Terpenoids are involved in the expression of systemic-induced resistance in Austrian pine

Terpenoids are defense metabolites that are induced upon infection or wounding. However, their role in systemic-induced resistance (SIR) is not known. Here, we explored the role of terpenoids in this phenomenon at a very early stage in the interaction between Austrian pine and the tip blight and canker pathogen Diplodia pinea. We induced Austrian pine saplings by either wounding or inoculating the lower stems with D. pinea. The seedlings were then challenged after 12 h, 72 h, or 10 days with D. pinea on the stem 15 cm above the induction. Lesion lengths and terpenoids were quantified at both induction and challenge locations. Key terpenoids were assayed for antifungal activity in in vitro bioassays. SIR increased with time and was correlated with the inducibility of several compounds. α-Pinene and a cluster of β-pinene, limonene, benzaldehyde, dodecanol, and n-dodecyl acrylate were positively correlated with SIR and were fungistatic in vitro, while other compounds were negatively correlated with SIR and appeared to serve as a carbon source for D. pinea. This study shows that, overall, terpenoids are involved in SIR in this system, but their role is nuanced, depending on the type of induction and time of incubation. We hypothesize that some, such as α-pinene, could serve in SIR signaling.

Bark structure is coordinated with xylem hydraulic properties in branches of five Cupressaceae species

The properties of bark and xylem contribute to tree growth and survival under drought and other types of stress conditions. However, little is known about the functional coordination of the xylem and bark despite the influence of selection on both structures in response to drought. To this end, we examined relationships between proportions of bark components (i.e. thicknesses of tissues outside the vascular cambium) and xylem transport properties in juvenile branches of five Cupressaceae species, focusing on transport efficiency and safety from hydraulic failure via drought-induced embolism. Both xylem efficiency and safety were correlated with multiple bark traits, suggesting that xylem transport and bark properties are coordinated. Specifically, xylem transport efficiency was greater in species with thicker secondary phloem, greater phloem-to-xylem thickness ratio and phloem-to-xylem cell number ratio. In contrast, species with thicker bark, living cortex and dead bark tissues were more resistant to embolism. Thicker phellem layers were associated with lower embolism resistance. Results of this study point to an important connection between xylem transport efficiency and phloem characteristics, which are shaped by the activity of vascular cambium. The link between bark and embolism resistance affirms the importance of both tissues to drought tolerance.

A Genome Sequence for the Threatened Whitebark Pine

Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in western contiguous US and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short-reads of haploid megagametophyte tissue and Oxford Nanopore long-reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gbp of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gbp). Approximately 87.2% (24.0 Gbp) of total sequence was placed on the twelve WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich-repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the three subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo assembled transcriptomes.

Differences in photoprotective strategy during winter in Eastern white pine and white spruce

Conifers growing in temperate forests utilize sustained forms of thermal dissipation during winter to protect the photosynthetic apparatus from damage, which can be monitored via pronounced reductions in photochemical efficiency (Fv/Fm) during winter. Eastern white pine (Pinus strobus L.) and white spruce (Picea  glauca (Moench) Voss) are known to recover from winter stress at different rates, with pine recovering more slowly than spruce, suggesting different mechanisms for sustained dissipation in these species. Our objectives were to monitor pine and spruce throughout spring recovery in order to provide insights into key mechanisms for sustained dissipation in both species. We measured chlorophyll fluorescence, pigments, and abundance and phosphorylation status of key photosynthetic proteins. We found that both species rely on two forms of sustained dissipation involving retention of high amounts of antheraxanthin (A) + zeaxanthin (Z), one that is very slowly reversible and temperature independent and one that is more dynamic and occurs only on subzero days. Differences in protein abundance suggest that spruce, but not pine, likely upregulates cyclic or alternative pathways of electron transport involving the cytochrome b6f complex and photosystem I (PSI). Both species show an increased sustained phosphorylation of the D1 protein on subzero days, and spruce additionally shows dramatic increases in the sustained phosphorylation of light-harvesting complex II (LHCII) and other PSII core proteins on subzero days only, suggesting that a mechanism of sustained dissipation that is temperature dependent requires sustained phosphorylation of photosynthetic proteins in spruce, possibly allowing for direct energy transfer from PSII to PSI as a mechanism of photoprotection. The data suggest differences in strategy among conifers in mechanisms of sustained thermal dissipation in response to winter stress. Additionally, the flexible induction of sustained A + Z and phosphorylation of photosynthetic proteins in response to subzero temperatures during spring recovery seem to be important in providing photoprotection during transitional periods with high temperature fluctuation.

Scots pine - panmixia and the elusive signal of genetic adaptation

Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.

Season of drought affects growth, but not nonstructural carbohydrates dynamics, in Pinus taeda saplings

In temperate evergreen conifers, growth occurs mostly in summer but photosynthesis precedes year-round; thus, nonstructural carbohydrates (NSC) increase in winter but decrease in summer. Given that mild drought reduces growth but not photosynthesis, a drought in summer should increase NSCs more than one in winter. However, the active regulation hypothesis suggests that to increase future drought resilience, plants might downregulate growth to increase NSCs after a winter drought even if NSCs do not increase during the drought. To test if so, potted Pinus taeda saplings (age $< 1$ yr) were subjected to six-month droughts in a greenhouse with one treatment receiving drought during winter (Sep-Mar), and another during summer (Mar-Sep). Both treatments were compared to a control. To measure dry biomass and NSCs, we harvested plants monthly following each drought, while to assess changes in growth rates, we measured height and diameter monthly. While we observed seasonal variation and an overall increase during the study, we found no drought-related changes in NSC dynamics; however, drought did reduce growth. Furthermore, drought in winter did reduce growth during the following summer, but the reduction was less than for a drought in summer. We conclude that the effect of drought on NSCs was too small to detect in our plants. While better control of soil water would have reduced a major source of uncertainty, plants with larger NSC reserves or more intense stress would also yield easier-to-detect effects. Although not definitive, our results suggest that water stress does not lead to dramatic changes in seasonal NSC dynamics in its aftermath, despite what one might expect under the active regulation hypothesis.

Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response

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 predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.

The phenotypic and genetic effects of drought-induced stress on wood specific conductivity and anatomical properties in white spruce seedlings, and relationships with growth and wood density

Drought frequency and intensity are projected to increase with climate change, thus amplifying stress on forest trees. Resilience to drought implicates physiological traits such as xylem conductivity and wood anatomical traits, which are related to growth and wood density. Integrating drought-stress response traits at the juvenile stage into breeding criteria could help promote the survival of planted seedlings under current and future climate and thus, improve plantation success. We assessed in greenhouse the influence of drought-induced stress on 600 two-year-old white spruce (Picea glauca) seedlings from 25 clonal lines after two consecutive growing seasons. Three levels of drought-induced stress were applied: control, moderate and severe. Seedlings were also planted at a 45° angle to clearly separate compression from normal wood. We looked at the phenotypic and genetic effects of drought stress on xylem specific hydraulic conductivity, lumen diameter, tracheid diameter and length, and the number of pits per tracheid in the normal wood. We detected no significant effects of drought stress except for tracheid length, which decreased with increasing drought stress. We found low to high estimates of trait heritability, which generally decreased with increasing drought stress. Genetic correlations were higher than phenotypic correlations for all treatments. Specific conductivity was genetically highly correlated positively with lumen diameter and tracheid length under all treatments. Tracheid length and diameter were always negatively correlated genetically, indicating a trade-off in resource allocation. Moderate to high genetic correlations sometimes in opposite direction were observed between physico-anatomical and productivity traits, also indicating trade-offs. A large variation was observed among clones for all physico-anatomical traits, but clonal ranks were generally stable between control and drought-induced treatments. Our results indicate the possibility of early screening of genetic material for desirable wood anatomical attributes under normal growing conditions, thus allowing to improve the drought resilience of young trees.

Changes in Polar Lipid Composition in Balsam Fir during Seasonal Cold Acclimation and Relationship to Needle Abscission

Needle abscission in balsam fir has been linked to both cold acclimation and changes in lipid composition. The overall objective of this research is to uncover lipid changes in balsam fir during cold acclimation and link those changes with postharvest abscission. Branches were collected monthly from September to December and were assessed for cold tolerance via membrane leakage and chlorophyll fluorescence changes at -5, -15, -25, -35, and -45 °C. Lipids were extracted and analyzed using mass spectrometry while postharvest needle abscission was determined gravimetrically. Cold tolerance and needle retention each significantly (p < 0.001) improved throughout autumn in balsam fir. There were concurrent increases in DGDG, PC, PG, PE, and PA throughout autumn as well as a decrease in MGDG. Those same lipids were strongly related to cold tolerance, though MGDG had the strongest relationship (R2 = 55.0% and 42.7% from membrane injury and chlorophyll fluorescence, respectively). There was a similar, albeit weaker, relationship between MGDG:DGDG and needle retention (R2 = 24.3%). Generally, a decrease in MGDG:DGDG ratio resulted in better cold tolerance and higher needle retention in balsam fir, possibly due to increased membrane stability. This study confirms the degree of cold acclimation in Nova Scotian balsam fir and presents practical significance to industry by identifying the timing of peak needle retention. It is suggested that MGDG:DGDG might be a beneficial tool for screening balsam fir genotypes with higher needle retention characteristics.

Time series DNA barcoding provides insight into factors influencing wood-boring and bark-feeding insect communities in Scots pine, Sitka spruce, and Noble fir stands

Bark-feeding and wood-boring insect pests can have significant negative impacts on conifers and wood production. The damage they cause is expected to increase in the future due to climate change and the growth of international trade. This study employed DNA barcoding of beetle juveniles (Coleoptera) sampled from standing trap trees and cut log piles at regular intervals over a 2-yr period to monitor the beetle community dynamics and associated environmental factors. Tree species was found to have a major influence on beetle communities, most strikingly at the start of early decay stages. Lower species diversity was reported from standing trap tree samples compared to log pile samples, likely due to higher residual defences in dying and recently dead trees. While the species identified from standing trap trees are more likely to be a threat to the forestry sector, the species found in the log piles are more likely to be beneficial due to their high abundance and their ability to compete with pests for breeding substrate. The analysis of beetles collected inside trees revealed additional information on ontogenetic niches and host preferences beyond that acquired solely from flight interception trap data. Our results offer insights on community composition and dynamics of bark-feeding and wood-boring insect species in Welsh conifer forests and provide resources for monitoring and management of potential pest species.

How Effective Are Push-Pull Semiochemicals as Deterrents for Bark Beetles? A Global Meta-Analysis of Thirty Years of Research

Bark beetles (Coleoptera: Curculionidae: Scolytinae) are among the most damaging tree pests globally. Rising temperatures, drought, fire, storms, cyclones, and poor forest management cause stress and loss of vigour in trees, and these conditions favour bark beetle outbreaks. While research has been conducted on push-pull strategies to deter bark beetles, using attractive and deterrent semiochemicals, the potential of this strategy to reduce bark beetle populations, particularly in the genera Dendroctonus and Ips, remains uncertain. Here, we conducted a global meta-analysis of 52 research articles to quantify the effects of semiochemical treatments on managing different species of Dendroctonus and Ips for forest protection. Based on this analysis, we found that push-pull semiochemicals can significantly reduce Dendroctonus and Ips populations measured by a reduction in the attraction to lure/trap catches, tree mortality, and attacks on trees. The overall efficacy of the push-pull semiochemical treatment shows a 66% reduction for Ips compared to control and a 54% reduction compared to control for Dendroctonus, while, at the species level, there was a 69% reduction for Dendroctonus ponderosae (Hopkins) and a 94% reduction in Ips perturbatus (Eichhoff), and a 93% reduction in Ips latidens (LeConte). Interestingly, among different treatment sources, the efficacy of conspecific semiochemicals in combination with heterospecific semiochemicals and non-host volatiles showed a 92% reduction in Dendroctonus spp., and conspecific semiochemicals in combination with non-host volatiles showed a 77% significant reduction in Ips spp., while the efficacy of heterospecific semiochemicals in reducing Ips population was about 69%, and 20% in Dendroctonus. Among different ecological regions, the use of a push-pull strategy showed a 70% reduction in Dendroctonus in central-west North America, and Ips showed a 75% reduction in southwest North America. Our results demonstrate that semiochemical-based push-pull techniques have the potential to reduce Dendroctonus and Ips bark beetle populations. Furthermore, based on our analysis, the efficacy of such eco-friendly interventions could be further improved and provide a good tool for forest managers to control these pests, at least under some circumstances.

Transcriptome features of stone cell development in weevil-resistant and susceptible Sitka spruce

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 apical shoots of trees resistant (R) to spruce weevil (Pissodes strobi) but being rare in susceptible (S) trees. To learn more about molecular mechanisms of stone cell formation in conifers, we used laser microdissection and RNA sequencing to develop cell-type-specific transcriptomes of developing stone cells from R and S trees. Using light, immunohistochemical, and fluorescence microscopy, we also visualized the deposition of cellulose, xylan, and lignin associated with stone cell development. A total of 1293 genes were differentially expressed at higher levels in developing stone cells relative to cortical parenchyma. Genes with potential roles in stone cell secondary cell wall formation (SCW) were identified and their expression evaluated over a time course of stone cell formation in R and S trees. The expression of several transcriptional regulators was associated with stone cell formation, including a NAC family transcription factor and several genes annotated as MYB transcription factors with known roles in SCW formation.

An Abies Extract Containing Nonvolatile Polyphenols Shows Virucidal Activity against SARS-CoV-2 That Is Enhanced in Increased pH Conditions

Researching the beneficial health properties of wood byproducts can prevent wastage by turning them into valuable resources. In this study, the virucidal activity of two extracts from Abies sachalinensis byproducts, ASE1, and ASE2, against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated. ASE1 is rich in monoterpenoid volatile compounds, whereas ASE2 contains nonvolatile polyphenols. SARS-CoV-2 solutions were mixed with ASE1 or ASE2, and viral titer reduction was evaluated. At their original acidic pH, ASE2 showed stronger virucidal activity than ASE1. The virucidal activity of ASE2 was also significantly enhanced when pH was increased to neutral or basic, which was not the case for ASE1. At a neutral pH, ASE2 induced statistically significant viral titer reduction in 1 min. HCl and NaOH solutions, which had a pH close to that of acidic and basic ASE2 test mixtures, respectively, exhibited no virucidal activity against SARS-CoV-2. Among the SARS-CoV-2 variants, Omicron showed the highest vulnerability to ASE2. Western blotting, RT-PCR, and electron microscopic analysis revealed that neutral ASE2 interacts with SARS-CoV-2 spike proteins and moderately disrupts the SARS-CoV-2 genome and viral envelope. These findings reveal the virucidal potential of ASE2.

Seasonal Developing Xylem Transcriptome Analysis of Pinus densiflora Unveils Novel Insights for Compression Wood Formation

Wood is the most important renewable resource not only for numerous practical utilizations but also for mitigating the global climate crisis by sequestering atmospheric carbon dioxide. The compressed wood (CW) of gymnosperms, such as conifers, plays a pivotal role in determining the structure of the tree through the reorientation of stems displaced by environmental forces and is characterized by a high content of lignin. Despite extensive studies on many genes involved in wood formation, the molecular mechanisms underlying seasonal and, particularly, CW formation remain unclear. This study examined the seasonal dynamics of two wood tissue types in Pinus densiflora: CW and opposite wood (OW). RNA sequencing of developing xylem for two consecutive years revealed comprehensive transcriptome changes and unique differences in CW and OW across seasons. During growth periods, such as spring and summer, we identified 2255 transcripts with differential expression in CW, with an upregulation in lignin biosynthesis genes and significant downregulation in stress response genes. Notably, among the laccases critical for monolignol polymerization, PdeLAC17 was found to be specifically expressed in CW, suggesting its vital role in CW formation. PdeERF4, an ERF transcription factor preferentially expressed in CW, seems to regulate PdeLAC17 activity. This research provides an initial insight into the transcriptional regulation of seasonal CW development in P. densiflora, forming a foundation for future studies to enhance our comprehension of wood formation in gymnosperms.

Topographic information improves simulated patterns of post-fire conifer regeneration in the southwest United States

The western United States is projected to experience more frequent and severe wildfires in the future due to drier and hotter climate conditions, exacerbating destructive wildfire impacts on forest ecosystems such as tree mortality and unsuccessful post-fire regeneration. While empirical studies have revealed strong relationships between topographical information and plant regeneration, ecological processes in ecosystem models have either not fully addressed topography-mediated effects on the probability of plant regeneration, or the probability is only controlled by climate-related factors, for example, water and light stresses. In this study, we incorporated seedling survival data based on a planting experiment in the footprint of the 2011 Las Conchas Fire into the Photosynthesis and EvapoTranspiration (PnET) extension of the LANDIS-II model by adding topographic and an additional climatic variable to the probability of regeneration. The modified algorithm included topographic parameters such as heat load index and ground slope and spring precipitation. We ran simulations on the Las Conchas Fire landscape for 2012-2099 using observed and projected climate data (i.e., Representative Concentration Pathway 4.5 and 8.5). Our modification significantly reduced the number of regeneration events of three common southwestern conifer tree species (piñon, ponderosa pine, and Douglas-fir), leading to decreases in aboveground biomass, regardless of climate scenario. The modified algorithm decreased regeneration at higher elevations and increased regeneration at lower elevations relative to the original algorithm. Regenerations of three species also decreased in eastern aspects. Our findings suggest that ecosystem models may overestimate post-fire regeneration events in the southwest United States. To better represent regeneration processes following wildfire, ecosystem models need refinement to better account for the range of factors that influence tree seedling establishment. This will improve model utility for projecting the combined effects of climate and wildfire on tree species distributions.

Different photorespiratory mechanisms in conifer leaves, where peroxisomes have intrinsically low catalase activity

Photorespiration is an essential metabolic mechanism associated with photosynthesis; however, little is known about the photorespiratory pathway of conifer gymnosperms. Metabolite analyses of the leaves of 27 tree species showed that the mean glycerate content in conifer leaves was lower than that in angiosperm leaves. We performed experiments where [13 C]-serine was fed to detached shoots of a conifer (Cryptomeria japonica), via the transpiration stream, and compared the labeling patterns of photorespiratory metabolites with those of an angiosperm tree (Populus nigra), because glycerate is produced from serine via hydroxypyruvate in peroxisomes. In P. nigra, hydroxypyruvate, glycerate and glycine were labeled with 13 C, whereas in C. japonica, glycolate and a non-canonical photorespiratory metabolite, formate, were also labeled, suggesting that an H2 O2 -mediated non-enzymatic decarboxylation (NED) reaction occurs in C. japonica. We analyzed changes in the metabolite contents of leaves kept in the dark and leaves exposed to illuminated photorespiration-promoting conditions: a positive relationship between formate and serine levels in C. japonica implied that the active C1 -metabolism pathway synthesizes serine from formate. Leaf gas exchange analyses revealed that CO2 produced through NED was recaptured by chloroplasts. Database analysis of the peroxisomal targeting signal motifs of an H2 O2 -scavenging enzyme, catalase, derived from various species, including nine coniferous species, as well as analyses of peroxisomal fractions isolated from C. japonica and P. nigra leaves indicated that conifer peroxisomes had less catalase activity. These results suggest that NED and the subsequent C1 metabolism are involved in the photorespiratory pathway of conifer leaves, where peroxisomes have intrinsically low catalase activity.

A single-nucleotide substitution of CjTKPR1 determines pollen production in the gymnosperm plant Cryptomeria japonica

Pollinosis, also known as pollen allergy or hay fever, is a global problem caused by pollen produced by various plant species. The wind-pollinated Japanese cedar (Cryptomeria japonica) is the largest contributor to severe pollinosis in Japan, where increasing proportions of people have been affected in recent decades. The MALE STERILITY 4 (MS4) locus of Japanese cedar controls pollen production, and its homozygous mutants (ms4/ms4) show abnormal pollen development after the tetrad stage and produce no mature pollen. In this study, we narrowed down the MS4 locus by fine mapping in Japanese cedar and found TETRAKETIDE α-PYRONE REDUCTASE 1 (TKPR1) gene in this region. Transformation experiments using Arabidopsis thaliana showed that single-nucleotide substitution ("T" to "C" at 244-nt position) of CjTKPR1 determines pollen production. Broad conservation of TKPR1 beyond plant division could lead to the creation of pollen-free plants not only for Japanese cedar but also for broader plant species.

Heat-Priming during Somatic Embryogenesis Increased Resilience to Drought Stress in the Generated Maritime Pine (Pinus pinaster) Plants

Drought stress is becoming the most important factor of global warming in forests, hampering the production of reproductive material with improved resilience. Previously, we reported that heat-priming maritime pine (Pinus pinaster) megagametophytes during SE produced epigenetic changes that generated plants better adapted to subsequent heat stress. In this work, we tested, in an experiment performed under greenhouse conditions, whether heat-priming will produce cross-tolerance to mild drought stress (30 days) in 3-year-old priming-derived plants. We found that they maintain constitutive physiological differences as compared to controls, such as higher proline, abscisic acid, starch, and reduced glutathione and total protein contents, as well as higher ΦPSII yield. Primed plants also displayed a constitutive upregulation of the WRKY transcription factor and the Responsive to Dehydration 22 (RD22) genes, as well as of those coding for antioxidant enzymes (APX, SOD, and GST) and for proteins that avoid cell damage (HSP70 and DHNs). Furthermore, osmoprotectants as total soluble sugars and proteins were early accumulated in primed plants during the stress. Prolongated water withdrawal increased ABA accumulation and negatively affected photosynthesis in all plants but primed-derived plants recovered faster than controls. We concluded that high temperature pulses during somatic embryogenesis resulted in transcriptomic and physiological changes in maritime pine plants that can increase their resilience to drought stress, since heat-primed plants exhibit permanent activation of mechanisms for cell protection and overexpression of stress pathways that pre-adapt them to respond more efficiently to soil water deficit.

Exploring the Seasonal Dynamics and Molecular Mechanism of Wood Formation in Gymnosperm Trees

Forests, comprising 31% of the Earth's surface, play pivotal roles in regulating the carbon, water, and energy cycles. Despite being far less diverse than angiosperms, gymnosperms account for over 50% of the global woody biomass production. To sustain growth and development, gymnosperms have evolved the capacity to sense and respond to cyclical environmental signals, such as changes in photoperiod and seasonal temperature, which initiate growth (spring and summer) and dormancy (fall and winter). Cambium, the lateral meristem responsible for wood formation, is reactivated through a complex interplay among hormonal, genetic, and epigenetic factors. Temperature signals perceived in early spring induce the synthesis of several phytohormones, including auxins, cytokinins, and gibberellins, which in turn reactivate cambium cells. Additionally, microRNA-mediated genetic and epigenetic pathways modulate cambial function. As a result, the cambium becomes active during the summer, resulting in active secondary xylem (i.e., wood) production, and starts to become inactive in autumn. This review summarizes and discusses recent findings regarding the climatic, hormonal, genetic, and epigenetic regulation of wood formation in gymnosperm trees (i.e., conifers) in response to seasonal changes.

Evidence for a trade-off between growth rate and xylem cavitation resistance in Callitris rhomboidea

The ideal plant water transport system is one that features high efficiency and resistance to drought-induced damage (xylem cavitation), however species rarely possess both. This may be explained by trade-offs between traits, yet thus far, no proposed trade-off has offered a universal explanation for the lack water transport systems that are both highly drought-resistant and highly efficient. Here we find evidence for a new trade-off, between growth rate and resistance to xylem cavitation, in the canopies of a drought-resistant tree species (Callitris rhomboidea). Wide variation in cavitation resistance (P50) was found in distal branch tips (< 2 mm in diameter), converging to low variation in P50 in larger diameter stems (> 2 mm). We found a significant correlation between cavitation resistance and distal branchlet internode length across branch tips in C. rhomboidea canopies. Branchlets with long internodes (8 mm or longer) were significantly more vulnerable to drought-induced xylem cavitation than shorter internodes (4 mm or shorter). This suggests that varying growth rates, leading to differences in internode length, drive differences in cavitation resistance in C. rhomboidea trees. The only distinct anatomical difference found between internodes was the pith size, with the average pith to xylem area in long internodes, 5x greater than in short internodes. Understanding whether this trade-off exists within and between species will help us to uncover what drives and limits drought resistance across the world's flora.

Pine has two glutamine synthetase paralogs, GS1b.1 and GS1b.2, exhibiting distinct biochemical properties

The enzyme glutamine synthetase (EC 6.3.1.2) is mainly responsible for the incorporation of inorganic nitrogen into organic molecules in plants. In the present work, a pine (Pinus pinaster) GS1 (PpGS1b.2) gene was identified, showing a high sequence identity with the GS1b.1 gene previously characterized in conifers. Phylogenetic analysis revealed that the presence of PpGS1b.2 is restricted to the genera Pinus and Picea and is not found in other conifers. Gene expression data suggest a putative role of PpGS1b.2 in plant development, similar to other GS1b genes from angiosperms, suggesting evolutionary convergence. The characterization of GS1b.1 and GS1b.2 at the structural, physicochemical, and kinetic levels has shown differences even though they have high sequence homology. GS1b.2 had a lower optimum pH (6 vs. 6.5) and was less thermally stable than GS1b.1. GS1b.2 exhibited positive cooperativity for glutamate and substrate inhibition for ammonium. However, GS1b.1 exhibited substrate inhibition behavior for glutamate and ATP. Alterations in the kinetic characteristics produced by site-directed mutagenesis carried out in this work strongly suggest an implication of amino acids at positions 264 and 267 in the active center of pine GS1b.1 and GS1b.2 being involved in affinity toward ammonium. Therefore, the amino acid differences between GS1b.1 and GS1b.2 would support the functioning of both enzymes to meet distinct plant needs.

From common gardens to candidate genes: exploring local adaptation to climate in red spruce

Local adaptation to climate is common in plant species and has been studied in a range of contexts, from improving crop yields to predicting population maladaptation to future conditions. The genomic era has brought new tools to study this process, which was historically explored through common garden experiments. In this study, we combine genomic methods and common gardens to investigate local adaptation in red spruce and identify environmental gradients and loci involved in climate adaptation. We first use climate transfer functions to estimate the impact of climate change on seedling performance in three common gardens. We then explore the use of multivariate gene-environment association methods to identify genes underlying climate adaptation, with particular attention to the implications of conducting genome scans with and without correction for neutral population structure. This integrative approach uncovered phenotypic evidence of local adaptation to climate and identified a set of putatively adaptive genes, some of which are involved in three main adaptive pathways found in other temperate and boreal coniferous species: drought tolerance, cold hardiness, and phenology. These putatively adaptive genes segregated into two 'modules' associated with different environmental gradients. This study nicely exemplifies the multivariate dimension of adaptation to climate in trees.

Phylogenetic risk assessment is robust for forecasting the impact of European insects on North American conifers

Some introduced species cause severe damage, although the majority have little impact. Robust predictions of which species are most likely to cause substantial impacts could focus efforts to mitigate those impacts or prevent certain invasions entirely. Introduced herbivorous insects can reduce crop yield, fundamentally alter natural and managed forest ecosystems, and are unique among invasive species in that they require certain host plants to succeed. Recent studies have demonstrated that understanding the evolutionary history of introduced herbivores and their host plants can provide robust predictions of impact. Specifically, divergence times between hosts in the native and introduced ranges of a nonnative insect can be used to predict the potential impact of the insect should it establish in a novel ecosystem. However, divergence time estimates vary among published phylogenetic datasets, making it crucial to understand if and how the choice of phylogeny affects prediction of impact. Here, we tested the robustness of impact prediction to variation in host phylogeny by using insects that feed on conifers and predicting the likelihood of high impact using four different published phylogenies. Our analyses ranked 62 insects that are not established in North America and 47 North American conifer species according to overall risk and vulnerability, respectively. We found that results were robust to the choice of phylogeny. Although published vascular plant phylogenies continue to be refined, our analysis indicates that those differences are not substantial enough to alter the predictions of invader impact. Our results can assist in focusing biosecurity programs for conifer pests and can be more generally applied to nonnative insects and their potential hosts by prioritizing surveillance for those insects most likely to be damaging invaders.

Exogenous 6-BA inhibited hypocotyl elongation under darkness in Picea crassifolia Kom revealed by transcriptome profiling

Hypocotyl elongation is an important process in plant growth and development, and is under hormonal regulatory signaling pathways. In our study, exogenous 6-BA significantly inhibited Picea crassifolia hypocotyl elongation more than ethylene in the dark, indicating the existence of different regulatory strategies in conifers, therefore, the P. crassifolia transcriptome was studied to explore the responsive genes and their regulatory pathways for exogenous N⁶-benzyladenine (6-BA) inhibition of hypocotyl elongation using RNA-Sequencing approach. We present the first transcriptome assembly of P. crassifolia obtained from 24.38 Gb clean data. With lowly-expressed and short contigs excluded, the assembly contains roughly 130,612 unigenes with an N50 length of 1,278 bp. Differential expression analysis found 3,629 differentially expressed genes (DEGs) and found that the differential expression fold of genes was mainly concentrated between 2 and 8 (1 ≤ log2FoldChange ≤ 3). Functional annotation showed that the GO term with the highest number of enriched genes (83 unigenes) was the shoot system development (GO: 0048367) and the KEGG category, plant hormone signal transduction (ko04075), was enriched 30 unigenes. Further analysis revealed that several cytokinin dehydrogenase genes (PcCTD1, PcCTD3 and PcCTD6) catabolized cytokinins, while xyloglucan endotransglucosylase hydrolase gene (PcXTH31), WALLS ARE THIN 1-like gene (PcWAT1-1) and Small auxin-induced gene (PcSAUR15) were strongly repressed thus synergistically completing the inhibition of hypocotyl elongation in P. crassifolia. Besides, PcbHLH149, PcMYB44 and PcERF14 were predicted to be potential core TFs that may form a multi-layered regulatory network with the above proteins for the regulation of hypocotyl growth.

Genetic Adaptation of Siberian Larch (Larix sibirica Ledeb.) to High Altitudes

Forest trees growing in high altitude conditions offer a convenient model for studying adaptation processes. They are subject to a whole range of adverse factors that are likely to cause local adaptation and related genetic changes. Siberian larch (Larix sibirica Ledeb.), whose distribution covers different altitudes, makes it possible to directly compare lowland with highland populations. This paper presents for the first time the results of studying the genetic differentiation of Siberian larch populations, presumably associated with adaptation to the altitudinal gradient of climatic conditions, based on a joint analysis of altitude and six other bioclimatic variables, together with a large number of genetic markers, single nucleotide polymorphisms (SNPs), obtained from double digest restriction-site-associated DNA sequencing (ddRADseq). In total, 25,143 SNPs were genotyped in 231 trees. In addition, a dataset of 761 supposedly selectively neutral SNPs was assembled by selecting SNPs located outside coding regions in the Siberian larch genome and mapped to different contigs. The analysis using four different methods (PCAdapt, LFMM, BayeScEnv and RDA) revealed 550 outlier SNPs, including 207 SNPs whose variation was significantly correlated with the variation of some of environmental factors and presumably associated with local adaptation, including 67 SNPs that correlated with altitude based on either LFMM or BayeScEnv and 23 SNPs based on both of them. Twenty SNPs were found in the coding regions of genes, and 16 of them represented non-synonymous nucleotide substitutions. They are located in genes involved in the processes of macromolecular cell metabolism and organic biosynthesis associated with reproduction and development, as well as organismal response to stress. Among these 20 SNPs, nine were possibly associated with altitude, but only one of them was identified as associated with altitude by all four methods used in the study, a nonsynonymous SNP in scaffold_31130 in position 28092, a gene encoding a cell membrane protein with uncertain function. Among the studied populations, at least two main groups (clusters), the Altai populations and all others, were significantly genetically different according to the admixture analysis based on any of the three SNP datasets as follows: 761 supposedly selectively neutral SNPs, all 25,143 SNPs and 550 adaptive SNPs. In general, according to the AMOVA results, genetic differentiation between transects or regions or between population samples was relatively low, although statistically significant, based on 761 neutral SNPs (F_ST = 0.036) and all 25,143 SNPs (F_ST = 0.017). Meanwhile, the differentiation based on 550 adaptive SNPs was much higher (F_ST = 0.218). The data showed a relatively weak but highly significant linear correlation between genetic and geographic distances (r = 0.206, p = 0.001).

Production and Characterization of Hydrothermal Extracts of the Needles from Four Conifer Tree Species: Scots Pine, Norway Spruce, Common Juniper, and European Larch

Coniferous trees are the most dominant trees in Finland with a great economic value for pulp, paper, and timber making. Thus, their utilization also results in large quantities of residues, especially bark and needles. Tree needles are a rich source of bioactive compounds, which have a considerable utilization potential in different pharmaceutical or techno-chemical applications. In this study, hydrothermal extraction (HTE) of the needles from four conifer tree species, namely, Scots pine, Norway spruce, common juniper, and European larch, was performed. Besides water, ethanol was also used as a solvent to enhance extraction efficiency and selectivity. All of the HTE experiments were conducted with a customized high-pressure reactor operated at 120 °C and 5 bar. The obtained needle extracts were then analyzed using a direct-infusion ultrahigh-resolution Fourier transform ion cyclotron (FT-ICR) mass spectrometry. The FT-ICR analysis of water and ethanol extracts allowed identification of over 200 secondary plant metabolites, including monosaccharides, organic acids, terpenoids, a variety of phenolic compounds, and nitrogen alkaloids. The use of ethanol as the extraction solvent considerably enhanced the recovery of lipids, especially terpenoids, some polyphenols, and other unsaturated hydrocarbon species.

Changing winter climate and snow conditions induce various transcriptional stress responses in Scots pine seedlings

In northern boreal forests the warming winter climate leads to more frequent snowmelt, rain-on-snow events and freeze-thaw cycles. This may be harmful or even lethal for tree seedlings that spend even a half of the year under snow. We conducted a snow cover manipulation experiment in a natural forest to find out how changing snow conditions affect young Scots pine (Pinus sylvestris L.) seedlings. The ice encasement (IE), absence of snow (NoSNOW) and snow compaction (COMP) treatments affected ground level temperature, ground frost and subnivean gas concentrations compared to the ambient snow cover (AMB) and led to the increased physical damage and mortality of seedlings. The expression responses of 28 genes related to circadian clock, aerobic and anaerobic energy metabolism, carbohydrate metabolism and stress protection revealed that seedlings were exposed to different stresses in a complex way depending on the thickness and quality of the snow cover. The IE treatment caused hypoxic stress and probably affected roots which resulted in reduced water uptake in the beginning of the growing season. Without protective snowpack in NoSNOW seedlings suffered from cold and drought stresses. The combination of hypoxic and cold stresses in COMP evoked unique transcriptional responses including oxidative stress. Snow cover manipulation induced changes in the expression of several circadian clock related genes suggested that photoreceptors and the circadian clock system play an essential role in the adaptation of Scots pine seedlings to stresses under different snow conditions. Our findings show that warming winter climate alters snow conditions and consequently causes Scots pine seedlings various abiotic stresses, whose effects extend from overwintering to the following growing season.

Accumulated effects of factors determining plant development from somatic embryos of Abies nordmanniana and Abies bornmuelleriana

Despite a much later inception of somatic embryogenesis (SE) propagation protocols for gymnosperms than for angiosperm species, SE is becoming increasingly important due to its applications for commercial forestry. For many conifers, there are however still major bottlenecks in the SE plant production process limiting the use of SE for forestry operations, Christmas tree production and research projects. In the present case study, the effects on plant growth from different cultural factors applied during the SE developmental process were studied in two conifer species of high value for Christmas tree production. Seven clones of Abies nordmanniana and two clones of Abies bornmuelleriana were included in the study. Accumulated effects from cultural treatments were recorded from the start of germination of mature embryos of different quality scores through development into plants in the third growing period. Experimental factors of the cultural treatments included were: germination temperature, germination time, light conditions, survival ex vitro and traits for plant growth and vitality. The results reveal that most of the studied experimental factors influenced plant growth during the first three years however their relative importance was different. Plant survival rate at end of the nursery stage was strongly impacted by germination temperature (p<0.001), initial embryo score (p=0.007), clone (p<0.001) and to a lesser extend week of germination (p=0.017). This case-study highlights and quantifies the strong interrelation between the developmental steps of somatic embryogenesis and show the importance of considering all cultural steps when optimizing SE plant production protocols.

Enhanced lignin synthesis and ecotypic variation in defense-related gene expression in response to shade in Norway spruce

During the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.

Transcriptome Analysis and Intraspecific Variation in Spanish Fir (Abies pinsapo Boiss.)

Spanish fir (Abies pinsapo Boiss.) is an endemic, endangered tree that has been scarcely investigated at the molecular level. In this work, the transcriptome of Spanish fir was assembled, providing a large catalog of expressed genes (22,769), within which a high proportion were full-length transcripts (12,545). This resource is valuable for functional genomics studies and genome annotation in this relict conifer species. Two intraspecific variations of A. pinsapo can be found within its largest population at the Sierra de las Nieves National Park: one with standard green needles and another with bluish-green needles. To elucidate the causes of both phenotypes, we studied different physiological and molecular markers and transcriptome profiles in the needles. "Green" trees showed higher electron transport efficiency and enhanced levels of chlorophyll, protein, and total nitrogen in the needles. In contrast, needles from "bluish" trees exhibited higher contents of carotenoids and cellulose. These results agreed with the differential transcriptomic profiles, suggesting an imbalance in the nitrogen status of "bluish" trees. Additionally, gene expression analyses suggested that these differences could be associated with different epigenomic profiles. Taken together, the reported data provide new transcriptome resources and a better understanding of the natural variation in this tree species, which can help improve guidelines for its conservation and the implementation of adaptive management strategies under climatic change.

Morpho-histology, endogenous hormone dynamics, and transcriptome profiling in Dacrydium pectinatum during female cone development

Dacrydium pectinatum de Laubenfels is a perennial dioeciously gymnosperm species dominant in tropical montane rain forests. Due to deforestation, natural disasters, long infancy, and poor natural regeneration ability, the population of this species has been significantly reduced and listed as an endangered protected plant. To better understand the female cone development in D. pectinatum, we examined the morphological and anatomical changes, analyzed the endogenous hormone dynamics, and profiled gene expression. The female reproductive structures were first observed in January. The morpho-histological observations suggest that the development of the D. pectinatum megaspore can be largely divided into six stages: early flower bud differentiation, bract primordium differentiation, ovule primordium differentiation, dormancy, ovule maturity, and seed maturity. The levels of gibberellins (GA), auxin (IAA), abscisic acid (ABA), and cytokinin (CTK) fluctuate during the process of female cone development. The female cones of D. pectinatum need to maintain a low level of GA3-IAA-ABA steady state to promote seed germination. The first transcriptome database for female D. pectinatum was generated, revealing 310,621 unigenes. Differential expression analyses revealed several floral (MADS2, AGL62, and LFY) and hormone biosynthesis and signal transduction (CKX, KO, KAO, ABA4, ACO, etc.) genes that could be critical for female cone development. Our study provides new insights into the cone development in D. pectinatum and the foundation for female cone induction with hormones.

Interaction of drought- and pathogen-induced mortality in Norway spruce and Scots pine

Pathogenic diseases frequently occur in drought-stressed trees. However, their contribution to the process of drought-induced mortality is poorly understood. We combined drought and stem inoculation treatments to study the physiological processes leading to drought-induced mortality in Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) saplings infected with Heterobasidion annosum s.s. We analysed the saplings' water status, gas exchange, nonstructural carbohydrates (NSCs) and defence responses, and how they related to mortality. Saplings were followed for two growing seasons, including an artificially induced 3-month dormancy period. The combined drought and pathogen treatment significantly increased spruce mortality; however, no interaction between these stressors was observed in pine, although individually each stressor caused mortality. Our results suggest that pathogen infection decreased carbon reserves in spruce, reducing the capacity of saplings to cope with drought, resulting in increased mortality rates. Defoliation, relative water content and the starch concentration of needles were predictors of mortality in both species under drought and pathogen infection. Infection and drought stress create conflicting needs for carbon to compartmentalize the pathogen and to avoid turgor loss, respectively. Heterobasidion annosum reduces the functional sapwood area and shifts NSC allocation patterns, reducing the capacity of trees to cope with drought.

Ammonium regulates the development of pine roots through hormonal crosstalk and differential expression of transcription factors in the apex

Ammonium is a prominent source of inorganic nitrogen for plant nutrition, but excessive amounts can be toxic for many species. However, most conifers are tolerant to ammonium, a relevant physiological feature of this ancient evolutionary lineage. For a better understanding of the molecular basis of this trait, ammonium-induced changes in the transcriptome of maritime pine (Pinus pinaster Ait.) root apex have been determined by laser capture microdissection and RNA sequencing. Ammonium promoted changes in the transcriptional profiles of multiple transcription factors, such as SHORT-ROOT, and phytohormone-related transcripts, such as ACO, involved in the development of the root meristem. Nano-PALDI-MSI and transcriptomic analyses showed that the distributions of IAA and CKs were altered in the root apex in response to ammonium nutrition. Taken together, the data suggest that this early response is involved in the increased lateral root branching and principal root growth, which characterize the long-term response to ammonium supply in pine. All these results suggest that ammonium induces changes in the root system architecture through the IAA-CK-ET phytohormone crosstalk and transcriptional regulation.

Genome-Wide Prediction of Transcription Start Sites in Conifers

The identification of promoters is an essential step in the genome annotation process, providing a framework for gene regulatory networks and their role in transcription regulation. Despite considerable advances in the high-throughput determination of transcription start sites (TSSs) and transcription factor binding sites (TFBSs), experimental methods are still time-consuming and expensive. Instead, several computational approaches have been developed to provide fast and reliable means for predicting the location of TSSs and regulatory motifs on a genome-wide scale. Numerous studies have been carried out on the regulatory elements of mammalian genomes, but plant promoters, especially in gymnosperms, have been left out of the limelight and, therefore, have been poorly investigated. The aim of this study was to enhance and expand the existing genome annotations using computational approaches for genome-wide prediction of TSSs in the four conifer species: loblolly pine, white spruce, Norway spruce, and Siberian larch. Our pipeline will be useful for TSS predictions in other genomes, especially for draft assemblies, where reliable TSS predictions are not usually available. We also explored some of the features of the nucleotide composition of the predicted promoters and compared the GC properties of conifer genes with model monocot and dicot plants. Here, we demonstrate that even incomplete genome assemblies and partial annotations can be a reliable starting point for TSS annotation. The results of the TSS prediction in four conifer species have been deposited in the Persephone genome browser, which allows smooth visualization and is optimized for large data sets. This work provides the initial basis for future experimental validation and the study of the regulatory regions to understand gene regulation in gymnosperms.

Cutting tree rings into time slices: how intra-annual dynamics of wood formation help decipher the space-for-time conversion

Tree-ring anatomy, microdensity and isotope records provide valuable intra-annual information. However, extracting signals at that scale is challenged by the complexity of xylogenesis, where two major processes - cell enlargement and wall thickening - occur at different times and rates. We characterized the space-for-time association in the tree rings of three conifer species by examining the duration, overlapping, inter-tree synchronicity and interannual stability during cell enlargement and wall thickening across regular tree-ring sectors (portions of equal tangential width). The number of cells and cell differentiation rates determined the duration of sector formation, which augmented more rapidly throughout the ring for wall thickening than for enlargement. Increasing the number of sectors above c. 15 had a limited effect on improving time resolution because consecutive sector formation overlapped greatly in time, especially in narrow rings and during wall thickening. Increasing the number of sectors also resulted in lower synchronicity and stability of intermediate-sector enlargement, whereas all sectors showed high synchronicity and stability during wall thickening. Increasing the number of sectors had a stronger effect on enhancing time-series resolution for enlargement- than for wall-thickening-related traits, which would nevertheless produce more reliable intra-annual chronologies as a result of the more similar calendars across trees and years in wall thickening.

Cryo-Treatment Enhances the Embryogenicity of Mature Somatic Embryos via the lncRNA-miRNA-mRNA Network in White Spruce

In conifers, somatic embryogenesis is uniquely initiated from immature embryos in a narrow time window, which is considerably hindered by the difficulty to induce embryogenic tissue (ET) from other tissues, including mature somatic embryos. In this study, the embryogenic ability of newly induced ET and DNA methylation levels was detected, and whole-transcriptome sequencing analyses were carried out. The results showed that ultra-low temperature treatment significantly enhanced ET induction from mature somatic embryos, with the induction rate from 0.4% to 15.5%, but the underlying mechanisms remain unclear. The newly induced ET showed higher capability in generating mature embryos than the original ET. DNA methylation levels fluctuated during the ET induction process. Here, WGCNA analysis revealed that OPT4, TIP1-1, Chi I, GASA5, GST, LAX3, WRKY7, MYBS3, LRR-RLK, PBL7, and WIN1 genes are involved in stress response and auxin signal transduction. Through co-expression analysis, lncRNAs MSTRG.505746.1, MSTRG.1070680.1, and MSTRG.33602.1 might bind to pre-novel_miR_339 to promote the expression of WRKY7 genes for stress response; LAX3 could be protected by lncRNAs MSTRG.1070680.1 and MSTRG.33602.1 via serving as sponges for novel_miR_495 to initiate auxin signal transduction; lncRNAs MSTRG.505746.1, MSTRG.1070680.1, and MSTRG.33602.1 might serve as sponges for novel_miR_527 to enhance the expression of Chi I for early somatic embryo development. This study provides new insight into the area of stress-enhanced early somatic embryogenesis in conifers, which is also attributable to practical applications.

In Vitro Propagation, Genetic Assessment, and Medium-Term Conservation of the Coastal Endangered Species Tetraclinis articulata (Vahl) Masters (Cupressaceae) from Adult Trees

Tetraclinis articulata (Vahl) Masters is an endangered tree growing in coastal and arid environments that is widely exploited by the timber and resin industry, among other applications. In this context, the use of in vitro techniques is highly encouraged for its propagation. We present a protocol for micropropagation using twigs from adult trees as a source of explants. The Schenk and Hildebrandt basal medium (SH) supplemented with 30 g L^-1 sucrose, 6.5 g L^-1 plant agar, 4.0 mg L^-1 6-benzyladenine (BA), and 0.05 mg L^-1 1-naphthaleneacetic acid (NAA) provided the optimum multiplication rate (90.48 ± 9.52 explants with basal shoots and 2.58 ± 0.29 basal shoots per explant). Application of activated charcoal (AC) or ½ Knop solution in a liquid overlay produced significantly longer shoots. Supplementation of solid media with indole-3-butyric acid (IBA) or NAA gave low rooting percentages (<17%). Addition of 0.9 g L^-1 AC improved rooting (40%) but rooting performance was optimal (66.7%) after a pulse treatment consisting of 4 h immersion in liquid SH medium without growth regulators, followed by 8 weeks of cultivation. Rooted microplants were successfully acclimatized (93.33%) in a peat moss and vermiculite mixture (1:1 v/v ratio). The genetic stability of the in vitro regenerated plantlets was confirmed using the randomly amplified polymorphic DNA (RAPD) technique. Explant survival and growth remained higher than 90% after 28 weeks of cold storage at both 4 °C and 10 °C. The protocol presented here allows for largescale T. articulata production and could be applied for both ex situ conservation strategies and industrial purposes.

Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin

Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.

In vivo monitoring of drought-induced embolism in Callitris rhomboidea trees reveals wide variation in branchlet vulnerability and high resistance to tissue death

Damage to the plant water transport system through xylem cavitation is known to be a driver of plant death in drought conditions. However, a lack of techniques to continuously monitor xylem embolism in whole plants in vivo has hampered our ability to investigate both how this damage propagates and the possible mechanistic link between xylem damage and tissue death. Using optical and fluorescence sensors, we monitored drought-induced xylem embolism accumulation and photosynthetic damage in vivo throughout the canopy of a drought-resistant conifer, Callitris rhomboidea, during drought treatments of c. 1 month duration. We show that drought-induced damage to the xylem can be monitored in vivo in whole trees during extended periods of water stress. Under these conditions, vulnerability of the xylem to cavitation varied widely among branchlets, with photosynthetic damage only recorded once > 90% of the xylem was cavitated. The variation in branchlet vulnerability has important implications for understanding how trees like C. rhomboidea survive drought, and the high resistance of branchlets to tissue damage points to runaway cavitation as a likely driver of tissue death in C. rhomboidea branch tips.

Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein-coding genes

Plastid genomes (plastomes) have a quadripartite structure, but some species have drastically reduced or lost inverted repeat (IR) regions. IR regions are important for genome stability and the evolution rate. In the evolutionary process of gymnosperms, the typical IRs of conifers were lost, possibly affecting the evolutionary rate and selection pressure of genomic protein-coding genes. In this study, we selected 78 gymnosperm species (51 genera, 13 families) for evolutionary analysis. The selection pressure analysis results showed that negative selection effects were detected in all 50 common genes. Among them, six genes in conifers had higher ω values than non-conifers, and 12 genes had lower ω values. The evolutionary rate analysis results showed that 9 of 50 common genes differed between conifers and non-conifers. It is more obvious that in non-conifers, the rates of psbA (trst, trsv, ratio, dN, dS, and ω) were 2.6- to 3.1-fold of conifers. In conifers, trsv, ratio, dN, dS, and ω of ycf2 were 1.2- to 3.6-fold of non-conifers. In addition, the evolution rate of ycf2 in the IR was significantly reduced. psbA is undergoing dynamic change, with an abnormally high evolution rate as a small portion of it enters the IR region. Although conifers have lost the typical IR regions, we detected no change in the substitution rate or selection pressure of most protein-coding genes due to gene function, plant habitat, or newly acquired IRs.

An assessment of temporal variability in mast seeding of North American Pinaceae

Our overall objective is to synthesize mast-seeding data on North American Pinaceae to detect characteristic features of reproduction (i.e. development cycle length, serotiny, dispersal agents), and test for patterns in temporal variation based on weather variables. We use a large dataset (n = 286 time series; mean length = 18.9 years) on crop sizes in four conifer genera (Abies, Picea, Pinus, Tsuga) collected between 1960 and 2014. Temporal variability in mast seeding (CVp) for 2 year genera (Abies, Picea, Tsuga) was higher than for Pinus (3 year), and serotinous species had lower CVp than non-serotinous species; there were no relationships of CVp with elevation or latitude. There was no difference in family-wide CVp across four tree regions of North America. Across all genera, July temperature differences between bud initiation and the prior year (ΔT) was more strongly associated with reproduction than absolute temperature. Both CVp and ΔT remained steady over time, while absolute temperature increased by 0.09°C per decade. Our use of the ΔT model included a modification for Pinus, which initiates cone primordia 2 years before seedfall, as opposed to 1 year. These findings have implications for how mast-seeding patterns may change with future increases in temperature, and the adaptive benefits of mast seeding. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.

Abundance and Diversity of Ophiostomatoid Fungi Associated With the Great Spruce Bark Beetle (Dendroctonus micans) in the Northeastern Qinghai-Tibet Plateau

The role of several virulent tree pathogens in host death has been overlooked because of the aggressiveness of their associated bark beetles. The great spruce bark beetle (Dendroctonus micans) is a widely distributed beetle that infests coniferous plants in Eurasia; however, its associated fungi have been poorly studied. Therefore, in this study, we elucidated the diversity of ophiostomatoid fungi associated with D. micans in the northeastern Qinghai-Tibet Plateau through field investigation, laboratory isolation, and culture analyses. A total of 220 strains of ophiostomatoid fungi were isolated from adults and tunnel galleries of D. micans infesting Picea crassifolia. We identified that the isolated strains belonged to eight ophiostomatoid species, including five new species (Ophiostoma huangnanense sp. nov., Ophiostoma maixiuense sp. nov., Ophiostoma sanum sp. nov., Leptographium sanjiangyuanense sp. nov., and Leptographium zekuense sp. nov.), one undefined species (Ophiostoma sp. 1), and two known species (Ophiostoma bicolor and Endoconidiophora laricicola), using phylogenetic analysis of multigene DNA sequences and morphological characteristics. This is the first time that E. laricicola, a pioneer invader and virulent pathogen, has been reported in China. We found that E. laricicola was the dominant species, accounting for 40.91% of the total number of ophiostomatoid communities. This study enriched the knowledge of the fungal associates of D. micans and elucidated that it carried the virulent pathogen E. laricicola at a surprisingly high frequency. Our findings show increased species association between D. micans and ophiostomatoid fungi and provide a basis for understanding the occurrence of forest diseases and pests.

[Radial growth responses of four coniferous species to climate change in the Potatso National Park, China]

Using the principles and methods of dendrochronology, we measured tree-ring width of four dominant coniferous species, i.e., Larix potaninii var. macrocarpa, Picea brachytyla, Pinus densata, and Abies georgei, in the Potatso National Park, and established the tree-ring width resi-dual chronologies. We analyzed the correlation of tree-ring width residual chronologies with daily and monthly climate data from the Shangrila meteorological station to analyze the response of radial growth to climate factors. The results showed that L. potaninii var. macrocarpa had the highest annual growth rate, and A. georgei had the lowest. Radial growth showed species-specific responses to climate changes, with the highest sensitivity of L. potaninii var. macrocarpa and the lowest sensitivity of P. brachytyla. Ring-width chronology of A. georgei correlated positively with mean temperature during previous winter (November and December) and current summer (July). Ring-width chronology of L. potaninii var. macrocarpa correlated positively with temperature during the early-growing season (June), but negatively with precipitation and relative humidity. Ring-width chronology of P. densata correlated positively with precipitation and humidity but negatively with maximum temperature during the early-growing season (May), indicating that its radial growth was primarily influenced by water availability during the early-growing season.

Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs

In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 giga base pairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers' accumulative genome evolution mode. For this, we applied low-coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs' organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.

Wood transcriptome analysis of Pinus densiflora identifies genes critical for secondary cell wall formation and NAC transcription factors involved in tracheid formation

Although conifers have significant ecological and economic value, information on transcriptional regulation of wood formation in conifers is still limited. Here, to gain insight into secondary cell wall (SCW) biosynthesis and tracheid formation in conifers, we performed wood tissue-specific transcriptome analyses of Pinus densiflora (Korean red pine) using RNA sequencing. In addition, to obtain full-length transcriptome information, PacBio single molecule real-time iso-sequencing was carried out using RNAs from 28 tissues of P. densiflora. Subsequent comparative tissue-specific transcriptome analysis successfully pinpointed critical genes encoding key proteins involved in biosynthesis of the major secondary wall components (cellulose, galactoglucomannan, xylan and lignin). Furthermore, we predicted a total of 62 NAC (NAM, ATAF1/2 and CUC2) family transcription factor members and identified seven PdeNAC genes preferentially expressed in developing xylem tissues in P. densiflora. Protoplast-based transcriptional activation analysis found that four PdeNAC genes, homologous to VND, NST and SND/ANAC075, upregulated GUS activity driven by an SCW-specific cellulose synthase promoter. Consistently, transient overexpression of the four PdeNACs induced xylem vessel cell-like SCW deposition in both tobacco (Nicotiana benthamiana) and Arabidopsis leaves. Taken together, our data provide a foundation for further research to unravel transcriptional regulation of wood formation in conifers, especially SCW formation and tracheid differentiation.

Isometric scaling to model water transport in conifer tree rings across time and environments

The hydraulic properties of xylem determine the ability of plants to efficiently and safely provide water to their leaves. These properties are key to understanding plant responses to environmental conditions and evaluating their fate under a rapidly changing climate. However, their assessment is hindered by the challenges of quantifying basic hydraulic components such as bordered pits and tracheids. Here, we use isometric scaling between tracheids and pit morphology to merge partial hydraulic models of the tracheid component and to upscale these properties to the tree-ring level in conifers. Our new model output is first cross-validated with the literature and then applied to cell anatomical measurements from Larix sibirica tree rings formed under harsh conditions in southern Siberia to quantify the intra- and inter-annual variability in hydraulic properties. The model provides a means of assessing how different-sized tracheid components contribute to the hydraulic properties of the ring. Upscaled results indicate that natural inter- and intra-ring anatomical variations have a substantial impact on the tree's hydraulic properties. Our model facilitates the assessment of important xylem functional attributes because it requires only the more accessible measures of cross-sectional tracheid size. This approach, if applied to dated tree rings, provides a novel way to investigate xylem structure-function relationships across time and environmental conditions.

Impact of chronic stylet-feeder infestation on folivore-induced signaling and defenses in a conifer

Our understanding of how conifers respond biochemically to multiple simultaneous herbivore attacks is lacking. Eastern hemlock (Tsuga canadensis; 'hemlock') is fed on by hemlock woolly adelgid (Adelges tsugae; 'adelgid') and by later-instar gypsy moth (Lymantria dispar; 'gypsy moth') caterpillars. The adelgid is a stylet-feeding insect that causes a salicylic acid (SA)-linked response in hemlock, and gypsy moth larvae are folivores that presumably cause a jasmonic acid (JA)-linked response. This system presents an opportunity to study how invasive herbivore-herbivore interactions mediated through host biochemical responses. We used a factorial field experiment to challenge chronically adelgid-infested hemlocks with gypsy moth caterpillars. We quantified 17 phytohormones, 26 phenolic and terpene metabolites, and proanthocyanidin, cell wall-bound (CW-bound) phenolic, and lignin contents. Foliage infested with adelgid only accumulated gibberellins and SA; foliage challenged by gypsy moth only accumulated JA phytohormones. Gypsy moth folivory on adelgid-infested foliage reduced the accumulation of JA phytohormones and increased the SA levels. Both herbivores increased CW-bound phenolics and gypsy moth increased lignin content when feeding alone but not when feeding on adelgid-infested foliage. Our study illustrates the importance of understanding the biochemical mechanisms and signaling antagonism underlying tree responses to multiple stresses and of disentangling local and systemic stress signaling in trees.

Proteometabolomic characterization of apical bud maturation in Pinus pinaster

Bud maturation is a physiological process that implies a set of morphophysiological changes that lead to the transition of growth patterns from young to mature. This transition defines tree growth and architecture, and in consequence traits such as biomass production and wood quality. In Pinus pinaster Aiton, a conifer of great timber value, bud maturation is closely related to polycyclism (multiple growth periods per year). This process causes a lack of apical dominance, and consequently increased branching that reduces its timber quality and value. However, despite its importance, little is known about bud maturation. In this work, proteomics and metabolomics were employed to study apical and basal sections of young and mature buds in P. pinaster. Proteins and metabolites in samples were described and quantified using (n)UPLC-LTQ-Orbitrap. The datasets were analyzed employing an integrative statistical approach, which allowed the determination of the interactions between proteins and metabolites and the different bud sections and ages. Specific dynamics of proteins and metabolites such as histones H3 and H4, ribosomal proteins L15 and L12, chaperonin TCP1, 14-3-3 protein gamma, gibberellins A1, A3 and A8, strigolactones and abscisic acid, involved in epigenetic regulation, proteome remodeling, hormonal signaling and abiotic stress pathways showed their potential role during bud maturation. Candidates and pathways were validated employing interaction databases and targeted transcriptomics. These results increase our understanding of the molecular processes behind bud maturation, a key step towards improving timber production and natural pine forests management in a future scenario of climate change. However, further studies are necessary using different P. pinaster populations that show contrasting wood quality and stress tolerance in order to generalize the results.

Genomic vulnerability to rapid climate warming in a tree species with a long generation time

The ongoing increase in global temperature affects biodiversity, especially in mountain regions where climate change is exacerbated. As sessile, long-lived organisms, trees are especially challenged in terms of adapting to rapid climate change. Here, we show that low rates of allele frequency shifts in Swiss stone pine (Pinus cembra) occurring near the treeline result in high genomic vulnerability to future climate warming, presumably due to the species' long generation time. Using exome sequencing data from adult and juvenile cohorts in the Swiss Alps, we found an average rate of allele frequency shift of 1.23 × 10^-2 /generation (i.e. 40 years) at presumably neutral loci, with similar rates for putatively adaptive loci associated with temperature (0.96 × 10^-2 /generation) and precipitation (0.91 × 10^-2 /generation). These recent shifts were corroborated by forward-in-time simulations at neutral and adaptive loci. Additionally, in juvenile trees at the colonisation front we detected alleles putatively beneficial under a future warmer and drier climate. Notably, the observed past rate of allele frequency shift in temperature-associated loci was decidedly lower than the estimated average rate of 6.29 × 10^-2 /generation needed to match a moderate future climate scenario (RCP4.5). Our findings suggest that species with long generation times may have difficulty keeping up with the rapid climate change occurring in high mountain areas and thus are prone to local extinction in their current main elevation range.

Characterization of Diaporthe spp. Associated With Spruce Decline on Colorado Blue Spruce in Michigan

Since 2006 there has been a decline in Colorado blue spruce (CBS; Picea pungens) planted as landscape trees and for Christmas tree production throughout the Lower Peninsula of Michigan. This decline is characterized by a slow loss of needles in the lower portion of the tree starting at branch tips, followed by entire branch dieback, which progresses upward over several years. This dieback has been linked to shallow branch cankers visible in the phloem when the bark layer is removed. Isolates in the fungal genus Diaporthe have been consistently isolated from lesion margins on symptomatic branches. Before the initial reports of declining CBS in landscape and Christmas trees, Diaporthe was known only as a nursery disease of CBS. To determine the species of Diaporthe linked to the decline of CBS in Michigan, seven gene regions were sequenced from a collection of Diaporthe isolates collected in 2011 through 2018 from CBS and other coniferous hosts. Subsequent phylogenetic analyses indicated that Diaporthe eres and a novel Diaporthe clade were present on symptomatic CBS in Michigan. The new species D. brevicancria nov. is described, and Koch's postulates were confirmed for D. brevicancria nov. and D. eres. D. brevicancria nov. produced the largest cankers in greenhouse pathogenicity trials, and dual inoculations of D. brevicancria nov. and D. eres produced intermediate cankers.