A5067300821- Plant biochemistry and biosynthesis
- Forest Insect Ecology and Management
- Plant Gene Expression Analysis
- Insect-Plant Interactions and Control
- Plant Disease Resistance and Genetics
- Plant and Fungal Interactions Research
- Insect and Pesticide Research
- Genetic diversity and population structure
- Microbial Natural Products and Biosynthesis
- Genetic and phenotypic traits in livestock
- Phytochemicals and Antioxidant Activities
- Fish Ecology and Management Studies
- Insect Resistance and Genetics
- Plant Pathogens and Fungal Diseases
- Genomics and Phylogenetic Studies
- Hemiptera Insect Studies
- Genetic Mapping and Diversity in Plants and Animals
- Forest Ecology and Biodiversity Studies
- Forest ecology and management
- Biochemical and biochemical processes
- Sesquiterpenes and Asteraceae Studies
- Bioinformatics and Genomic Networks
- Plant Reproductive Biology
- Natural product bioactivities and synthesis
- Bioactive Natural Diterpenoids Research
University of British Columbia
2015-2024
Canada's Michael Smith Genome Sciences Centre
2015-2024
Ministry of Forests
2013-2016
Government of British Columbia
2013
Simon Fraser University
2013
Guy's Hospital
1984
Abstract White spruce (Picea glauca) is a dominant conifer of the boreal forests North America, and providing genomics resources for this commercially valuable tree will help improve forest management conservation efforts. Sequencing assembling large highly repetitive genome though pushes boundaries current technology. Here, we describe whole-genome shotgun sequencing strategy using two Illumina platforms an assembly approach ABySS software. We report 20.8 giga base pairs draft in 4.9...
The mountain pine beetle, Dendroctonus ponderosae Hopkins, is the most serious insect pest of western North American forests. A recent outbreak destroyed more than 15 million hectares forests, with major environmental effects on forest health, and economic industry. has in part been driven by climate change, will contribute to increased carbon emissions through decaying We developed a genome sequence resource for beetle better understand unique aspects this insect's biology. draft de novo...
The European spruce bark beetle, Ips typographus, and the North American mountain pine Dendroctonus ponderosae (Coleoptera: Curculionidae: Scolytinae), are severe pests of coniferous forests. Both beetle species utilize aggregation pheromones to coordinate mass-attacks on host trees, while odorants from non-host trees modulate pheromone response. Thus, olfactory sense is utmost importance for fitness. However, information genes underlying detection has been lacking in beetles limited...
White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe draft genome assemblies two white genotypes, PG29 and WS77111, innovative tools assembly very large genomes, genomics resources developed in this process. The genotypes originate from distant geographic regions western (PG29) eastern (WS77111) North America, represent elite trees Canadian tree-breeding programs. present an update (V3 V4) previously reported V2 introduce...
Cryptococcus gattii recently emerged as the causative agent of cryptococcosis in healthy individuals western North America, despite previous characterization fungus a pathogen tropical or subtropical regions. As foundation to study genetics virulence this pathogen, we sequenced genomes strain (WM276) representing predominant global molecular type (VGI) and clinical (R265) major genotype (VGIIa) causing disease America. We compared these C. with each other representative strains two varieties...
Abstract Plants produce over 10,000 different diterpenes of specialized (secondary) metabolism, and fewer general (primary) metabolism. Specialized may have functions in ecological interactions plants with other organisms also benefit humanity as pharmaceuticals, fragrances, resins, industrial bioproducts. Examples high-value are taxol forskolin pharmaceuticals or ambroxide fragrances. Yields purity obtained from natural sources by chemical synthesis often insufficient for large-volume...
Summary Tropical sandalwood ( Santalum album ) produces one of the world's most highly prized fragrances, which is extracted from mature heartwood. However, in some places such as southern India, natural populations this slow‐growing tree are threatened by over‐exploitation. Sandalwood oil contains four major and fragrance‐defining sesquiterpenols: Z )‐α‐santalol, )‐β‐santalol, )‐ epi ‐β‐santalol )‐α‐ exo‐ bergamotol. The first committed step their biosynthesis catalyzed a multi‐product...
Abstract Cannabis (Cannabis sativa) resin is the foundation of a multibillion dollar medicinal and recreational plant bioproducts industry. Major components cannabis are cannabinoids terpenes. Variations terpene profiles contribute much to different flavor fragrance phenotypes that affect consumer preferences. A major problem in industry lack proper metabolic characterization many existing cultivars, combined with sometimes incorrect cultivar labeling. We characterized foliar plants grown...
Abstract Background We present a biological data warehouse called Atlas that locally stores and integrates sequences, molecular interactions, homology information, functional annotations of genes, ontologies. The goal the system is to provide data, as well software infrastructure for bioinformatics research development. Description based on relational models we developed each source types. Data stored within these are managed through Structured Query Language (SQL) calls implemented in set...
Abstract The biosynthesis of the tetracyclic diterpene ent-kaurene is a critical step in general (primary) metabolism gibberellin hormones. ent-Kaurene formed by two-step cyclization geranylgeranyl diphosphate via intermediate ent-copalyl diphosphate. In lower land plant, moss Physcomitrella patens, single bifunctional synthase (diTPS) catalyzes both steps. contrast, angiosperms, two consecutive cyclizations are catalyzed distinct monofunctional enzymes, (CPS) and (KS). enzyme, or...
Abstract Diterpene resin acids (DRAs) are major components of pine (Pinus spp.) oleoresin. They play critical roles in conifer defense against insects and pathogens as a renewable resource for industrial bioproducts. The core structures DRAs formed secondary (i.e. specialized) metabolism via cycloisomerization geranylgeranyl diphosphate (GGPP) by diterpene synthases (diTPSs). Previously described gymnosperm diTPSs DRA biosynthesis bifunctional enzymes that catalyze the initial bicyclization...
The labdanoid diterpene alcohol cis-abienol is a major component of the aromatic oleoresin balsam fir (Abies balsamea) and serves as valuable bioproduct material for fragrance industry. Using high-throughput 454 transcriptome sequencing metabolite profiling bark tissue, we identified candidate synthase sequences full-length cDNA cloning functional characterization. We discovered bifunctional class I/II (AbCAS), along with paralogous levopimaradiene/abietadiene isopimaradiene synthase, all...
The mountain pine beetle (MPB; Dendroctonus ponderosae Hopkins), a major forest pest native to western North America, has extended its range north and eastward during an ongoing outbreak. Determining how the MPB expanded breach putative barriers, whether physical (nonforested prairie high elevation of Rocky Mountains) or climatic (extreme continental climate where temperatures can be below −40 °C), may contribute our general understanding changes as well management current epidemic. Here, we...
Abstract Background Expansion of polyglutamine-encoding CAG trinucleotide repeats has been identified as the pathogenic mutation in nine different genes associated with neurodegenerative disorders. The majority individuals clinically diagnosed spinocerebellar ataxia do not have mutations within known disease genes, and it is likely that additional ataxias or Huntington disease-like disorders will be found to caused by this common mutational mechanism. We set out determine length...
Abstract Background The mountain pine beetle (MPB, Dendroctonus ponderosae ) epidemic has affected lodgepole ( Pinus contorta across an area of more than 18 million hectares forests in western Canada, and is a threat to the boreal jack banksiana forest. Defence pines against MPB associated fungal pathogens, as well other pests, involves oleoresin monoterpenes, which are biosynthesized by families terpene synthases (TPSs). Volatile monoterpenes also serve host recognition cues for precursors...
Cytochrome P450 enzymes of the CYP720B subfamily play a central role in biosynthesis diterpene resin acids (DRAs), which are major component conifer oleoresin defense system. CYP720Bs exist families up to dozen different members genomes and fall into four clades (I-IV). Only two members, loblolly pine (Pinus taeda) PtCYP720B1 Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both multisubstrate multifunctional clade III enzymes, catalyze consecutive three-step...
Plant specialized metabolism serves as a rich resource of biologically active molecules for drug discovery. The acylated flavonol glycoside montbretin A (MbA) and its precursor myricetin 3-
Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance enormous contributions to global carbon sequestration. harbor very genomes high repetitiveness, hampering their comparative analysis. Here, we present compare four different North American spruces: genome assemblies for Engelmann spruce engelmannii) Sitka sitchensis) together improved more contiguous white glauca) a naturally occurring introgress...
Abstract Background Conifers are a large group of gymnosperm trees which separated from the angiosperms by more than 300 million years independent evolution. Conifer genomes extremely and contain considerable amounts repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed tags (ESTs) full-length (FL)cDNAs. There is no genome available for or any other gymnosperm. defence-related genes often into families with closely related members. The goals this study to...
The mountain pine beetle, Dendroctonus ponderosae, is a native species of bark beetle (Coleoptera: Curculionidae) that caused unprecedented damage to the forests British Columbia and other parts western North America currently expanding its range into boreal central eastern Canada USA. We conducted large-scale gene expression analysis (RNA-seq) male female adults either starved or fed in male-female pairs for 24 hours on lodgepole host tree tissues. Our aim was uncover transcripts involved...
Plant defenses often involve specialized cells and tissues. In conifers, of the bark are important for defense against insects pathogens. Using laser microdissection, we characterized transcriptomes cortical resin duct cells, phenolic phloem white spruce (Picea glauca) under constitutive methyl jasmonate (MeJa)-induced conditions, compared these with transcriptome tissue complex. Overall, ~3700 transcripts were differentially expressed in response to MeJa. Approximately 25% only one cell...
The plant metabolite montbretin A (MbA) and its precursor mini-MbA are potential new drugs for treating type 2 diabetes. These complex acylated flavonol glycosides only occur in small amounts the corms of ornamental montbretia (Crocosmia × crocosmiiflora). Our goal is to metabolically engineer Nicotiana benthamiana using genes achieve increased production MbA. Two UDP-dependent glycosyltransferases (UGTs), CcUGT1 CcUGT2, catalyze formation first two pathway-specific intermediates MbA...
We assembled the 9.8-Gbp genome of western redcedar (WRC; Thuja plicata), an ecologically and economically important conifer species Cupressaceae. The assembly, derived from a uniquely inbred tree produced through five generations self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis, one most assemblies for conifer. Population genomic analysis revealed WRC genetically depauperate wild plant species, with effective population size approximately 300 no significant...