Jörg Bohlmann

• University of British Columbia

Forests face many threats. While traditional breeding may be too slow to deliver well‐adapted trees, genomic selection (GS) can accelerate the process. We describe a comprehensive study of GS from proof of concept to operational application in western redcedar (WRC, Thuja plicata). Using genomic data, we developed models on a training population (T...

Nucleotide-binding domain and Leucine-rich Repeat (NLR) immune receptor genes form a major line of defence in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis) but it is unknown how widespread this genomic architecture may be among the extan...

Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and βglu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its...

The plant‐specialized metabolite montbretin A (MbA) is being developed as a new treatment option for type‐2 diabetes, which is among the ten leading causes of premature death and disability worldwide. MbA is a complex acylated flavonoid glycoside produced in small amounts in below‐ground organs of the perennial plant Montbretia ( Crocosmia × crocos...

Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were...

Research conducted Nucleotide-binding domain and Leucine-rich Repeat (NLR) immune receptor genes form a major line of defence in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in pine but it is unknown how widespread this genomic architecture may be among the extant spe...

Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5 / Ugt5b and βglu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce ( Picea glauca ) against...

Background The mountain pine beetle, Dendroctonus ponderosae , is an irruptive bark beetle that causes extensive mortality to many pine species within the forests of western North America. Driven by climate change and wildfire suppression, a recent mountain pine beetle (MPB) outbreak has spread across more than 18 million hectares, including areas...

Stone cells are a specialized, highly lignified cell type found in both angiosperms and gymnosperms. In conifers, abundance of stone cells in the cortex provides a robust constitutive physical defense against stem feeding insects. Stone cells are a major insect‐resistance trait in Sitka spruce (Picea sitchensis), occurring in dense clusters in apic...

Insects and plants dominate terrestrial ecosystems in terms of both species numbers and biomass. Ecological relationships between insects and plants are ubiquitous and insect-plant interactions are important for ecosystem structuring and functioning.

Vaccinium corymbosum (highbush blueberry) in British Columbia relies on honeybee pollination for a reliable fruit set. As floral volatiles may help explain pollinator preference for blueberry, we surveyed components of variation for volatiles using gas chromatography-mass spectrometry (GC/MS). Principal component analysis of GC chromatogram peaks r...

Background: The mountain pine beetle, Dendroctonus ponderosae, is an irruptive bark beetle that causes extensive mortality to many pine species within the forests of western North America. Driven by climate change and wildfire suppression, a recent MPB outbreak has spread across more than 18 million hectares, including areas to the east of the Rock...

Diet-derived polysaccharides are an important carbon source for gut bacteria and shape the human gut microbiome. Acarbose, a compound used clinically to treat type 2 diabetes, is known to inhibit the growth of some bacteria on starches based on its activity as an inhibitor of α-glucosidases and α-amylases. In contrast to acarbose, montbretin A, a n...

Western redcedar (WRC; Thuja plicata) is a conifer of the Pacific Northwest of North America prized for its durable and rot‐resistant wood. WRC has naturally low outcrossing rates and readily self‐fertilizes in nature. Challenges faced in WRC breeding and propagation involve selecting trees for accelerated growth while also ensuring enhanced heartw...

We assembled the 9.8 Gbp genome of western redcedar (WRC, Thuja plicata ), an ecologically and economically important conifer species of the Cupressaceae. The genome assembly, derived from a uniquely inbred tree produced through five generations of self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis - one of the most c...

We assembled the 9.8 Gbp genome of western redcedar (WRC, Thuja plicata ), an ecologically and economically important conifer species of the Cupressaceae. The genome assembly, derived from a uniquely inbred tree produced through five generations of self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis - one of the most c...

Western redcedar (WRC) is an ecologically and economically important forest tree species characterized by low genetic diversity with high self‐compatibility and high heartwood durability. Using sequence capture genotyping of target genic and non‐genic regions, we genotyped 44 parent trees and 1520 offspring trees representing 26 polycross (PX) fami...

Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of f...

The mountain pine beetle epidemic has highlighted the complex interactions of bark beetles with conifer host defenses. In these interactions, oleoresin terpenoids and volatiles, produced and released by the host tree, can be both harmful and beneficial to the beetle's success in colonizing a tree and completing its life cycle. The insect spends alm...

The highly diverse insect family of true weevils, Curculionidae, includes many agricultural and forest pests. Pissodes strobi, commonly known as the spruce weevil or white pine weevil, is a major pest of spruce and pine forests in North America. P. strobi larvae feed on the apical shoots of young trees, causing stunted growth and can destroy regene...

The cereal scutellum is a hub for diverse specialized defense metabolism and pathway discovery.

Background Montbretins are rare specialized metabolites found in montbretia (Crocosmia x crocosmiiflora) corms. Montbretin A (MbA) is of particular interest as a novel therapeutic for type-2 diabetes and obesity. There is no scalable production system for this complex acylated flavonol glycoside. MbA biosynthesis has been reconstructed in Nicotiana...

Spruce weevil (Pissodes strobi) is a significant pest of regenerating spruce (Picea) and pine (Pinus) forests in North America. Weevil larvae feed in the bark, phloem, cambium, and outer xylem of apical shoots, causing stunted growth or mortality of young trees. We identified and characterized constitutive and weevil‐induced patterns of Sitka spruc...

The mountain pine beetle, Dendroctonus ponderosae, has infested over ~16 Mha of pine forests in British Columbia killing >50% of mature lodgepole pine, Pinus contorta, trees in affected stands. At present, it is functionally an invasive species in Alberta, killing and reproducing in evolutionarily naïve populations of lodgepole pine (P. contorta),...

Specialized metabolites constitute key layers of immunity that underlie disease resistance in crops; however, challenges in resolving pathways limit our understanding of the functions and applications of these metabolites. In maize (Zea mays), the inducible accumulation of acidic terpenoids is increasingly considered to be a defence mechanism that...

Here, we present the chloroplast genome sequence of black spruce (Picea mariana), a conifer widely distributed throughout North American boreal forests. This complete and annotated chloroplast sequence is 123,961 bp long and will contribute to future studies on the genetic basis of evolutionary change in spruce and adaptation in conifers.

With climate change, the pressure on tree breeding to provide varieties with improved resilience to biotic and abiotic stress is increasing. As such, pest resistance is of high priority but has been neglected in most tree breeding programs, given the complexity of phenotyping for these traits and delays to assess mature trees. In addition, the exis...

Within seed plants, the genomes of the conifer lineage are extraordinarily large and complex. While the evolutionary mechanisms driving this expansion are poorly understood, increasing evidence implicates retrotransposon activity as the driving force. We have isolated in targeted fashion and sequenced two independent white spruce genomic BAC clones...

Glandular trichomes (GTs) are defensive structures that produce and accumulate specialized metabolites and protect plants against herbivores, pathogens, and abiotic stress. GTs have been extensively studied in angiosperms for their roles in defense and biosynthesis of high-value metabolites. In contrast, trichomes of gymnosperms have been described...

Diabetes and obesity are affecting human health worldwide. Their occurrence is increasing with lifestyle choices, globalization of food systems, and economic development. The specialized plant metabolite montbretin A (MbA) is being developed as an anti-diabetes and anti-obesity treatment due to its potent and specific inhibition of the human pancre...

Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent (“decoupled”) axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally...

Cannabis (Cannabis sativa) resin is the foundation of a multi-billion dollar medicinal and recreational plant bioproducts industry. Major components of the cannabis resin are the cannabinoids and terpenes. Variations of cannabis terpene profiles contribute much to the different flavor and fragrance phenotypes that affect consumer preferences. A maj...

Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5 Mbp mitochondria...

We review a recently discovered white spruce (Picea glauca) chemical defense against spruce budworm (Choristoneura fumiferana) involving hydroxyacetophenones. These defense metabolites detected in the foliage accumulate variably as the aglycons, piceol and pungenol, or the corresponding glucosides, picein and pungenin. We summarize current knowledg...

Duplication and divergence of primary pathway genes underlie the evolution of plant specialized metabolism; however, mechanisms partitioning parallel hormone and defence pathways are often speculative. For example, the primary pathway intermediate ent-kaurene is essential for gibberellin biosynthesis and is also a proposed precursor for maize antib...

The cannabis leaf is iconic, but it is the flowers of cannabis that are consumed for the psychoactive and medicinal effects of their specialized metabolites. Cannabinoid metabolites, together with terpenes, are produced in glandular trichomes. Superficially, stalked and sessile trichomes in cannabis only differ in size and whether they have a stalk...

Type 2 diabetes (T2D) affects over 320 million people worldwide. Healthy lifestyles, improved drugs and effective nutraceuticals are different components of a response against the growing T2D epidemic. The specialized metabolite montbretin A (MbA) is being developed for treatment of T2D and obesity due to its unique pharmacological activity as a hi...

Conifers have evolved complex oleoresin terpene defenses against herbivores and pathogens. In co‐evolved bark beetles, conifer terpenes also serve chemo‐ecological functions as pheromone precursors, chemical barcodes for host identification, or nutrients for insect‐associated microbiomes. We highlight the genomic, molecular and biochemical underpin...

Western Redcedar (Thuja plicata; WRC) is an ecologically and economically important conifer species of the Pacific Northwest. Ungulate consumption of young WRC foliage and fungal heartwood decay in older trees are both significant problems facing planting of new-growth WRC and are a major focus of the WRC improvement program in British Columbia. Re...

Engelmann spruce ( Picea engelmannii ) is a conifer found primarily on the west coast of North America. Here, we present the complete chloroplast genome sequence of Picea engelmannii genotype Se404-851. This chloroplast sequence will benefit future conifer genomic research and contribute resources to further species conservation efforts.

Here, we present the complete chloroplast genome sequence of white spruce (Picea glauca, genotype WS77111), a coniferous tree widespread in the boreal forests of North America. This sequence contributes to genomic and phylogenetic analyses of the Picea genus that are part of ongoing research to understand their adaptation to environmental stress.

Motivation: In the modern genomics era, genome sequence assemblies are routine practice. However, depending on the methodology, resulting drafts may contain considerable base errors. Although utilities exist for genome base polishing, they work best with high read coverage and do not scale well. We developed ntEdit, a Bloom filter-based genome seq...

The mountain pine beetle (MPB; Dendroctonus ponderosae) is a forest insect pest that attacks several different pine (Pinus) species in its native range of distribution in western North America. MPB are exposed for most of their life cycle to the chemical defenses of their hosts. These defenses are dominated by oleoresin secretions containing mostly...

Denatured CYP6DJ1, CYP6BW1, CYP6BW3 and empty vector control microsomes on a 12% SDS-Page gel. Lane 1: Precision Plus Protein ladder (Bio-rad). Lane 2: empty vector microsomes. Lane 3: CYP6BW1 microsomes, protein band is visible between 75 kDa and 50 kDa. Lane 4: CYP6BW3 microsomes, protein band is visible between 75 kDa and 50 kDa. Lane 5: Precisi...

CO Spectra of CYP6DJ1, CYP6BW1, CYP6BW3 and empty vector control microsomes. (PDF)

Mass spectra of peaks 1–8 from the gas chromatograms of extracts of CYP6DJ1 or female beetles treated with (–)-(4S)-limonene along with the standards. Gas chromatograms with peak numbers can be found in Fig 2. (PDF)

Mass spectra of peaks 15–18 from the gas chromatograms of extracts of CYP6BW1 or CYP6BW3 or female beetles treated with isopimaric, palustric, or dehydroabietic acid. Gas chromatograms with peak numbers can be found in Fig 7A–7C. (PDF)

Mass spectra of peaks 3–9 from the gas chromatograms of extracts of CYP6DJ1 or female beetles treated with (+)-(4R)-limonene along with the standards. Gas chromatograms with peak numbers can be found in Fig 1. (PDF)

Mass spectra of peaks 9 and 10 from the gas chromatograms of extracts of CYP6DJ1 or female beetles treated with with (–)-(4S)-limonene along with the standards. Gas chromatograms with peak numbers can be found in Fig 2. (PDF)

Mass spectra of peaks 11–14 from the gas chromatograms of extracts of CYP6DJ1 or female beetles treated with terpinolene. Gas chromatograms with peak numbers can be found in Fig 3. (PDF)

Mass spectra of peaks 19–21 from the gas chromatograms of extracts of CYP6BW1 or CYP6BW3 or female beetles treated with levopimaric, abietic or neoabietic acid. Gas chromatograms with peak numbers can be found in Fig 7D–7F. (PDF)

Activity assay of CYP6DJ1, CYP6BW1 and CYP6BW3 with ten selected monoterpenes and six diterpene resin acid substrates. Red crosses indicate that no product was detected in GC chromatograms of the assay, green checkmarks indicate that one or more products were detected in the assay. (PDF)

The retention index of all limonene and terpinolene products of CYP6DJ1 and from extracts of MPB after treatment. All samples were injected onto a DB-Wax column. See Figs 1–5 and S3–S6 Figs. for the gas chromatograms, structures and mass spectra of these peaks. (PDF)

The retention index of diterpene resin acid products of CYP6BW1 and CYP6BW3 and from extracts of MPB after treatment. All samples were injected onto a HP-5 column. See Fig 7 and S7 and S8 Figs for the gas chromatograms and mass spectra of these peaks. (PDF)

Insect pests are part of natural forest ecosystems contributing to forest rejuvenation, but can also cause ecological disturbance and economic losses that are expected to increase with climate change. The white pine or spruce weevil (Pissodes strobi) is a pest of conifer forests in North America. Weevil‐host interactions with various spruce (Picea)...

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 in the corms of the ornamental plant montbretia (Crocosmia × crocosmiiflora). Our goal is to metabolically engineer Nicotiana benthamiana using montbretia gen...

Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the 5.5 Mbp mitochondrial genome...

Cannabis sativa (cannabis) produces a resin that is valued for its psychoactive and medicinal properties. Despite being the foundation of a multi-billion dollar global industry, scientific knowledge and research on cannabis is lagging behind compared to other high-value crops. This is largely due to legal restrictions that have prevented many resea...

In the modern genomics era, genome sequence assemblies are routine practice. However, depending on the methodology, resulting drafts may contain considerable base errors. Although utilities exist for genome base polishing, they work best with high read coverage and do not scale well. We developed ntEdit, a Bloom filter-based genome sequence editing...

The recent outbreak of the mountain pine beetle (Dendroctonus ponderosae; MPB) has affected over 20 M hectares of pine forests in western North America. During the colonization of host trees, female MPB release the aggregation pheromone (−)-trans-verbenol. (−)-trans-Verbenol is thought to be produced from the pine defense compound (−)-α-pinene by c...

The mountain pine beetle (MPB, Dendroctonus ponderosae) is a forest insect pest endemic to western North America. During dispersal and host colonization, MPB identify suitable host trees by olfaction of monoterpene volatiles, contend with host terpene defenses, and communicate with conspecifics using terpenoid and other pheromones. Cytochromes P450...

Chardonnay is the basis of some of the world’s most iconic wines and its success is underpinned by a historic program of clonal selection. There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mutations during centuries of asexual propa...

Background Genome sequencing yields the sequence of many short snippets of DNA (reads) from a genome. Genome assembly attempts to reconstruct the original genome from which these reads were derived. This task is difficult due to gaps and errors in the sequencing data, repetitive sequence in the underlying genome, and heterozygosity. As a result, as...

Conifers depend on complex defense systems against herbivores. Stone cells (SC) and oleoresin are physical and chemical defenses of Sitka spruce that have been separately studied in previous work. Weevil oviposit at the tip of the previous year's apical shoot (PYAS). We investigated interactions between weevil larvae and trees in controlled oviposi...

Plant genomes encode isopentenyl phosphate kinases (IPKs) that reactivate isopentenyl phosphate (IP) via ATP-dependent phosphorylation, forming the primary metabolite isopentenyl diphosphate (IPP) used generally for isoprenoid/terpenoid biosynthesis. Therefore, the existence of IPKs in plants raises unanswered questions concerning the origin and re...

Chardonnay is the basis of some of the world’s most iconic wines and its success is underpinned by a historic program of clonal selection. There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mutations during centuries of asexual propa...

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 mini-MbA are potent inhibitors of human pancreatic α-amylase and are being developed as drug candidates for the treatment of type-2 diabetes. MbA occurs in corms of the orna...

The seed coats of several conifers contain terpene-filled resin vesicles, which may be involved in the protection of the dormant embryo and the seed storage tissue against herbivores or pathogens. We analyzed the terpenoid composition of seeds from four Abies species (Abiesamabilis Douglas ex J. Forbes, Abiesbalsamea (L.) Mill., Abiesgrandis (Dougl...

Western redcedar (Thuja plicata; Cupressaceae; WRC) is an ecologically and economically important conifer species of the Pacific Northwest. Regeneration of WRC forests is affected by ungulate browsing, which removes current growth and hampers development of young trees. Monoterpenes make WRC foliage less palatable and can deter browsing. Genomic re...

Genome sequencing yields the sequence of many short snippets of DNA (reads) from a genome. Genome assembly attempts to reconstruct the original genome from which these reads were derived. This task is difficult due to gaps and errors in the sequencing data, repetitive sequence in the underlying genome, and heterozygosity, and assembly errors are co...

Significance trans -Verbenol is a critical aggregation pheromone of the female mountain pine beetle. It is derived from a compound of the host defense, the monoterpene α-pinene. We found that beetles accumulate monoterpenyl esters during early life stages. These may serve as a previously unknown reservoir for the sex-specific release of aggregation...

Terpenoids are a major component of maize (Zea mays) chemical defenses that mediate responses to herbivores, pathogens and other environmental challenges. Here, we describe the biosynthesis and elicited production of a class of maize diterpenoids, named dolabralexins. Dolabralexin biosynthesis involves the sequential activity of two diterpene synth...

Acetophenones are phenolic metabolites of plant species. A metabolic route for the biosynthesis and release of two defense-related hydroxyacetophenones in white spruce (Picea glauca) was recently proposed to involve three phases: (i) biosynthesis of the acetophenone aglycons catalyzed by a currently unknown set of enzymes, (ii) formation and accumu...

The mountain pine beetle (Dendroctonus ponderosae; MPB) is an eruptive bark beetle species affecting pine forests of western North America. MPB are exposed to volatile monoterpenes, which are important host defense chemicals. We assessed the toxicity of the ten most abundant monoterpenes of lodgepole pine (Pinus contorta), a major host in the curre...

Acetophenones are phenolic compounds involved in resistance of white spruce (Picea glauca) against spruce budworm (Choristoneura fumiferiana), a major forest pest in North America. The acetophenones pungenol and piceol commonly accumulate in spruce foliage in the form of the corresponding glycosides, pungenin and picein. These glycosides appear to...

Plant defenses often involve specialized cells and tissues. In conifers, specialized cells of the bark are important for defense against insects and pathogens. Using laser microdissection, we characterized the transcriptomes of cortical resin duct cells, phenolic cells, and phloem of white spruce (Picea glauca) bark under constitutive and methyl ja...

Eastern spruce budworm ( Choristoneura fumiferiana Clemens) (ESBW) is a major forest pest which feeds on young shoots of white spruce ( Picea glauca ) and can cause landscape level economic and ecological losses. Release of acetophenone metabolites, piceol and pungenol, from their corresponding glycosides, picein and pungenin, can confer natural re...

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The development of heartwood (HW) and the associated accumulation of secondary metabolites, which are also known as 'specialized metabolites' or 'extractives', is an important feature of tree biology. Heartwood development can affect tree health with broader implications for forest health. Heartwood development also defines a variety of wood qualit...

West Australian sandalwood (Santalum spicatum) has long been exploited for its fragrant, sesquiterpene-rich heartwood; however sandalwood fragrance qualities vary substantially, which is of interest to the sandalwood industry. We investigated metabolite profiles of trees from the arid northern and southeastern and semi-arid southwestern regions of...

The range of many Holarctic forest insects does not comprise the entire range of their hosts, as they are often limited to more southern latitudes by the adverse effects of cold temperatures. Global climate warming has led to the increased potential for forest insects to invade novel habitats of native hosts within the same landmass. The mountain p...

Cannabis (Cannabis sativa) plants produce and accumulate a terpene-rich resin in glandular trichomes, which are abundant on the surface of the female inflorescence. Bouquets of different monoterpenes and sesquiterpenes are important components of cannabis resin as they define some of the unique organoleptic properties and may also influence medicin...

qPCR primers. (XLSX)