A5062507839- Plant Gene Expression Analysis
- Plant biochemistry and biosynthesis
- Biochemical and biochemical processes
- Plant Molecular Biology Research
- Photosynthetic Processes and Mechanisms
- Plant nutrient uptake and metabolism
- Plant-Microbe Interactions and Immunity
- Plant Reproductive Biology
- Genetic and phenotypic traits in livestock
- Plant tissue culture and regeneration
- Genetic Mapping and Diversity in Plants and Animals
- Plant Stress Responses and Tolerance
- Microbial Natural Products and Biosynthesis
- Forest ecology and management
- Genetic diversity and population structure
- Biofuel production and bioconversion
- Microbial Metabolic Engineering and Bioproduction
- Insect and Arachnid Ecology and Behavior
- Lignin and Wood Chemistry
- Plant Pathogens and Fungal Diseases
- Plant Micronutrient Interactions and Effects
- Insect Resistance and Genetics
- Forest Insect Ecology and Management
- Plant Pathogens and Resistance
- Lipid metabolism and biosynthesis
University of Victoria
2013-2025
Canada's Michael Smith Genome Sciences Centre
2005-2014
Institut de Biologie Moléculaire des Plantes
2005-2014
Université de Strasbourg
2008-2014
University of British Columbia
2001-2014
Forest Research
2013
Czech Academy of Sciences, Biology Centre
2013
Centre National de la Recherche Scientifique
2005-2008
Oak Ridge National Laboratory
2006
Umeå University
2006
We report the draft genome of black cottonwood tree, Populus trichocarpa . Integration shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction genome. More than 45,000 putative protein-coding genes were identified. Analysis assembled revealed a whole-genome duplication event; about 8000 pairs duplicated from that event survived in A second, older is indistinguishably coincident divergence and Arabidopsis lineages. Nucleotide substitution, tandem gene...
Summary The enzyme 4‐coumarate:CoA ligase (4CL) plays a key role in channelling carbon flow into diverse branch pathways of phenylpropanoid metabolism which serve important functions plant growth and adaptation to environmental perturbations. Here we report on the cloning 4CL gene family from Arabidopsis thaliana demonstrate that its three members, At4CL1 , At4CL2 At4CL3 encode isozymes with distinct substrate preference specificities. Expression studies revealed differential behaviour genes...
Abstract Background The protein phosphatase 2Cs (PP2Cs) from various organisms have been implicated to act as negative modulators of kinase pathways involved in diverse environmental stress responses and developmental processes. A genome-wide overview the PP2C gene family plants is not yet available. Results comprehensive computational analysis identified 80 78 genes Arabidopsis thaliana (AtPP2Cs) Oryza sativa (OsPP2Cs), respectively, which denotes one largest families plants. Phylogenic...
Abstract Lignin, one of the most abundant biopolymers on Earth, derives from plant phenolic metabolism. It appeared upon terrestrialization and is thought critical for colonization land. Early diverging land plants do not form lignin, but already have elements its biosynthetic machinery. Here we delete in a moss P450 oxygenase that defines entry point angiosperm lignin metabolism, find pre-lignin pathway essential development. This does involve biochemical regulation via shikimate coupling,...
Summary Different stages of vascular and interfascicular fiber differentiation can be identified along the axis bolting stems in Arabidopsis. To gain insights into metabolic, developmental, regulatory events that control this pattern, we applied global transcript profiling employing an Arabidopsis full‐genome longmer microarray. More than 5000 genes were differentially expressed, among which more 3000 changed twofold, placed eight expression clusters based on polynomial regression models....
Summary In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions black cottonwood ( Populus trichocarpa ) from much its range in western North America. Extensive data large‐scale phenotyping (with spatial and temporal replications within a common garden) genotyping 34 K single nucleotide polymorphism SNP array) all were for gene discovery genome‐wide association study GWAS ). We performed with 40 biomass, ecophysiology phenology traits 29 355...
The primary inflorescence stem of Arabidopsis thaliana is rich in lignified cell walls, both vascular bundles and interfascicular fibres. Previous gene expression studies demonstrated a correlation between phenylpropanoid biosynthetic genes subset encoding ATP-binding cassette (ABC) transporters, especially the ABCB/multi-drug resistance/P-glycoprotein (ABCB/MDR/PGP) ABCG/pleiotropic drug resistance (ABCG/PDR) subfamilies. objective this study was to characterize these ABC transporters terms...
From Retrogene to Phenolic Metabolism Metabolic plasticity, which involves the creation of new genes, is an essential feature plant adaptation and speciation. Studying plants from mustard family, Matsuno et al. (p. 1688 ) show that variants cytochrome P450 enzyme family were derived through retroposition, duplication, subsequent mutaton. Evolutionary changes increased volume substrate pocket altering with what sorts substrates enzymes could interact. The formed basis for a metabolic pathway,...
Summary Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement economically important plant species. Our work represents the first genome‐wide association study inherently complex currently poorly understood architecture industrially relevant wood traits. Here, we employed an Illumina Infinium 34 K single nucleotide polymorphism ( SNP ) genotyping array that generated 29 233 high‐quality s in c . 3500 broad‐based candidate...
Nitrogen uptake, reallocation within the plant, and between subcellular compartments involves ammonium, nitrate peptide transporters. Ammonium transporters are separated into two distinct families (AMT1 AMT2), each comprised of five members on average in angiosperms. Nitrate also form discrete (NRT1 NRT2), with angiosperms having four NRT2s, average. NRT1s share an evolutionary history (PTRs). The NRT1/PTR family land plants usually has more than 50 contains activities, such as glucosinolate...
The cytochrome P450 family encompasses the largest of enzymes in plant metabolism, and functions many its members Arabidopsis thaliana are still unknown. Gene coexpression analysis pointed to two P450s that were coexpressed with monoterpene synthases flowers thus predicted be involved monoterpenoid metabolism. We show all four selected genes, terpene (TPS10 TPS14) (CYP71B31 CYP76C3), simultaneously expressed at anthesis, mainly upper anther filaments petals. Upon transient expression...
Abstract Cytochromes P450 monooxygenases from the CYP98 family catalyze meta-hydroxylation step in phenylpropanoid biosynthetic pathway. The ref8 Arabidopsis (Arabidopsis thaliana) mutant, with a point mutation CYP98A3 gene, was previously described to show developmental defects, changes lignin composition, and lack of soluble sinapoyl esters. We isolated T-DNA insertion mutant that this leads more drastic inhibition plant development cell growth. Similar has reduced content, stem...
Abstract Background Sequencing of the first plant genomes has revealed that cytochromes P450 have evolved to become largest family enzymes in secondary metabolism. The proportion with characterized biochemical function(s) is however very small. If diversification mirrors evolution chemical diversity, this points an unexpectedly poor understanding We assumed extensive analysis gene expression might guide towards function enzymes, and highlight overlooked aspects Results created a...
Abstract Background Plants are exposed to attack from a large variety of herbivores. Feeding insects can induce substantial changes the host plant transcriptome. Arabidopsis thaliana has been established as relevant system for discovery genes associated with response herbivory, including specialized (i.e. secondary) metabolism well involved in plant-insect defence signalling. Results Using 70-mer oligonulceotide microarray covering 26,090 gene-specific elements, we monitored leaf...
Abstract Genetic mapping of quantitative traits requires genotypic data for large numbers markers in many individuals. For such studies, the use single nucleotide polymorphism ( SNP ) genotyping arrays still offers most cost‐effective solution. Herein we report on design and performance a array Populus trichocarpa (black cottonwood). This was designed with s pre‐ascertained 34 wild accessions covering species latitudinal range. We adopted candidate gene approach to that resulted selection...
We tested the hypothesis that Arabidopsis can recognize and respond differentially to insect species at transcriptional level using a genome wide microarray. Transcriptional reprogramming was characterized co-expression analysis in damaged undamaged leaves two times response mechanical wounding four species. In all, 2778 (10.6%) of annotated genes on array were expressed least one treatment. Responses differed mainly between aphid caterpillar sampling times. aphids caterpillars shared only...
The phenylpropanoid enzyme 4-coumarate:coenzyme A ligase (4CL) plays a key role in general metabolism. 4CL is related to larger class of prokaryotic and eukaryotic adenylateforming enzymes shares several conserved peptide motifs with these enzymes. In order better characterize the nature gene families poplar, parsley, tobacco, we used degenerate primers amplify sequences from species. each species additional, divergent genes were found. Complete cDNA clones for two new poplar obtained,...
4‐Coumarate:coenzyme A ligase (4CL) is a key enzyme of general phenylpropanoid metabolism which provides the precursors for large variety important plant secondary products, such as lignin, flavonoids, or phytoalexins. To identify amino acids 4CL activity, eight mutations were introduced into Arabidopsis thaliana At4CL2. Determination specific activities and K m values ATP caffeate heterologously expressed purified proteins identified four distinct classes mutants: enzymes with little no...
Abstract NADPH:cytochrome P450 reductase (CPR) provides reducing equivalents to diverse cytochrome monooxygenases. We isolated cDNAs for three CPR genes (CPR1,CPR2, and CPR3) from hybrid poplar (Populus trichocarpa × Populus deltoides). Deduced CPR2 CPR3 amino acid sequences were 91% identical, but encoded isoforms divergent CPR1 (72% identity). co-expressed together with the enzyme cinnamate-4-hydroxylase (C4H) in yeast (Saccharomyces cerevisiae). Microsomes strains expressing CPR1/C4H or...
An approach based on an in silico analysis predicted that CYP77A4, a cytochrome P450 so far has no identified function, might be fatty acid-metabolizing enzyme. CYP77A4 was heterologously expressed Saccharomyces cerevisiae strain (WAT11) engineered for expression. Lauric acid (C(12:0)) converted into mixture of hydroxylauric acids when incubated with microsomes from yeast expressing CYP77A4. A variety physiological C(18) were tested as potential substrates. Oleic (cis-Delta(9)C(18:1))...