Genome, Plant

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  Subject Areas on Research

  • 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. 
  • A COSII genetic map of the pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus Capsicum. 
  • A comprehensive structure-function analysis of Arabidopsis SNI1 defines essential regions and transcriptional repressor activity. 
  • A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions 
  • A host plant genome (Zizania latifolia) after a century-long endophyte infection. 
  • A linkage map reveals a complex basis for segregation distortion in an interpopulation cross in the moss Ceratodon purpureus. 
  • A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism. 
  • A novel chloroplast gene reported for flagellate plants 
  • A proteogenomic survey of the Medicago truncatula genome. 
  • A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily. 
  • Allotetraploid Mimulus sookensis are highly interfertile despite independent origins. 
  • An Exploration of Fern Genome Space 
  • An international bioinformatics infrastructure to underpin the Arabidopsis community. 
  • Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta). 
  • Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. 
  • Arabidopsis functional genomics. 
  • Asexual reproduction in a close relative of Arabidopsis: a genetic investigation of apomixis in Boechera (Brassicaceae). 
  • Biotic interactions. Genomics and coevolution. 
  • Boechera, a model system for ecological genomics. 
  • Cell identity regulators link development and stress responses in the Arabidopsis root. 
  • Comparative genetic mapping in Boechera stricta, a close relative of Arabidopsis. 
  • Comparative genomics in the Brassicaceae: a family-wide perspective. 
  • Contribution of chromosomal polymorphisms to the G-matrix of Mimulus guttatus. 
  • Cytosolic hydroxymethyldihydropterin pyrophosphokinase/dihydropteroate synthase from Arabidopsis thaliana: a specific role in early development and stress response. 
  • Deciding among green plants for whole genome studies. 
  • Differential regulation of genes by retrotransposons in rice promoters. 
  • Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae (Bryophyta). 
  • Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome. 
  • Evolutionary genetics: jumping into a new species. 
  • Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus. 
  • Fern genomes elucidate land plant evolution and cyanobacterial symbioses 
  • Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea). 
  • Genes and networks regulating root anatomy and architecture. 
  • Genetic evidence for hybridization in red oaks (Quercus sect. Lobatae, Fagaceae). 
  • Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe. 
  • Genome Sequencing of Arabidopsis abp1-5 Reveals Second-Site Mutations That May Affect Phenotypes. 
  • Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. 
  • Genome wide analyses reveal little evidence for adaptive evolution in many plant species. 
  • Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca. 
  • Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular patterning through cytokinin homeostasis. 
  • Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. 
  • Genome-wide transcriptional analysis of the Arabidopsis thaliana interaction with the plant pathogen Pseudomonas syringae pv. tomato DC3000 and the human pathogen Escherichia coli O157:H7. 
  • Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research. 
  • Harnessing epigenetic variability for crop improvement: current status and future prospects. 
  • High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq. 
  • High-resolution mapping of open chromatin in the rice genome. 
  • Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. 
  • Integrative systems biology: an attempt to describe a simple weed. 
  • Intergenic and genic sequence lengths have opposite relationships with respect to gene expression. 
  • Interploidal hybridization and mating patterns in the Sphagnum subsecundum complex. 
  • Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. 
  • Mapping of ionomic traits in Mimulus guttatus reveals Mo and Cd QTLs that colocalize with MOT1 homologues. 
  • Multilocus patterns of nucleotide diversity, population structure and linkage disequilibrium in Boechera stricta, a wild relative of Arabidopsis. 
  • One thousand plant transcriptomes and the phylogenomics of green plants. 
  • Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss). 
  • Origin, fate, and architecture of ecologically relevant genetic variation. 
  • Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. 
  • Partial shotgun sequencing of the Boechera stricta genome reveals extensive microsynteny and promoter conservation with Arabidopsis. 
  • Philip Benfey. 
  • Phylotranscriptomic analysis of the origin and early diversification of land plants. 
  • Plant evolutionary genomics. 
  • Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters. 
  • Population structure and local selection yield high genomic variation in Mimulus guttatus. 
  • Quantitative trait locus mapping reveals regions of the maize genome controlling root system architecture. 
  • Re-annotation of the woodland strawberry (Fragaria vesca) genome. 
  • Recombination and gene conversion in a 170-kb genomic region of Arabidopsis thaliana. 
  • Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia. 
  • Refugial isolation and range expansions drive the genetic structure of Oxyria sinensis (Polygonaceae) in the Himalaya-Hengduan Mountains. 
  • Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. 
  • Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. 
  • Solution NMR studies of the plant peptide hormone CEP inform function. 
  • Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid. 
  • Strong selection genome-wide enhances fitness tradeoffs across environments and episodes of selection 
  • The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. 
  • The Arabidopsis GRAS-type SCL28 transcription factor controls the mitotic cell cycle and division plane orientation. 
  • The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project. 
  • The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) 
  • The draft genome of tropical fruit durian (Durio zibethinus). 
  • The fast and transient transcriptional network of gravity and mechanical stimulation in the Arabidopsis root apex. 
  • The genome of a cave plant, Primulina huaijiensis, provides insights into adaptation to limestone karst habitats. 
  • The standing pool of genomic structural variation in a natural population of Mimulus guttatus. 
  • Three-genome mosses: complex double allopolyploid origins for triploid gametophytes in Sphagnum. 
  • Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. 
  • Transmission ratio distortion in intraspecific hybrids of Mimulus guttatus: implications for genomic divergence. 
  • Unifying genetic canalization, genetic constraint, and genotype-by-environment interaction: QTL by genomic background by environment interaction of flowering time in Boechera stricta. 
  • Using cauliflower to find conserved non-coding regions in Arabidopsis. 
  • What can patterns of differentiation across plant genomes tell us about adaptation and speciation? 
  • Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. 
  • Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences. 
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  Keywords of People

  • Mitchell-Olds, Thomas, Newman Ivey White Distinguished Professor of Biology, Biology