Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

Our objective was to assess the photosynthetic responses of loblolly pine trees (Pinus taedaL.) during the first full growth season (1997) at the Brookhaven National Lab/Duke University Free Air CO2Enrichment (FACE) experiment. Gas exchange, fluorescence characteristics, and leaf biochemistry of ambient CO2(control) needles and ambient + 20 Pa CO2(elevated) needles were examined five times during the year. The enhancement of photosynthesis by elevated CO2in mature loblolly pine trees varied across the season and was influenced by abiotic and biotic factors. Photosynthetic enhancement by elevated CO2was strongly correlated with leaf temperature. The magnitude of photosynthetic enhancement was zero in March but was as great as 52% later in the season. In March, reduced sink demand and lower temperatures resulted in lower net photosynthesis, lower carboxylation rates and higher excess energy dissipation from the elevated CO2needles than from control needles. The greatest photosynthetic enhancement by CO2enrichment was observed in July during a period of high temperature and low precipitation, and in September during recovery from this period of low precipitation. In July, loblolly pine trees in the control rings exhibited lower net photosynthetic rates, lower maximum rates of photosynthesis at saturating CO2and light, lower values of carboxylation and electron transport rates (modelled fromA–Cicurves), lower total Rubisco activity, and lower photochemical quenching of fluorescence in comparison to other measurement periods. During this period of low precipitation trees in the elevated CO2rings exhibited reduced net photosynthesis and photochemical quenching of fluorescence, but there was little effect on light‐ and CO2‐saturated rates of photosynthesis, modelled rates of carboxylation or electron transport, or Rubisco activity. These first‐year data will be used to compare with similar measurements from subsequent years of the FACE experiment in order to determine whether photosynthetic acclimation to CO2occurs in these canopy loblolly pine trees growing in a forest ecosystem.

BackgroundLoblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees.ResultsThe exons were captured in the ADEPT2 association mapping population of 375 clonally-propagated loblolly pine trees using NimbleGen oligonucleotide hybridization probes, and then exome-enriched genomic DNA fragments were sequenced using the Illumina HiSeq 2500 platform. Oligonucleotide probes were designed based on 199,723 exons (≈49 Mbp) partitioned from the loblolly pine reference genome (PineRefSeq v. 1.01). The probes covered 90.2 % of the target regions. Capture efficiency was high; on average, 67 % of the sequence reads generated for each tree could be mapped to the capture target regions, and more than 70 % of the captured target bases had at least 10X sequencing depth per tree. A total of 972,720 high quality SNPs were identified after filtering. Among them, 53 % were located in coding regions (CDS), 5 % in 5’ or 3’ untranslated regions (UTRs) and 42 % in non-target and non-coding regions, such as introns and adjacent intergenic regions collaterally captured. We found that linkage disequilibrium (LD) decayed very rapidly, with the correlation coefficient (r2) between pairs of SNPs linked within single scaffolds decaying to half maximum (r2 = 0.22) within 55 bp, to r2 = 0.1 within 192 bp, and to r2 = 0.05 within 451 bp. Population structure analysis using unlinked SNPs demonstrated the presence of two main distinct clusters representing western and eastern parts of the loblolly pine range included in our sample of trees.ConclusionsThe obtained results demonstrated the efficiency of exome capture for genotyping species such as loblolly pine with a large and complex genome. The highly diverse genetic variation reported in this study will be a valuable resource for future genetic and genomic research in loblolly pine.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3081-8) contains supplementary material, which is available to authorized users.

The Chromosome-Level Reference Genome of Tea Tree Unveils Recent Bursts of Non-autonomous LTR Retrotransposons in Driving Genome Size Evolution

Cultural intensity and planting density effects on aboveground biomass of 12-year-old loblolly pine trees in the Upper Coastal Plain and Piedmont of the southeastern United States

Branches of field-grown mature loblolly pine (Pinus taeda L.) trees were exposed for 2 years (1992 and 1993) to ambient or elevated CO(2) concentrations (ambient + 165 micro mol mol(-1) or ambient + 330 micro mol mol(-1) CO(2)). Exposure to elevated CO(2) concentrations enhanced rates of net photosynthesis (P(n)) by 53-111% compared to P(n) of foliage exposed to ambient CO(2). At the same CO(2) measurement concentration, the ratio of intercellular to atmospheric CO(2) concentration (C(i)/C(a)) and stomatal conductance to water vapor did not differ among foliage grown in an ambient or enriched CO(2) concentration. Analysis of the relationship between P(n) and C(i) indicated no significant change in carboxylation efficiency of ribulose-1,5-bisphosphate carboxylase/oxygenase during growth in elevated CO(2) concentrations. Based on estimates derived from P(n)/C(i) curves, there were no apparent treatment differences in dark respiration, CO(2) compensation point or P(n) at the mean C(i). In 1992, foliage in the three CO(2) treatments yielded similar estimates of CO(2)-saturated P(n) (P(max)), whereas in 1993, estimates of P(max) were higher for branches grown in elevated CO(2) than in ambient CO(2). We conclude that field-grown loblolly pine trees do not exhibit downward acclimation of leaf-level photosynthesis in their long-term response to elevated CO(2) concentrations.

A stochastic model to simulate the processes of initiation, diameter growth, death, and self-pruning of branches in loblolly pine ( Pinus taeda L.) trees is presented. Information on whorl formation and branch growth was obtained from destructive sampling of whorl sections from 34 trees growing under 10 different initial spacings. Three different components were modeled and hierarchically connected: whorl, branches, and knots. For each new growing season, whorls and branches are assigned stochastically along and around the stem. Thereafter, branch diameter growth is predicted as a function of relative location within the live crown and stem growth. The branch model was linked to an individual-tree growth model, PTAEDA3.1, to simulate the dynamics of first-order branches arising from the main stem. Information on (i) vertical trend of branch diameter along and around the stem, (ii) volume of knots (live and dead portions), and (iii) spatial location, size, and type (live and dead) of knots can be obtained. In its current stage, the framework allows evaluation of the quality of trees and sawlogs produced, inclusion of additional wood properties, and linkage with industrial conversion processes (e.g., sawing simulation). However, further research is needed to obtain data on branch dynamics to validate the overall performance of the model and improve developed submodels.

Equations are needed to estimate the green weight of loblolly pine (Pinus taeda L.) trees across the commercial range in the South. Thus, a study was conducted to derive models for predicting green weight of total and merchantable bole portions. Equations were fitted to sectional tree stem observations where a serial correlation was discerned among the data, indicating an intratree relationship. Linear equations utilizing a correction for serial correlation did not outperform an uncorrected nonlinear equation form. Three data sets were combined, and regionwide prediction models for total green weight, green weight to any upper merchantable diameter, and green weight to any upper merchantable height were developed for loblolly pine trees. Implicit taper functions were derived from the green weight prediction equations to enable estimation of upper stem diameters and heights. South. J. Appl. For. 27(2):153–159.

Penaeid shrimp (family Penaeidae) represents one of the most economically and ecologically important groups of crustaceans. However, their genome sequencing and assembly have encountered extreme difficulties during the last 20 years. In this study, based on our previous genomic data, we investigated the genomic characteristics of four penaeid shrimp species and identified potential factors that result in their poor genome assembly, including heterozygosity, polyploidization, and repeats. Genome sequencing and comparison of somatic cells (diploid) of the four shrimp species and a single sperm cell (haploid) of Litopenaeus vannamei identified a common bimodal distribution of K-mer depths, suggesting either high heterozygosity or abundant homo-duplicated sequences present in their genomes. However, penaeids have not undergone whole-genome duplication as indicated by a series of approaches. Besides, the remarkable expansion of simple sequence repeats was another outstanding character of penaeid genomes, which also made the genome assembly highly fragmented. Due to this situation, we tried to assemble the genome of penaeid shrimp using various genome sequencing and assembly strategies and compared the quality. Therefore, this study provides new insights about the genomic characteristics of penaeid shrimps while improving their genome assemblies.

Crown architecture and size influence leaf area distribution within tree crowns and have large effects on the light environment in forest canopies. The use of selected genotypes in combination with silvicultural treatments that optimize site conditions in forest plantations provide both a challenge and an opportunity to study the biological and environmental determinants of forest growth. We investigated tree growth, crown development and leaf traits of two elite families of loblolly pine (Pinus taeda L.) and one family of slash pine (P. elliottii Mill.) at canopy closure. Two contrasting silvicultural treatments -- repeated fertilization and control of competing vegetation (MI treatment), and a single fertilization and control of competing vegetation treatment (C treatment) -- were applied at two experimental sites in the West Gulf Coastal Plain in Texas and Louisiana. At a common tree size (diameter at breast height), loblolly pine trees had longer and wider crowns, and at the plot-level, intercepted a greater fraction of photosynthetic photon flux than slash pine trees. Leaf-level, light-saturated assimilation rates (A(max)) and both mass- and area-based leaf nitrogen (N) decreased, and specific leaf area (SLA) increased with increasing canopy depth. Leaf-trait gradients were steeper in crowns of loblolly pine trees than of slash pine trees for SLA and leaf N, but not for A(max). There were no species differences in A(max), except in mass-based photosynthesis in upper crowns, but the effect of silvicultural treatment on A(max) differed between sites. Across all crown positions, A(max) was correlated with leaf N, but the relationship differed between sites and treatments. Observed patterns of variation in leaf properties within crowns reflected acclimation to developing light gradients in stands with closing canopies. Tree growth was not directly related to A(max), but there was a strong correlation between tree growth and plot-level light interception in both species. Growth efficiency was unaffected by silvicultural treatment. Thus, when coupled with leaf area and light interception at the crown and canopy levels, A(max) provides insight into family and silvicultural effects on tree growth.

: Throughout the southeastern United States, upland sites that were once dominated by longleaf pine (Pinus palustris Mill.) have been widely converted to faster growing species such as loblolly pine (P. taeda L.). Consequently, existing populations of the federally endangered redcockaded woodpecker (RCW; Picoides borealis) are currently occupying mature loblolly pine stands. Reports of declining loblolly pine health in some locations raised concerns about the longevity of existing RCW habitat and underscored the need to convert upland forests back to longleaf pine. Forest managers needed protocols to restore longleaf pine on sites where canopy pines are retained. Further, because protocol suitability is likely to vary among site types based on productivity and the structure and composition of the canopy and ground layer vegetation protocol development on a range of site conditions was necessary. The need for such protocols were deemed critical at Fort Benning, Georgia, where as many as 70% of the active RCW cavities were found in loblolly pine trees. Because longleaf pine seedling growth tends to decrease as canopy cover increases, the conversion of loblolly pine stands to longleaf was expected to require a balance between canopy removal to increase the growth of planted longleaf pine seedlings and canopy retention for RCW habitat and other ecosystem services (e.g., fuel inputs from needlefall). Retaining the trees likely to live the longest would secure the most RCW habitat value through time; thus, a model for predicting tree longevity would be a valuable management tool. Additionally, an increased understanding of environmental factors associated with reduced loblolly pine health was needed to inform RCW management decisions at Fort Benning.

ACORN Review: NPK fertilizer use in loblolly pine plantations: Who are we really feeding?

Genome assemblers are computational tools for de novo genome assembly, based on a plenitude of primary sequencing data. The quality of genome assemblies is estimated by their contiguity and the occurrences of misassemblies (duplications, deletions, translocations or inversions). The rapid development of sequencing technologies has enabled the rise of novel de novo genome assembly strategies. The ultimate goal of such strategies is to utilise the features of each sequencing platform in order to address the existing weaknesses of each sequencing type and compose a complete and correct genome map. In the present study, the hybrid strategy, which is based on Illumina short paired-end reads and Nanopore long reads, was benchmarked using MaSuRCA and Wengan assemblers. Moreover, the long-read assembly strategy, which is based on Nanopore reads, was benchmarked using Canu or PacBio HiFi reads were benchmarked using Hifiasm and HiCanu. The assemblies were performed on a computational cluster with limited computational resources. Their outputs were evaluated in terms of accuracy and computational performance. PacBio HiFi assembly strategy outperforms the other ones, while Hi-C scaffolding, which is based on chromatin 3D structure, is required in order to increase continuity, accuracy and completeness when large and complex genomes, such as the human one, are assembled. The use of Hi-C data is also necessary while using the hybrid assembly strategy. The results revealed that HiFi sequencing enabled the rise of novel algorithms which require less genome coverage than that of the other strategies making the assembly a less computationally demanding task. Taken together, these developments may lead to the democratisation of genome assembly projects which are now approachable by smaller labs with limited technical and financial resources.

Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.

This study examined several aspects of canopy structure and their influence on growth of loblolly pine (Pinus taeda L.) plantations. Foliage distribution, crown hydraulic architecture, and the effect of chronological changes in canopy structure on stand development were explored as possible components of a future process-based model intended for management purposes. A model based on the Johnson’s SB distribution was developed to predict leaf area distribution of loblolly pine trees. This is a preliminary step for building a submodel capable of simulating chronological changes in canopy structure and stand growth. The model accurately predicted the cumulative distribution of leaf area in the crown. It has the potential to be included in forest growth models where an accurate description of leaf area distribution is needed. A novel process-related, non-carbon-based growth model for predicting the growth of closed, unthinned, loblolly pine stands was developed. Its ability to represent the dynamics of the canopy and stand growth was evaluated. Overall, model predictions were in agreement with reported observations or proposed theories in relation to stand growth, size-density relations, and relationships between canopy dynamics and stand growth. Modeling the hydraulic architecture of the crown is important because it controls crown recession. Patterns in branch permeability with crown depth and permeability at the top of the main stem were analyzed for loblolly pine trees from families selected for differences in growth rate and crown size. The results showed that branch permeability decreased significantly from the top to the bottom of the crown and that genetic-based differences might exist in patterns of stem and branch permeability. The study showed the potential of using a process approach to develop a forest growth model and utilizing mechanistic and empirical elements in the construction of the simulator. In addition, the integration and synthesis of information coming from diverse sources in the model allow the possibility of detecting deficiencies in the understanding of key processes and provide a guide for formulating hypotheses and planning experiments to fill the gaps in knowledge of the processes regulating stand development.

In the context of increasing droughts related to climate change, our results showed that heavy thinning and/or very low initial planting density can increase CO 2 assimilation rate in needles, and may be used as a short-term management strategy for loblolly pine plantation across sites prone to drought. The dry summer of 2013 provided us an opportunity to understand the CO2 assimilation rate and stomatal conductance after density manipulation treatments using the dual isotope (δ13C and δ18O) signatures in needles of planted loblolly pine (Pinus taeda L.) trees in the southeastern USA. To our knowledge, this is the first study using the dual isotope approach to examine the physiological response of loblolly pine trees, one of the most widely planted tree species in the world, to stand density manipulation treatments (i.e., thinning intensity and planting density). In 2001–2003, trees were planted with five different planting densities, 494, 1111, 1729, 2346, and 2964 trees ha−1 at three sites. In 2009–2011, two thinning treatments (none and moderate thinning) were applied in the 1111 trees ha−1 plots, whereas three treatments (none, light and heavy thinning) were applied in the 1729 trees ha−1 plots. Response variables (specific leaf area (SLA), foliar N, δ13C and δ18O) were measured in February 2014. SLA was lower, while δ18O was higher in the 494 trees ha−1 plots than the 2964 trees ha−1 plots without thinning. In plots planted to 1729 trees ha−1 SLA was lower, while δ13C and δ18O were higher following heavy thinning than in the unthinned control. These responses plus increased crown length, DBH, and height following heavy thinning may reflect an increased tree-level CO2 assimilation rate. Our results showed that heavy thinning and/or very low initial planting density can be used as a short-term management strategy for loblolly pine plantation across sites prone to drought.