The epiphytic lichen Letharia vulpina has been commonly sampled in-situ for nitrogen (N) deposition biomonitoring studies but has never before been transplanted for this purpose. In the high-elevation wilderness areas of southern California Letharia vulpina is generally uncommon, making in-situ sampling difficult. In this study, we compared thallus N accumulation...
The role of small secreted peptides in plant defense responses to viruses has been seldom investigated. Here, we report a role for potato (Solanum tuberosum) PIP1, a gene predicted to encode a member of the PAMP-induced peptide (PIP) family, in the response of potato to potato virus Y infection (PVY)....
The objectives of this study are to isolate and characterize pathogenic agrobacteria that cause crown gall in grapevines and test hot water dips as a method for eradicating the infectious bacteria . Crown gall is commonly found among Oregon vineyards and the causative agent, Agrobacterium vitis, is known to be...
The sweet potato is one of the world’s most widely consumed crops, yet its evolutionary history is poorly understood. In this paper, we present a comprehensive phylogenetic study of all species closely related to the sweet potato and address several questions pertaining to the sweet potato that remained unanswered. Our...
Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low‐copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to...
Micronutrient deficiency, also known as the hidden hunger, affects over two billion people worldwide. Potato is the third most consumed food crops in the world, and is therefore a fundamental element of food security for millions of people. Increasing the amount of micronutrients in food crop could help alleviate worldwide...
The dataset here is used as a document file for presenting supplementary videos in the dissertation Tao, K. (2018). Investigating protein-lipid-membrane interactions in Plant Cells using Bimolecular Fluorescence Complementation (Doctoral dissertation).
Keywords: Protein, Lipid, Membrane, Plant Cells, Fluorescent Imaging
Explaining restoration failure can be as important as touting success. We used a series of studies to understand the failure of techniques commonly used to restore wetland prairies in the Willamette Valley of western Oregon. Burning, fallowing, and solarization (covering tilled plots with plastic sheeting to heat the soil) had...
Question: Most results of restoration efforts are species-specific and/or site-specific and therefore are not general enough to be easily applied to other species and other sites. Our research addresses the issue of species-specific results by investigating the feasibility of using plant traits instead of taxonomic species to characterize species responses...
Questions: Are traits related to the performance of plant species in restoration? Are the relationships between traits and performance consistent across the functional groups of annual forbs, perennial forbs, and grasses? Do the relationships between traits and performance depend on neighboring functional groups? Location: A former agricultural field, being restored...
To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of...
Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, exhibits a clonal reproductive lifestyle in North America. Phenotypes such as fungicide sensitivity and host preference are conserved among individuals within clonal lineages, while substantial phenotypic differences can exist between lineages. Whole P. infestans genomes were...
Host resistance, both quantitative and qualitative, is the preferred long-term approach for disease management in many pathosystems, including powdery mildew of hop (Podosphaera macularis). In 2012, an epidemic of powdery mildew occurred in Washington and Idaho on previously resistant cultivars whose resistance was putatively based on the gene designated R6....
This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Genetics Society of America. The published article can be found at: https://doi.org/10.1534/g3.116.027045
Mountain environments are currently among the ecosystems least invaded by non-native species; however, mountains are increasingly under threat of non-native plant invasion. The slow pace of exotic plant invasions in mountain ecosystems is likely due to a combination of low anthropogenic disturbances, low propagule supply, and extreme/steep environmental gradients. The...
Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native...
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize...
RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data...
Nitrogen-fixing lichens (cyanolichens) are an important source of nitrogen (N) in Pacific Northwest forests, but limitation of lichen growth by elements essential for N fixation is poorly understood. To investigate how nutrient limitation may affect cyanolichen growth rates, we fertilized a tripartite cyanobacterial lichen (Lobaria pulmonaria) and a green algal...
Optimum timing and use of fungicides for disease control are improved by an understanding of the characteristics of fungicide physical mode of action. Greenhouse and field experiments were conducted to quantify and model the duration of pre- and postinfection activity of fungicides most commonly used for control of hop downy...
Results of 28 field trials conducted over a 12-year period investigating management of hop powdery mildew caused by Podosphaera macularis were quantitatively summarized by meta-analysis to compare product efficacy and use patterns by mode of action as defined by Fungicide Resistance Action Committee (FRAC) groups. Availability of original observations enabled...
The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of...
In eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has...
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across...
Phytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013,...
Correction:
21 Jan 2015: The PLOS ONE Staff (2015) Correction: Separate Introns Gained within Short and Long Soluble Peridinin-Chlorophyll a-Protein Genes during Radiation of Symbiodinium (Dinophyceae) Clade A and B Lineages. PLOS ONE 10(1): e0117735. https://doi.org/10.1371/journal.pone.0117735
Viruses are obligatory parasites that depend on host cellular factors for their replication as well as for their local and systemic movement to establish infection. Although myosin motors are thought to contribute to plant virus infection, their exact roles in the specific infection steps have not been addressed. Here we...
Primula sect. Parryi comprises five species endemic to western North America: P. parryi, P. angustifolia, P. rusbyi, P. capillaris, and P. cusickiana with four varieties. This section, derived from a clade with representatives in Asia and Europe, exemplifies a phytogeographic pattern in which a widespread species is accompanied by multiple...
Convergent evolution is common throughout the tree of life, but the molecular mechanisms causing similar phenotypes to appear repeatedly are obscure. Yeasts have arisen in multiple fungal clades, but the genetic causes and consequences of their evolutionary origins are unknown. Here we show that the potential to develop yeast forms...
Impact and relevance are valued by both plant pathologists and
the supporters of research and extension. Impact has been characterized
as the “So what?” of research results, and in applied research
in agriculture typically involves some change in human
behavior. This might involve, for instance, avoidance of broad
spectrum pesticides,...
Members of Gram-positive Actinobacteria cause economically important diseases to plants. Within the Rhodococcus genus,
some members can cause growth deformities and persist as pathogens on a wide range of host plants. The current model
predicts that phytopathogenic isolates require a cluster of three loci present on a linear plasmid, with...
Introduction: Biotic soil crust communities contribute valuable ecosystem services and biodiversity in steppe ecosystems. The uncommon crust lichens Acarospora schleicheri, Fuscopannaria cyanolepra, Rhizocarpon diploschistidina, and Texosporium sancti-jacobi are associated with fine-textured soils along rivers of the Columbia Basin. A. schleicheri and R. diploschistidina indicate late-successional habitat and may serve as...
Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms
describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The
widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth...
The Arabidopsis Information Portal (AIP), a resource expected to provide access to all community data and combine outputs into
a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began
during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics...
The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop,
maintain and use a set of structured, controlled
vocabularies for the annotation of genes, gene
products and sequences. The GO ontologies
are expanding both in content and in structure.
Several new relationship types have been introduced
and used, along with...
Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops
and a community resource for rice. We are populating and curating Gramene with
annotated rice (Oryza sativa) genomic sequence data and associated biological information
including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait
Loci (QTL). In order to support queries...
The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative
effort among several plant databases and experts in plant systematics, botany
and genomics. A primary goal of the POC is to develop simple yet robust
and extensible controlled vocabularies that accurately reflect the biology of plant
structures and developmental stages. These...
Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require
uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative
studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is
used to describe...
The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort
among model plant genome databases and plant
researchers that aims to create, maintain and
facilitate the use of a controlled vocabulary
(ontology) for plants. The ontology allows users to
ascribe attributes of plant structure (anatomy and
morphology) and developmental stages...
The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the
application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity
is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the...
Gramene (www.gramene.org) is a curated resource
for genetic, genomic and comparative genomics
data for the major crop species, including rice,
maize, wheat and many other plant (mainly grass)
species. Gramene is an open-source project.
All data and software are freely downloadable
through the ftp site (ftp.gramene.org/pub/gramene)
and available for use...
Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. Rice, in addition to being an economically important crop, is also a model monocot for understanding other agronomically important grass genomes. Gramene replaces the existing AceDB database ‘RiceGenes’ with a relational database based on...
Rice, maize, sorghum, wheat, barley and the other
major crop grasses from the family Poaceae
(Gramineae) are mankind’s most important source
of calories and contribute tens of billions of dollars
annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov).
Continued improvement of Poaceae crops is necessary
in order...
Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article,
we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate
both the forward and reverse genetics research. The QTL database contains the...
BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental
changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a
substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day.
Synchronized...
Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with...
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
PREMISE OF THE STUDY: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum
(slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis,
Oregon, USA.
METHODS AND RESULTS: More than 350 million sequence reads from the mRNA libraries...
Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst tethering complex, we...
Pseudomonas syringae is a phylogenetically diverse species of Gram-negative bacterial plant pathogens responsible for crop diseases around the world. The HrpL sigma factor drives expression of the major P. syringae virulence regulon. HrpL controls expression of the genes encoding the structural and functional components of the type III secretion system...