A5054417776- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Research in Cotton Cultivation
- Plant Virus Research Studies
- Plant Pathogens and Fungal Diseases
- Forest ecology and management
- Plant and Fungal Interactions Research
- Identification and Quantification in Food
- Rangeland and Wildlife Management
- Plant Diversity and Evolution
- Environmental DNA in Biodiversity Studies
- Plant and Fungal Species Descriptions
- Forest Ecology and Biodiversity Studies
- Plant Disease Resistance and Genetics
- Ecology and Vegetation Dynamics Studies
- Phytochemistry and Bioactive Compounds
- Plant Pathogens and Resistance
- Fungal Biology and Applications
- HIV Research and Treatment
- Plant and animal studies
- Mycorrhizal Fungi and Plant Interactions
- Plant Taxonomy and Phylogenetics
- Yeasts and Rust Fungi Studies
- Botany, Ecology, and Taxonomy Studies
Pacific Northwest Research Station
2015-2024
US Forest Service
2006-2018
United States Department of Agriculture
1998-2018
Oregon State University
2011-2015
Iowa State University
1996-2003
Washington University in St. Louis
2003
Centre for Australian National Biodiversity Research
2001
Commonwealth Scientific and Industrial Research Organisation
2001
Plant Industry
2001
Gembloux Agro-Bio Tech
2001
Most eukaryotes have genomes that exhibit high levels of gene redundancy, much which seems to arisen from one or more cycles genome doubling. Polyploidy has been particularly prominent during flowering plant evolution, yielding duplicated genes (homoeologs) whose expression may be retained lost either as an immediate consequence polyploidization on evolutionary timescale. Expression 40 homoeologous pairs was assayed by cDNA-single-stranded conformation polymorphism in natural (1-...
Just as Sanger sequencing did more than 20 years ago, next-generation (NGS) is poised to revolutionize plant systematics. By combining multiplexing approaches with NGS throughput, systematists may no longer need choose between taxa or characters. Here we describe a genome skimming (shallow sequencing) approach for systematics.Through simulations, evaluated optimal depth and performance of single-end paired-end short read sequences assembly nuclear ribosomal DNA (rDNA) plastomes addressed the...
Organellar DNA sequences are widely used in evolutionary and population genetic studies, however, the conservative nature of chloroplast gene genome evolution often limits phylogenetic resolution statistical power. To gain maximal access to historical record contained within genomes, we have adapted multiplex sequencing-by-synthesis (MSBS) simultaneously sequence multiple genomes using Illumina Genome Analyzer. We PCR-amplified ∼120 kb plastomes from eight species (seven Pinus , one Picea )...
Phylogenetic resolution is often low within groups of recently diverged taxa due to a paucity phylogenetically informative characters. We tested the relative utility seven noncoding cpDNA regions and pair homoeologous nuclear genes for resolving recent divergences, using tetraploid cottons ( Gossypium ) as model system. The five species are monophyletic assemblage derived from an allopolyploidization event that probably occurred last 0.5–2 million years. Previous analysis restriction site...
Molecular data have had a profound impact on the field of plant systematics, and application DNA-sequence to phylogenetic problems is now routine. The majority used in molecular studies derives from chloroplast DNA nuclear rDNA, while use low-copy genes has not been widely adopted. This due, at least part, greater difficulty isolating characterising relative rDNA sequences that are readily amplified with universal primers. higher level sequence variation characteristic genes, however, often...
Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes high-copy genomic targets plant systematics evolution studies. •Genome transcriptome assemblies milkweed (Asclepias syriaca) were used to design probes 3385 exons from 768 (>1.6 Mbp) followed by Illumina sequencing enriched libraries. Hyb-Seq 12 individuals (10 Asclepias species two related genera) resulted in at least partial assembly 92.6% 99.7% an average...
• Premise of the study: The dramatic advances offered by modern DNA sequencers continue to redefine limits what can be accomplished in comparative plant biology. Even with recent achievements, however, genomes present obstacles that make it difficult execute large‐scale population and phylogenetic studies on next‐generation sequencing platforms. Factors like large genome size, extensive variation proportion organellar total DNA, polyploidy, gene number/redundancy contribute these challenges,...
Recent work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes the early generations following polyploid synthesis. To address question of whether rapid also occur cotton (Gossypium) species, amplified fragment length polymorphism (AFLP) analysis was performed to evaluate nine sets newly synthesized allotetraploid and allohexaploid plants, their parents, selfed progeny from colchicine-doubled synthetics. Using both...
Molecular evolutionary rate variation in Gossypium (cotton) was characterized using sequence data for 48 nuclear genes from both genomes of allotetraploid cotton, models its diploid progenitors, and an outgroup. Substitution rates varied widely among the genes, with silent replacement substitution levels varying 0.018 to 0.162 0.000 0.073, respectively, comparisons between orthologous outgroup sequences. However, about 90% had spanning a more narrow threefold range. Because there no evidence...
Previous molecular phylogenetic studies have failed to resolve the branching order among major cotton ( Gossypium ) lineages, and it has been unclear whether this reflects actual history (rapid radiation) or sampling properties of genes evaluated. In paper, we reconsider relationships diploid genome groups using DNA sequences from 11 single‐copy nuclear loci (10 293 base pairs [bp]), ribosomal (695 bp), four chloroplast (7370 bp). Results individual combined partitions reveal that radiated...
Of the many processes that generate gene duplications, polyploidy is unique in entire genomes are duplicated. This process has been important evolution of eukaryotic groups, and it occurs with high frequency plants. Recent evidence suggests polyploidization may be accompanied by rapid genomic changes, but evolutionary fate discrete loci recently doubled (homoeologues) not studied. Here we use locus-specific isolation techniques comparative mapping to characterize homoeologous allopolyploid...
Silent mutation rate estimates for Pinus vary 50-fold, ranging from angiosperm-like to among the slowest reported plants. These differences either reflect extraordinary genomic processes or inconsistent fossil calibration, and they have important consequences population biogeographical inferences. Here we estimate rates 4 species that represent major lineages using 11 nuclear chloroplast loci. Calibration was tested at divergence of subgenera with oldest leaf subg. Strobus (Eocene; 45 MYA) a...
Phylogenetic relationships among Pinus species from subgenus Strobus remain unresolved despite combined efforts based on nrITS and cpDNA. To provide greater resolution these taxa, a 900-bp intron late embryogenesis abundant (LEA)-like gene (IFG8612)was sequenced 39 pine species, with two or more alleles representing 33 species. Nineteen of exhibited allelic nonmonphyly in the strict consensus tree, 10 deviated significantly monophyly topology incongruence tests. Intraspecific nucleotide...
Horizontal gene transfer (HGT) of DNA from the plastid to nuclear and mitochondrial genomes higher plants is a common phenomenon; however, (plastomes) are highly conserved have generally been regarded as impervious HGT. We sequenced 158 kb plastome 690 genome milkweed (Asclepias syriaca [Apocynaceae]) found evidence intracellular HGT for 2.4-kb segment rps2–rpoC2 intergenic spacer plastome. The transferred region contains an rpl2 pseudogene flanked by sequence in genome, including rpoC2...
Randy Johnson, Larry Stritch, Peggy Olwell, Scott Lambert, Matthew E Horning and Richard Cronn
Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate compliment these studies. This study explored how low coverage genome sequencing the common milkweed syriaca could be useful characterizing a plant without prior genomic information for development as step toward further developing A. model ecology evolution. A 0.5× was produced using Illumina sequencing. virtually...
A reference genome sequence for Pseudotsuga menziesii var. (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a third genus of the family Pinaceae. The contiguity and quality assembly far exceeds that other conifer sequences (contig N50 = 44,136 bp scaffold 340,704 bp). Incremental improvements in sequencing technologies are part responsible higher genome, but it may also be due to slightly lower exact repeat content Douglas-fir vs. pine spruce. Comparative annotation with...
Polyploidy, or whole-genome duplication often with hybridization, is common in eukaryotes and thought to drive ecological evolutionary success, especially plants. The mechanisms of polyploid success ecologically relevant contexts, however, remain largely unknown. We conducted an extensive test functional trait divergence plasticity conferring fitness advantage heterogeneous environments, by growing clonal replicates a worldwide genotype collection six allopolyploid five diploid wild...