén et al. (2021) Tracking the Ancestry of Known and ‘Ghost’ Homeologous Subgenomes in Model Grass Brachypodium Polyploids. The Plant Journal . 10.1111/tpj.15650
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Scavuzzo-Duggan, Tess et al. (2021) Cell Wall Compositions of Sorghum bicolor Leaves and Roots Remain Relatively Constant Under Drought Conditions. Frontiers in Plant Science 12, 747225. 10.3389/fpls.2021.747225
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Singer, Esther et al. (2021) Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome. Phytobiomes Journal 5(2). 10.1094/pbiomes-05-20-0042-rvw
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Wu, G. A. et al. (2021) Diversification of mandarin citrus by hybrid speciation and apomixis. Nature Communications 12. 10.1038/s41467-021-24653-0
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Yates, Timothy B et al. (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). 10.1093/gbe/evab198
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Zhou, M. et al. (2021) Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers. Journal of visualized experiments : JoVE (169). 10.3791/61707
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2020

Bahri, B. A. et al. (2020) Natural Variation in Lignin and Pectin Biosynthesis-Related Genes in Switchgrass (Panicum virgatum L.) and Association of SNP Variants with Dry Matter Traits. Bioenergy Research 13(1), 79-99. 10.1007/s12155-020-10090-2
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Borowska-Zuchowska, N. et al. (2020) The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum. Plant J . 10.1111/tpj.14869
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Brenton, Z. W. et al. (2020) Species-Specific Duplication Event Associated with Elevated Levels of Nonstructural Carbohydrates in Sorghum bicolor. G3 (Bethesda) 10(5), 1511-1520. 10.1534/g3.119.400921
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Casarrubia, S. et al. (2020) Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus. Front Microbiol 11, 341. 10.3389/fmicb.2020.00341
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Chen, Z. J. et al. (2020) Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nat Genet 52(5), 525-533. 10.1038/s41588-020-0614-5
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Dong, O. X. et al. (2020) Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9. Nat Commun 11(1), 1178. 10.1038/s41467-020-14981-y
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Gao, C. et al. (2020) Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics. Nat Commun 11(1), 34. 10.1038/s41467-019-13913-9
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Gordon, S. P. et al. (2020) Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors. Nat Commun 11(1), 3670. 10.1038/s41467-020-17302-5
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Hofmeister, B. T. et al. (2020) A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biol 21(1), 259. 10.1186/s13059-020-02162-5
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Li, Z. et al. (2020) Single-parent expression drives dynamic gene expression complementation in maize hybrids. Plant J . 10.1111/tpj.15042
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MacKinnon, K. J. M. et al. (2020) Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation. New Phytologist . 10.1111/nph.16507
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MacQueen, A. H. et al. (2020) Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean. Genetics 215(1), 267-284. 10.1534/genetics.120.303038
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Mamidi, S. et al. (2020) A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. Nat Biotechnol 38(10), 1203-1210. 10.1038/s41587-020-0681-2
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Mitros, T. et al. (2020) Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nature Communications 11(1). 10.1038/s41467-020-18923-6
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Peng, Z. et al. (2020) A chromosome-scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease resistance, cold tolerance and genome evolution in Citrus. Plant J 104(5), 1215-1232. 10.1111/tpj.14993
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Piatkowski, B. T. et al. (2020) Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway. Mol Phylogenet Evol 151, 106904. 10.1016/j.ympev.2020.106904
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Schmidt, J. E. et al. (2020) Impacts of directed evolution and soil management legacy on the maize rhizobiome. Soil Biology & Biochemistry 145. ARTN 107794 10.1016/j.soilbio.2020.107794
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Stover, E. et al. (2020) Rationale for reconsidering current regulations restricting use of hybrids in orange juice. Horticulture Research 7(1). 10.1038/s41438-020-0277-5
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Toubiana, D. et al. (2020) Correlation-based network analysis combined with machine learning techniques highlight the role of the GABA shunt in Brachypodium sylvaticum freezing tolerance. Sci Rep 10(1), 4489. 10.1038/s41598-020-61081-4
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Woods, D. P. et al. (2020) Mutations in the predicted DNA polymerase subunit POLD3 result in more rapid flowering of Brachypodium distachyon. New Phytol . 10.1111/nph.16546
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Xie, M. et al. (2020) Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect. Plant Direct 4(1), e00178. 10.1002/pld3.178
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Zhang, J. et al. (2020) Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoe fedtschenkoi, a plant with crassulacean acid metabolism. Gigascience 9(3). 10.1093/gigascience/giaa018
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Zhou, R. et al. (2020) A willow sex chromosome reveals convergent evolution of complex palindromic repeats. Genome Biol 21(1), 38. 10.1186/s13059-020-1952-4
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2019

Ali, S. et al. (2019) High-density linkage map reveals QTL underlying growth traits in AP13xVS16 biparental population of switchgrass. Global Change Biology Bioenergy 11(5), 672-690. 10.1111/gcbb.12592
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Bertioli, D. J. et al. (2019) The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat Genet 51(5), 877-884. 10.1038/s41588-019-0405-z
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Brisson, V. et al. (2019) A New Method to Correct for Habitat Filtering in Microbial Correlation Networks. Frontiers in Microbiology 10. 10.3389/fmicb.2019.00585
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Brisson, V. L. et al. (2019) Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil. Sci Rep 9(1), 15611. 10.1038/s41598-019-52148-y
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Chen, F. et al. (2019) Agrobacterium-Mediated Transformation of Brachypodium distachyon. Curr Protoc Plant Biol , e20088. 10.1002/cppb.20088
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Chen, F. et al. (2019) Agrobacterium-Mediated Transformation of Brachypodium distachyon. Curr Protoc Plant Biol , e20088. 10.1002/cppb.20088
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Chhetri, H. B. et al. (2019) Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits. New Phytol 223(1), 293-309. 10.1111/nph.15777
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Chiniquy, D. et al. (2019) PMR5, an acetylation protein at the intersection of pectin biosynthesis and defense against fungal pathogens. Plant J 100(5), 1022-1035. 10.1111/tpj.14497
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Cooper, E. A. et al. (2019) A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism. BMC Genomics 20(1), 420. 10.1186/s12864-019-5734-x
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Fernandez-Pozo, N. et al. (2019) PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens. Plant J . 10.1111/tpj.14607
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Furches, A. et al. (2019) Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence. Front Plant Sci 10, 1249. 10.3389/fpls.2019.01249
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Handakumbura, P. P. et al. (2019) Metabotyping as a Stopover in Genome-to-Phenome Mapping. Sci Rep 9(1), 1858. 10.1038/s41598-019-38483-0
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Jain, R. et al. (2019) Genome sequence of the model rice variety KitaakeX. BMC Genomics 20(1), 905. 10.1186/s12864-019-6262-4
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Jiang, L. R. et al. (2019) Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9-1. Rice 12. 10.1186/s12284-019-0308-8
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Khasanova, A. et al. (2019) The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass. Front Plant Sci 10, 366. 10.3389/fpls.2019.00366
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Labbe, J. et al. (2019) Mediation of plant-mycorrhizal interaction by a lectin receptor-like kinase. Nat Plants 5(7), 676-680. 10.1038/s41477-019-0469-x
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Larson, S. et al. (2019) Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium). Theor Appl Genet . 10.1007/s00122-019-03357-6
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Lowry, D. B. et al. (2019) QTL x environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient. Proc Natl Acad Sci U S A 116(26), 12933-12941. 10.1073/pnas.1821543116
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Masonbrink, R. et al. (2019) The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC Genomics 20(1), 119. 10.1186/s12864-019-5485-8
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Mazaheri, M. et al. (2019) Genome-wide association analysis of stalk biomass and anatomical traits in maize. BMC Plant Biol 19(1), 45. 10.1186/s12870-019-1653-x
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Na, G. et al. (2019) Enhancing microRNA167A expression in seed decreases the alpha-linolenic acid content and increases seed size in Camelina sativa. Plant J . 10.1111/tpj.14223
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Panchy, N. L. et al. (2019) Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication. BMC Evol Biol 19(1), 77. 10.1186/s12862-019-1398-z
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Ramstein, G. P. et al. (2019) Extensions of BLUP Models for Genomic Prediction in Heterogeneous Populations: Application in a Diverse Switchgrass Sample. G3 (Bethesda) 9(3), 789-805. 10.1534/g3.118.200969
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Rao, X. et al. (2019) Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum). Plant Biotechnol J 17(3), 580-593. 10.1111/pbi.13000
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Ullah, C. et al. (2019) Salicylic acid activates poplar defense against the biotrophic rust fungus Melampsora larici-populina via increased biosynthesis of catechin and proanthocyanidins. New Phytol 221(2), 960-975. 10.1111/nph.15396
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Valliyodan, B. et al. (2019) Construction and comparison of three reference-quality genome assemblies for soybean. Plant J 100(5), 1066-1082. 10.1111/tpj.14500
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Varoquaux, N. et al. (2019) Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. Proc Natl Acad Sci U S A . 10.1073/pnas.1907500116
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Wang, B. et al. (2019) Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. Genome Biol 20(1), 126. 10.1186/s13059-019-1729-9
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Weighill, D. et al. (2019) Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation. Front Genet 10, 487. 10.3389/fgene.2019.00487
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Wilson, P. B. et al. (2019) Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate. Genetics 211(1), 317-331. 10.1534/genetics.118.301589
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Zhang, J. et al. (2019) Overexpression of a Prefoldin beta subunit gene reduces biomass recalcitrance in the bioenergy crop Populus. Plant Biotechnol J . 10.1111/pbi.13254
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2018

Bachy, C. et al. (2018) Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions. Environ Microbiol 20(8), 2898-2912. 10.1111/1462-2920.14273
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Bahri, B. A. et al. (2018) Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.). BMC Evol Biol 18(1), 91. 10.1186/s12862-018-1193-2
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Wu, G. A. et al. (2018) Genomics of the origin and evolution of Citrus. Nature 554(7692), 311-316. 10.1038/nature25447
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2017

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Li, G. et al. (2017) The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. Plant Cell 29(6), 1218-1231. 10.1105/tpc.17.00154
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2015

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Song, Q. et al. (2015) SNP Assay Development for Linkage Map Construction, Anchoring Whole Genome Sequence and Other Genetic and Genomic Applications in Common Bean. G3 (Bethesda) . 10.1534/g3.115.020594
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Yang, X. et al. (2015) A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world. New Phytol 207(3), 491-504. 10.1111/nph.13393
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2014

Bartholome, J. et al. (2014) High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytol . 10.1111/nph.13150
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Beissinger, T. M. et al. (2014) A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number. Genetics 196(3), 829-40. 10.1534/genetics.113.160655
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Lewis, S. M., Gross, S., Visel, A., Kelly, M. and Morrow, W. et al. (2014) Fuzzy GIS-based multi-criteria evaluation for US Agave production as a bioenergy feedstock. GCB Bioenergy . 10.1111/gcbb.12116
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Lowry, D. B. et al. (2014) The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. New Phytol . 10.1111/nph.13027
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Marcussen, T. et al. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. Science 345(6194), 1250092. 10.1126/science.1250092
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Martin, J. A. et al. (2014) A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing. Sci Rep 4, 4519. 10.1038/srep04519
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Myburg, A. A. et al. (2014) The genome of Eucalyptus grandis. Nature 509(7505), 356-62. 10.1038/nature13308
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Pfeifer, M. et al. (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. Science 345(6194), 1250091. 10.1126/science.1250091
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Schmutz, J. et al. (2014) A reference genome for common bean and genome-wide analysis of dual domestications.. Nature 46(7), 707-713. 10.1038/ng.3008
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Wang, W. et al. (2014) The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun 5, 3311. 10.1038/ncomms4311
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Weston, D. J. et al. (2014) Sphagnum physiology in the context of changing climate: Emergent influences of genomics, modeling and host-microbiome interactions on understanding ecosystem function. Plant Cell Environ . 10.1111/pce.12458
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Wu, G. A. et al. (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 32(7), 656-62. 10.1038/nbt.2906
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2013

Barling, A. et al. (2013) A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes. BMC Genomics 14, 864. 10.1186/1471-2164-14-864
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Geraldes, A. et al. (2013) A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species. Mol Ecol Resour 13(2), 306-23. 10.1111/1755-0998.12056
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Gross, S. M. et al. (2013) De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Genomics 14, 563. 10.1186/1471-2164-14-563
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Hellsten, U. et al. (2013) Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing. Proc Natl Acad Sci U S A 110(48), 19478-82. 10.1073/pnas.1319032110
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Iwata, A. et al. (2013) Identification and characterization of functional centromeres of the common bean. Plant J 76(1), 47-60. 10.1111/tpj.12269
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Mascher, M. et al. (2013) Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J 76(4), 718-27. 10.1111/tpj.12319
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Peiffer, J. A. et al. (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci U S A 110(16), 6548-53. 10.1073/pnas.1302837110
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Read, B. A. et al. (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499(7457), 209-13. 10.1038/nature12221
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Rice, D. W. et al. (2013) Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science 342(6165), 1468-73. 10.1126/science.1246275
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Slotte, T. et al. (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet 45(7), 831-5. 10.1038/ng.2669
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Verde, I. et al. (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45(5), 487-94. 10.1038/ng.2586
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Wullschleger, S. D. et al. (2013) Revisiting the sequencing of the first tree genome: Populus trichocarpa. Tree Physiol 33(4), 357-64. 10.1093/treephys/tps081
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Yang, R. et al. (2013) The Reference Genome of the Halophytic Plant Eutrema salsugineum. Front Plant Sci 4, 46. 10.3389/fpls.2013.00046
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Zarzycki, J. et al. (2013) Cyanobacterial-based approaches to improving photosynthesis in plants. J Exp Bot 64(3), 787-98. 10.1093/jxb/ers294
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Zhang, J. Y. et al. (2013) Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.). Plant J 74(1), 160-73. 10.1111/tpj.12104
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2012

Abraham, P. et al. (2012) Defining the Boundaries and Characterizing the Landscape of Functional Genome Expression in Vascular Tissues of Populus using Shotgun Proteomics. Journal of Proteome Research 11(1), 449-460. Doi 10.1021/Pr200851y
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Bennetzen, J. L. et al. (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30(6), 555-61. 10.1038/nbt.2196
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Chan, C. X. et al. (2012) Porphyra (Bangiophyceae) Transcriptomes Provide Insights Into Red Algal Development And Metabolism. Journal of Phycology 48(6), 1328-1342. DOI 10.1111/j.1529-8817.2012.01229.x
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Chan, C. X. et al. (2012) Analysis of Porphyra Membrane Transporters Demonstrates Gene Transfer among Photosynthetic Eukaryotes and Numerous Sodium-Coupled Transport Systems. Plant Physiology 158(4), 2001-2012. DOI 10.1104/pp.112.193896
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Cui, Y. et al. (2012) Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One 7(6), e38333. 10.1371/journal.pone.0038333
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Goodstein, D. M. et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research 40(D1), D1178-D1186. Doi 10.1093/Nar/Gkr944
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Jones, F. C. et al. (2012) A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks. Curr Biol 22(1), 83-90. 10.1016/j.cub.2011.11.045
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Lorenz, W. W. et al. (2012) Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species. Tree Genetics & Genomes 8(6), 1477-1485. Doi 10.1007/S11295-012-0547-Y
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Paterson, A. H. et al. (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492(7429), 423-7. 10.1038/nature11798
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Prochnik, S. et al. (2012) The Cassava Genome: Current Progress, Future Directions. Trop Plant Biol 5(1), 88-94. 10.1007/s12042-011-9088-z
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Sharma, M. K. et al. (2012) A genome-wide survey of switchgrass genome structure and organization. PLoS One 7(4), e33892. 10.1371/journal.pone.0033892
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Slavov, G. T. et al. (2012) Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol 196(3), 713-25. 10.1111/j.1469-8137.2012.04258.x
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Swaminathan, K. et al. (2012) A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy. Bmc Genomics 13. Artn 142Doi 10.1186/1471-2164-13-142
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2011

Bresson, A. et al. (2011) Qualitative and quantitative resistances to leaf rust finely mapped within two nucleotide-binding site leucine-rich repeat (NBS-LRR)-rich genomic regions of chromosome 19 in poplar. New Phytologist 192(1), 151-163. DOI 10.1111/j.1469-8137.2011.03786.x
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Casler, M. D. et al. (2011) The Switchgrass Genome: Tools and Strategies. Plant Genome 4(3), 273-282. DOI 10.3835/plantgenome2011.10.0026
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Chapman, J. A. et al. (2011) Meraculous: de novo genome assembly with short paired-end reads. PLoS One 6(8), e23501. 10.1371/journal.pone.0023501
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Foston, M. et al. (2011) Chemical, ultrastructural and supramolecular analysis of tension wood in Populus tremula x alba as a model substrate for reduced recalcitrance. Energy & Environmental Science 4(12), 4962-4971. Doi 10.1039/C1ee02073k
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Hsu, C. Y. et al. (2011) FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar. Proc Natl Acad Sci U S A 108(26), 10756-61. 10.1073/pnas.1104713108
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Karpowicz, S. J. et al. (2011) The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. J Biol Chem 286(24), 21427-39. 10.1074/jbc.M111.233734
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Studer, M. H. et al. (2011) Lignin content in natural Populus variants affects sugar release. Proc Natl Acad Sci U S A 108(15), 6300-5. 10.1073/pnas.1009252108
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Swarbreck, S. M. et al. (2011) Analysis of leaf and root transcriptomes of soil-grown Avena barbata plants. Plant Cell Physiol 52(2), 317-32. 10.1093/pcp/pcq188
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Yang, X. H. et al. (2011) Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics. Plant Science 181(6), 675-687. DOI 10.1016/j.plantsci.2011.01.020
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Ye, C. Y. et al. (2011) Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis. Plant Science 181(6), 688-695. DOI 10.1016/j.plantsci.2011.01.021
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2010

Chan, Y. F. et al. (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 327(5963), 302-5. 10.1126/science.1182213
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Chapman, J. A. et al. (2010) The dynamic genome of Hydra. Nature 464(7288), 592-596. Doi 10.1038/Nature08830
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Ferris, P. et al. (2010) Evolution of an expanded sex-determining locus in Volvox. Science 328(5976), 351-4. 10.1126/science.1186222
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Fritz-Laylin, L. K. et al. (2010) The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell 140(5), 631-42. 10.1016/j.cell.2010.01.032
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Hyten, D. L. et al. (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. Bmc Genomics 11. Artn 38Doi 10.1186/1471-2164-11-38
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International Brachypodium Initiative et al. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282), 763-8. 10.1038/nature08747
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Jackson, D. J. et al. (2010) Parallel evolution of nacre building gene sets in molluscs. Mol Biol Evol 27(3), 591-608. 10.1093/molbev/msp278
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Kim, M. Y. et al. (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proceedings of the National Academy of Sciences of the United States of America 107(51), 22032-22037. DOI 10.1073/pnas.1009526107
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Prochnik, S. E. et al. (2010) Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science 329(5988), 223-6. 10.1126/science.1188800
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Schmutz, J. et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463(7278), 178-83. 10.1038/nature08670
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Schmutz, J. et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463(7278), 178-83. 10.1038/nature08670
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Srivastava, M. et al. (2010) Early evolution of the LIM homeobox gene family. BMC Biol 8, 4. 10.1186/1741-7007-8-4
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Voelker, S. L. et al. (2010) Antisense down-regulation of 4CL expression alters lignification, tree growth, and saccharification potential of field-grown poplar. Plant Physiol 154(2), 874-86. 10.1104/pp.110.159269
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Wang, Z. et al. (2010) SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol 10, 14. 10.1186/1471-2229-10-14
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2009

Gray, J. et al. (2009) A recommendation for naming transcription factor proteins in the grasses. Plant Physiol 149(1), 4-6. 10.1104/pp.108.128504
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Jiang, Z. H. et al. (2009) Old can be new again: HAPPY whole genome sequencing, mapping and assembly. International Journal of Biological Sciences 5(4), 298-303.
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Kawashima, T. et al. (2009) Domain shuffling and the evolution of vertebrates. Genome Res 19(8), 1393-403. 10.1101/gr.087072.108
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Marlow, H. Q. et al. (2009) Anatomy and development of the nervous system of Nematostella vectensis, an anthozoan cnidarian. Dev Neurobiol 69(4), 235-54. 10.1002/dneu.20698
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Paterson, A. H. et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229), 551-6. 10.1038/nature07723
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Vogel, C. J. et al. (2009) Brachypodium distachyon: a New Model for Biomass Crops. In Vitro Cellular & Developmental Biology-Animal 45, S6-S6.
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2008

Bowler, C. et al. (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456(7219), 239-44. 10.1038/nature07410
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Gomez, L. D. et al. (2008) Analysis of saccharification in Brachypodium distachyon stems under mild conditions of hydrolysis. Biotechnol Biofuels 1(1), 15. 10.1186/1754-6834-1-15
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Grimson, A. et al. (2008) Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455(7217), 1193-7. 10.1038/nature07415
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Hendrix, D. A. et al. (2008) Promoter elements associated with RNA Pol 11 stalling in the Drosophila embryo. Proceedings of the National Academy of Sciences of the United States of America 105(22), 7762-7767. DOI 10.1073/pnas.0802406105
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Holland, L. Z. et al. (2008) The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Research 18(7), 1100-1111. DOI 10.1101/gr.073676.107
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Horton, A. C. et al. (2008) Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs. Dev Genes Evol 218(11-12), 613-28. 10.1007/s00427-008-0249-5
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King, N. et al. (2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451(7180), 783-788. Doi 10.1038/Nature06617
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Larroux, C. et al. (2008) Genesis and expansion of metazoan transcription factor gene classes. Mol Biol Evol 25(5), 980-96. 10.1093/molbev/msn047
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Opperman, C. H. et al. (2008) Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proc Natl Acad Sci U S A 105(39), 14802-7. 10.1073/pnas.0805946105
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Putnam, N. H. et al. (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453(7198), 1064-71. 10.1038/nature06967
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Quesada, T. et al. (2008) Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms. New Phytol 180(2), 408-20. 10.1111/j.1469-8137.2008.02586.x
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Ralph, S. G. et al. (2008) Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. Bmc Genomics 9. Artn 57Doi 10.1186/1471-2164-9-57
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Sela, D. A. et al. (2008) The genome sequence of Bifidobacterium longum subsp infantis reveals adaptations for milk utilization within the infant microbiome. Proceedings of the National Academy of Sciences of the United States of America 105(48), 18964-18969. DOI 10.1073/pnas.0809584105
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Smith, D. R. et al. (2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research 18(10), 1638-1642. DOI 10.1101/gr.077776.108
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Srivastava, M. et al. (2008) The Trichoplax genome and the nature of placozoans. Nature 454(7207), 955-60. 10.1038/nature07191
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Yin, T. et al. (2008) Genome structure and emerging evidence of an incipient sex chromosome in Populus. Genome Res 18(3), 422-30. 10.1101/gr.7076308
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2007

Grossman, A. R. et al. (2007) Novel metabolism in Chlamydomonas through the lens of genomics. Current Opinion in Plant Biology 10(2), 190-198. Doi 10.1016/J.Pbi.2007.01.012
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Kalluri, U. C. et al. (2007) Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. Bmc Plant Biology 7. Artn 59Doi 10.1186/1471-2229-7-59
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Kelleher, C. T. et al. (2007) A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant Journal 50(6), 1063-1078. Doi 10.1111/J.1365-313x.2007.03112.X
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Merchant, S. S. et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318(5848), 245-251. Doi 10.1126/Science.1143609
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Montsant, A. et al. (2007) Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana. Journal of Phycology 43(3), 585-604. Doi 10.1111/J.1529-8817.2007.00342.X
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2006

Tuskan, G. A. et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793), 1596-1604. Doi 10.1126/Science.1128691
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2004

Martin, J. et al. (2004) The sequence and analysis of duplication-rich human chromosome 16. Nature 432(7020), 988-94. 10.1038/nature03187
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Schmutz, J. et al. (2004) The DNA sequence and comparative analysis of human chromosome 5. Nature 431(7006), 268-74. 10.1038/nature02919
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Metcalfe, Cushla J. et al. Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification. Theoretical and Applied Genetics , 1-14. 10.1007/s00122-022-04030-1
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Poosapati, Sowmya et al. 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. 10.1007/s00425-021-03814-x
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