Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome.

Nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes form a major line of defense 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 extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity, and genomic distribution of NLR genes.

High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers.

In species with large and complex genomes such as conifers, dense linkage maps are a useful resource for supporting genome assembly and laying the genomic groundwork at the structural, populational, and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 single nucleotide polymorphism (SNP) markers in Sitka spruce (Picea sitchensis [Bong.

Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce.

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 primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.

Comparing DNA isolation methods for forest trees: quality, plastic footprint, and time-efficiency.

Background: Genetic and genomic studies are seeing an increase in sample sizes together with a wider range of species investigated in response to environmental change concerns. In turn, these changes may come with challenges including the time and difficulty to isolate nucleic acids (DNA or RNA), the sequencing cost and environmental impacts of the growing amount of plastic waste generated in the process. Pseudotsuga menziesii var.

Range-wide differential adaptation and genomic offset in critically endangered Asian rosewoods.

In the billion-dollar global illegal wildlife trade, rosewoods have been the world's most trafficked wild product since 2005. and are the most sought-after rosewoods in the Greater Mekong Subregion. They are exposed to significant genetic risks and the lack of knowledge on their adaptability limits the effectiveness of conservation efforts.

Comparative transcriptomic responses of European and Japanese larches to infection by Phytophthora ramorum.

Background And Objectives: Phytophthora ramorum severely affects both European larch (EL) and Japanese larch (JL) trees as indicated by high levels of mortality particularly in the UK. Field observations suggested that EL is less severely affected and so may be less susceptible to P. ramorum than JL; however, controlled inoculations have produced inconsistent or non-statistically significant differences.

Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes.

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.

Physiological responses of rosewoods and under drought and heat stresses.

and are classified as vulnerable and endangered, respectively, in the IUCN Red List and under continued threat from deforestation and illegal harvesting for rosewood. Despite emerging efforts to conserve and restore these species, little is known of their responses to drought and heat stress, which are expected to increase in the Greater Mekong Subregion where the species co-occur and are endemic. In this study of isolated and combined drought and heat effects, we found that had an earlier stomatal closure and more constant midday water potential in response to increasing drought level, suggesting that is relatively isohydric while is relatively anisohydric.

Association genetics of acetophenone defence against spruce budworm in mature white spruce.

Background: Outbreaks of spruce budworm (SBW, Choristoneura fumiferana Clem.) cause major recurrent damage in boreal conifers such as white spruce (Picea glauca [Moench] Voss) and large losses of forest biomass in North America. Although defensive phenolic compounds have recently been linked to chemical resistance against SBW, their genetic basis remains poorly understood in forest trees, especially in conifers.

Evolution of the biosynthesis of two hydroxyacetophenones in plants.

Acetophenones are phenolic metabolites of plant species. A metabolic route for the biosynthesis and release of 2 defence-related hydroxyacetophenones in white spruce (Picea glauca) was recently proposed to involve 3 phases: (a) biosynthesis of the acetophenone aglycons catalysed by a currently unknown set of enzymes, (b) formation and accumulation of the corresponding glycosides catalysed by a glucosyltransferase, and (c) release of the aglycons catalysed by a glucosylhydrolase (PgβGLU-1). We tested if this biosynthetic model is conserved across Pinaceae and land plant species.

Insect herbivory (Choristoneura fumiferana, Tortricidea) underlies tree population structure (Picea glauca, Pinaceae).

Variation in insect herbivory can lead to population structure in plant hosts as indicated by defence traits. In annual herbaceous, defence traits may vary between geographic areas but evidence of such patterns is lacking for long-lived species. This may result from the variety of selection pressures from herbivores, long distance gene flow, genome properties, and lack of research.

Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function.

Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20-24 gigabases have been sequenced for several conifers, with several others expected in the near future.

Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures.

Transcript profiling has shown the molecular bases of several biological processes in plants but few studies have developed an understanding of overall transcriptome variation. We investigated transcriptome structure in white spruce (Picea glauca), aiming to delineate its modular organization and associated functional and evolutionary attributes. Microarray analyses were used to: identify and functionally characterize groups of co-expressed genes; investigate expressional and functional diversity of vascular tissue preferential genes which were conserved among Picea species, and identify expression networks underlying wood formation.

Expression of the β-glucosidase gene Pgβglu-1 underpins natural resistance of white spruce against spruce budworm.

Periodic outbreaks of spruce budworm (SBW) affect large areas of ecologically and economically important conifer forests in North America, causing tree mortality and reduced forest productivity. Host resistance against SBW has been linked to growth phenology and the chemical composition of foliage, but the underlying molecular mechanisms and population variation are largely unknown. Using a genomics approach, we discovered a β-glucosidase gene, Pgβglu-1, whose expression levels and function underpin natural resistance to SBW in mature white spruce (Picea glauca) trees.

Large-scale screening of transcription factor-promoter interactions in spruce reveals a transcriptional network involved in vascular development.

This research aimed to investigate the role of diverse transcription factors (TFs) and to delineate gene regulatory networks directly in conifers at a relatively high-throughput level. The approach integrated sequence analyses, transcript profiling, and development of a conifer-specific activation assay. Transcript accumulation profiles of 102 TFs and potential target genes were clustered to identify groups of coordinately expressed genes.

Opposite action of R2R3-MYBs from different subgroups on key genes of the shikimate and monolignol pathways in spruce.

Redundancy and competition between R2R3-MYB activators and repressors on common target genes has been proposed as a fine-tuning mechanism for the regulation of plant secondary metabolism. This hypothesis was tested in white spruce [Picea glauca (Moench) Voss] by investigating the effects of R2R3-MYBs from different subgroups on common targets from distinct metabolic pathways. Comparative analysis of transcript profiling data in spruces overexpressing R2R3-MYBs from loblolly pine (Pinus taeda L.

Are long-lived trees poised for evolutionary change? Single locus effects in the evolution of gene expression networks in spruce.

Genetic variation in gene expression traits contributes to phenotypic diversity and may facilitate adaptation following environmental change. This is especially important in long-lived organisms where adaptation to rapid changes in the environment must rely on standing variation within populations. However, the extent of expression variation in most wild species remains to be investigated.

A white spruce gene catalog for conifer genome analyses.

Several angiosperm plant genomes, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), poplar (Populus trichocarpa), and grapevine (Vitis vinifera), have been sequenced, but the lack of reference genomes in gymnosperm phyla reduces our understanding of plant evolution and restricts the potential impacts of genomics research. A gene catalog was developed for the conifer tree Picea glauca (white spruce) through large-scale expressed sequence tag sequencing and full-length cDNA sequencing to facilitate genome characterizations, comparative genomics, and gene mapping. The resource incorporates new and publicly available sequences into 27,720 cDNA clusters, 23,589 of which are represented by full-length insert cDNAs.

Gene family structure, expression and functional analysis of HD-Zip III genes in angiosperm and gymnosperm forest trees.

Background: Class III Homeodomain Leucine Zipper (HD-Zip III) proteins have been implicated in the regulation of cambium identity, as well as primary and secondary vascular differentiation and patterning in herbaceous plants. They have been proposed to regulate wood formation but relatively little evidence is available to validate such a role. We characterised and compared HD-Zip III gene family in an angiosperm tree, Populus spp.

High nitrogen fertilization and stem leaning have overlapping effects on wood formation in poplar but invoke largely distinct molecular pathways.

Previous studies indicated that high nitrogen fertilization may impact secondary xylem development and alter fibre anatomy and composition. The resulting wood shares some resemblance with tension wood, which has much thicker cell walls than normal wood due to the deposition of an additional layer known as the G-layer. This report compares the short-term effects of high nitrogen fertilization and tree leaning to induce tension wood, either alone or in combination, upon wood formation in young trees of Populus trichocarpa (Torr.

Prepublication data sharing.

Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.

Effects of increased nitrogen supply on the lignification of poplar wood.

The short-term influence of adequate and high nitrogen fertilization on poplar lignification was investigated. The high nitrogen supply decreased lignin staining in the newly formed secondary xylem, indicating that lignin deposition was affected. Acetyl bromide determinations gave a 9-10% decrease in lignin content; however, Klason lignin content was unchanged.

RECENT ADVANCES IN UNDERSTANDING LIGNIN BIOSYNTHESIS.

After a long period of little change, the basic concepts of lignin biosynthesis have been challenged by new results from genetic modification of lignin content and composition. New techniques for making directed genetic changes in plants, as well as improvements in the analytical techniques used to determine lignin content and composition in plant cell walls, have been used in experimental tests of the accepted lignin biosynthetic pathway. The lignins obtained from genetically modified plants have shown unexpected properties, and these findings have extended the known range of variation in lignin content and composition.