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Jörg Bohlmann - One of the best experts on this subject based on the ideXlab platform.
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oleoresin defenses in Conifers chemical diversity terpene synthases and limitations of oleoresin defense under climate change
New Phytologist, 2019Co-Authors: Jose M Celedon, Jörg BohlmannAbstract: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 underpinnings of the large chemical space of conifer oleoresin terpenes and volatiles. Conifer terpenes are predominantly the products of the conifer terpene synthase (TPS) gene family. Terpene diversity is increased by cytochromes P450 of the CYP720B class. Many conifer TPS are multiproduct enzymes. Multisubstrate CYP720B enzymes catalyse multistep oxidations. We summarise known terpenoid gene functions in various different conifer species with reference to the annotated terpenoid gene space in a spruce genome. Overall, biosynthesis of terpene diversity in Conifers is achieved through a system of biochemical radiation and metabolic grids. Expression of TPS and CYP720B genes can be specific to individual cell types of constitutive or traumatic resin duct systems. Induced terpenoid transcriptomes in resin duct cells lead to dynamic changes of terpene composition and quantity to fend off herbivores and pathogens. While terpenoid defenses have contributed much to the evolutionary success of Conifers, under new conditions of climate change, these defences may become inconsequential against range-expanding forest pests.
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slow but not low genomic comparisons reveal slower evolutionary rate and higher dn ds in Conifers compared to angiosperms
BMC Evolutionary Biology, 2012Co-Authors: Emmanuel Buschiazzo, Jörg Bohlmann, Carol Ritland, Kermit RitlandAbstract:Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two Conifers, Sitka spruce (Picea sitchensis) and loblolly pine (Pinus taeda), together with full genome sequences for two angiosperms, Arabidopsis thaliana and poplar (Populus trichocarpa), offer an opportunity to infer the evolutionary processes underlying thousands of orthologous protein-coding genes in gymnosperms compared with an angiosperm orthologue set. Based upon pairwise comparisons of 3,723 spruce and pine orthologues, we found an average synonymous genetic distance (dS) of 0.191, and an average dN/dS ratio of 0.314. Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10-9 synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in Conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar-Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in Conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution. Our results are in line with documented reduced nucleotide diversity, conservative genome evolution and low rates of diversification in Conifers on the one hand and numerous examples of local adaptation in Conifers on the other hand. We propose that reduced levels of nucleotide mutation in large and long-lived conifer trees, coupled with large effective population size, were the main factors leading to slow substitution rates but retention of beneficial mutations.
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cytochrome p450 mono oxygenases in conifer genomes discovery of members of the terpenoid oxygenase superfamily in spruce and pine
Biochemical Society Transactions, 2006Co-Authors: Bjorn Hamberger, Jörg BohlmannAbstract:Diterpene resin acids, together with monoterpenes and sesquiterpenes, are the most prominent defence chemicals in Conifers. These compounds belong to the large group of structurally diverse terpenoids formed by enzymes known as terpenoid synthases. CYPs (cytochrome P450-dependent mono-oxygenases) can further increase the structural diversity of these terpenoids. While most terpenoids are characterized as specialized or secondary metabolites, some terpenoids, such as the phytohormones GA (gibberellic acid), BRs (brassinosteroids) and ABA (abscisic acid), have essential functions in plant growth and development. To date, very few CYP genes involved in conifer terpenoid metabolism have been functionally characterized and were limited to two systems, yew (Taxus) and loblolly pine (Pinus taeda). The characterized yew CYP genes are involved in taxol diterpene biosynthesis, while the only characterized pine terpenoid CYP gene is part of DRA (diterpene resin acid) biosynthesis. These CYPs from yew and pine are members of two apparently conifer-specific CYP families within the larger CYP85 clan, one of four plant CYP multifamily clans. Other CYP families within the CYP85 clan were characterized from a variety of angiosperms with functions in terpenoid phytohormone metabolism of GA, BR, and ABA. The recent development of EST (expressed sequence tag) and FLcDNA (where FL is full-length) sequence databases and cDNA collections for species of two Conifers, spruce (Picea) and pine, allows for the discovery of new terpenoid CYPs in gymnosperms by means of large-scale sequence mining, phylogenetic analysis and functional characterization. Here, we present a snapshot of conifer CYP data mining, discovery of new conifer CYPs in all but one family within the CYP85 clan, and suggestions for their functional characterization. This paper will focus on the discovery of conifer CYPs associated with diterpene metabolism and CYP with possible functions in the formation of GA, BR, and ABA in Conifers.
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Characterization of EST-SSRs in loblolly pine and spruce
Tree Genetics & Genomes, 2006Co-Authors: Yanik Bérubé, Jörg Bohlmann, Jun Zhuang, Dainis Rungis, Steven G. Ralph, Kermit RitlandAbstract:In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases were characterized for EST-SSRs. One database was from “interior spruce” (white and Engelmann spruce in Southern British Columbia) and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce, respectively. 3′ ESTs contained 14% more SSRs than 5′ EST reads in loblolly pine and 41% more in spruce. Conifer EST-SSRs differed conspicuously from angiosperm EST-SSRs in several aspects. EST-SSRs were considerably less frequent in Conifers (one EST-SSR every ∼50 kb) than in angiosperms (one EST-SSR every ∼20 kb). Dinucleotide repeats were the most abundant repeat class in Conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these EST-SSRs in Conifers could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for in-silico approaches for marker development.
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genes enzymes and chemicals of terpenoid diversity in the constitutive and induced defence of Conifers against insects and pathogens
New Phytologist, 2006Co-Authors: Christopher I Keeling, Jörg BohlmannAbstract:Contents Summary 657 I. Introduction 658 II. Identification and functional characterization of terpenoid pathway genes 658 III. Insect interactions with Conifers 667 IV. Conclusions and outlook 670 Acknowledgements 671 References 671 Summary Insects select their hosts, but trees cannot select which herbivores will feed upon them. Thus, as long-lived stationary organisms, Conifers must resist the onslaught of varying and multiple attackers over their lifetime. Arguably, the greatest threats to Conifers are herbivorous insects and their associated pathogens. Insects such as bark beetles, stem- and wood-boring insects, shoot-feeding weevils, and foliage-feeding budworms and sawflies are among the most devastating pests of conifer forests. Conifer trees produce a great diversity of compounds, such as an enormous array of terpenoids and phenolics, that may impart resistance to a variety of herbivores and microorganisms. Insects have evolved to specialize in resistance to these chemicals – choosing, feeding upon, and colonizing hosts they perceive to be best suited to reproduction. This review focuses on the plant–insect interactions mediated by conifer-produced terpenoids. To understand the role of terpenoids in conifer–insect interactions, we must understand how Conifers produce the wide diversity of terpenoids, as well as understand how these specific compounds affect insect behaviour and physiology. This review examines what chemicals are produced, the genes and proteins involved in their biosynthesis, how they work, and how they are regulated. It also examines how insects and their associated pathogens interact with, elicit, and are affected by conifer-produced terpenoids.
Wenzhi Wang - One of the best experts on this subject based on the ideXlab platform.
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mortality predispositions of Conifers across western usa
New Phytologist, 2021Co-Authors: Wenzhi Wang, Nathan B English, Charlotte Grossiord, Arthur Gessler, Adrian J Das, Nathan L Stephenson, Christopher H Baisan, Craig D Allen, Nate G McdowellAbstract:Conifer mortality rates are increasing in western North America, but the physiological mechanisms underlying this trend are not well understood. We examined tree-ring-based radial growth along with stable carbon (C) and oxygen (O) isotope composition (δ13 C and δ18 O, respectively) of dying and surviving Conifers at eight old-growth forest sites across a strong moisture gradient in the western USA to retrospectively investigate mortality predispositions. Compared with surviving trees, lower growth of dying trees was detected at least one decade before mortality at seven of the eight sites. Intrinsic water-use efficiency increased over time in both dying and surviving trees, with a weaker increase in dying trees at five of the eight sites. C starvation was a strong correlate of conifer mortality based on a conceptual model incorporating growth, δ13 C, and δ18 O. However, this approach does not capture processes that occur in the final months of survival. Ultimately, C starvation may lead to increased mortality vulnerability, but hydraulic failure or biotic attack may dominate the process during the end stages of mortality in these Conifers.
Kenji Seiwa - One of the best experts on this subject based on the ideXlab platform.
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Role of thinning intensity in creating mixed hardwood and conifer forests within a Cryptomeria japonica conifer plantation: A 14-year study
Forest Ecology and Management, 2020Co-Authors: Yuki Negishi, Yukino Eto, Masahiro Hishita, Sachi Negishi, Masanori Suzuki, Kazuhiko Masaka, Kenji SeiwaAbstract:Abstract For managers of conifer plantations, conversion to mixed hardwood and conifer forests is an important management goal. However, the extent to which thinning intensity affects stand volume and timber quantity and quality remains unclear. We investigated the growth of conifer and hardwood trees over 14 years (at 5 and 9 years after the first and second thinning operations, respectively) under unthinned (Control), 33% thinned (Weak), and 67% thinned (Intensive) treatments in a Cryptomeria japonica plantation. The diameter growth of both Conifers and hardwoods, stand volume of hardwoods, and relative increment of stand volume of Conifers increased with greater thinning intensity in the order of Control
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Effects of thinning intensity on species diversity and timber production in a conifer (Cryptomeria japonica) plantation in Japan
Journal of Forest Research, 2012Co-Authors: Kenji Seiwa, Masahiro Hishita, Kazuhiko MasakaAbstract:In conifer plantations, enhancement of species diversity has become an important management goal. Although thinning is a useful method to enhance diversity, determining optimum thinning intensities may be rather complicated because of potential trade-offs among a broad array of management goals (e.g., recovery of biodiversity, increasing individual tree sizes, increasing net primary production, saving management costs). To evaluate the optimum thinning intensity by analyzing these relationships, we conducted a thinning experiment with three different thinning intensities—unthinned, 33% thinned, and 67% thinned—in a Cryptomeria japonica plantation in 2003, and investigated the number, diameter at breast height (DBH), and diversity of hardwoods (height > 1.5 m) in 2008, and the growth of Conifers over five years. In hardwoods, the number of individuals, number of species, mean DBH, and total basal area were greatest in the 67% thinned treatment, irrespective of successional status. However, Shannon’s diversity index did not differ among the three treatments due to a disproportionate increase with thinning intensity in the abundance of a mid-successional species, Cornus controversa . Diameter growth of Conifers was also highest in the 67% thinned and lowest in the unthinned treatment, whereas the reverse was true for stand volume increment. These results suggest that intensive thinning is a reliable method to convert conifer plantations into conifer–hardwood mixed forests at canopy level much more quickly and consistently than weak thinning, although primary production is to some extent reduced. If forest managers prefer sustainable timber production of Conifers rather than full recovery of diversity, weak thinning may be suitable.
Kermit Ritland - One of the best experts on this subject based on the ideXlab platform.
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insights into conifer giga genomes
Plant Physiology, 2014Co-Authors: Amanda R De La Torre, Stefan Jansson, Ove Nilsson, John Mackay, Inanc Birol, Par K Ingvarsson, Christopher I Keeling, Steven J.m. Jones, Jean Bousquet, Kermit RitlandAbstract:Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, Conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.
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Genomics of a phylum distant from flowering plants: Conifers
Tree Genetics & Genomes, 2012Co-Authors: Kermit RitlandAbstract:Conifers are evolutionarily distant from angiosperms, separated by 300 million years of evolution. The genomes of coniferous species are very large, among the largest of any nonpolyploid plant species. Their genomes are characterized by reduced evolutionary rate for coding genes, accumulation of noncoding DNA, and evolutionarily distance from angiosperms. I highlight both the advantages and disadvantages for Conifers as model organism for genomics. With advances of new high-throughput sequencing technologies, we are at a watershed in conifer genomics.
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slow but not low genomic comparisons reveal slower evolutionary rate and higher dn ds in Conifers compared to angiosperms
BMC Evolutionary Biology, 2012Co-Authors: Emmanuel Buschiazzo, Jörg Bohlmann, Carol Ritland, Kermit RitlandAbstract:Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two Conifers, Sitka spruce (Picea sitchensis) and loblolly pine (Pinus taeda), together with full genome sequences for two angiosperms, Arabidopsis thaliana and poplar (Populus trichocarpa), offer an opportunity to infer the evolutionary processes underlying thousands of orthologous protein-coding genes in gymnosperms compared with an angiosperm orthologue set. Based upon pairwise comparisons of 3,723 spruce and pine orthologues, we found an average synonymous genetic distance (dS) of 0.191, and an average dN/dS ratio of 0.314. Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10-9 synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in Conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar-Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in Conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution. Our results are in line with documented reduced nucleotide diversity, conservative genome evolution and low rates of diversification in Conifers on the one hand and numerous examples of local adaptation in Conifers on the other hand. We propose that reduced levels of nucleotide mutation in large and long-lived conifer trees, coupled with large effective population size, were the main factors leading to slow substitution rates but retention of beneficial mutations.
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Genetic Mapping in Conifers
2011Co-Authors: Kermit Ritland, Jean Bousquet, Konstantin V. Krutovsky, Y. Tsumura, Betty Pelgas, Nathalie Isabel, C. Piomion, Chittaranjan KoleAbstract:This chapter summarizes the history and current status of genetic mapping in Conifers. We review the development of molecular markers, methods to construct genetic maps, and the resulting conifer genetic maps. Genetic maps are subdivided into (1) linkage maps of genetic markers, (2) quantitative trait loci (QTL) maps, and (3) comparative maps. Comparative maps involve alignment of marker genes and even QTLs between species. Physical mapping is also briefl y discussed. Emphasis is placed up problems and approaches unique to Conifers, and the involvement of new genomics technologies.
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Characterization of EST-SSRs in loblolly pine and spruce
Tree Genetics & Genomes, 2006Co-Authors: Yanik Bérubé, Jörg Bohlmann, Jun Zhuang, Dainis Rungis, Steven G. Ralph, Kermit RitlandAbstract:In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases were characterized for EST-SSRs. One database was from “interior spruce” (white and Engelmann spruce in Southern British Columbia) and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce, respectively. 3′ ESTs contained 14% more SSRs than 5′ EST reads in loblolly pine and 41% more in spruce. Conifer EST-SSRs differed conspicuously from angiosperm EST-SSRs in several aspects. EST-SSRs were considerably less frequent in Conifers (one EST-SSR every ∼50 kb) than in angiosperms (one EST-SSR every ∼20 kb). Dinucleotide repeats were the most abundant repeat class in Conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these EST-SSRs in Conifers could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for in-silico approaches for marker development.
Nate G Mcdowell - One of the best experts on this subject based on the ideXlab platform.
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mortality predispositions of Conifers across western usa
New Phytologist, 2021Co-Authors: Wenzhi Wang, Nathan B English, Charlotte Grossiord, Arthur Gessler, Adrian J Das, Nathan L Stephenson, Christopher H Baisan, Craig D Allen, Nate G McdowellAbstract:Conifer mortality rates are increasing in western North America, but the physiological mechanisms underlying this trend are not well understood. We examined tree-ring-based radial growth along with stable carbon (C) and oxygen (O) isotope composition (δ13 C and δ18 O, respectively) of dying and surviving Conifers at eight old-growth forest sites across a strong moisture gradient in the western USA to retrospectively investigate mortality predispositions. Compared with surviving trees, lower growth of dying trees was detected at least one decade before mortality at seven of the eight sites. Intrinsic water-use efficiency increased over time in both dying and surviving trees, with a weaker increase in dying trees at five of the eight sites. C starvation was a strong correlate of conifer mortality based on a conceptual model incorporating growth, δ13 C, and δ18 O. However, this approach does not capture processes that occur in the final months of survival. Ultimately, C starvation may lead to increased mortality vulnerability, but hydraulic failure or biotic attack may dominate the process during the end stages of mortality in these Conifers.