Dataset Information

A reference genome of the European beech (Fagus sylvatica L.).

ABSTRACT: Background:The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany. Findings:Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12% of Ns. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high-molecular-weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum. Conclusions:The assembled genome will be a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g., involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.

SUBMITTER: Mishra B

PROVIDER: S-EPMC6014182 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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A reference genome of the European beech (Fagus sylvatica L.).

Mishra Bagdevi B Gupta Deepak K DK Pfenninger Markus M Hickler Thomas T Langer Ewald E Nam Bora B Paule Juraj J Sharma Rahul R Ulaszewski Bartosz B Warmbier Joanna J Burczyk Jaroslaw J Thines Marco M

GigaScience 20180601 6

<h4>Background</h4>The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany.<h4>Findings</h4>Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained a ...[more]

PMID: 29893845

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Project description:In this article, we outline the set-up and the application of an eco-hydrological box model, with the aim to describe the water balance of deciduous (Fagus Sylvatica L.) forest stands. The water balance model (WBM) uses standard meteorological parameters as input variables and runs on a daily time step. It consists of two modules. The aboveground module (1) comprises routines for fog precipitation generation, precipitation interception and snowfall/snowmelt dynamics. Covered belowground processes (2) are bypass flow, percolation, soil evaporation and transpiration, where the latter two processes are considered separately. Preceding to the WBM, a routine is introduced, specifying the intra-annual foliage dynamics of beech. Emphasis is also laid on the inter-annual variation of beech phenology. Leaf sprouting and leaf senescence are calculated as functions of day-length and air temperature. The WBM was applied to four European beech dominated forest stands in the northeastern part of Austria. They are located on a gradient of declining annual precipitation (from west to east). The two easterly sites are located close to the (dry) limit of the natural distribution of beech. Records of soil moisture were used for the adjustment of 26 parameters. On all sites the calibration process (simulated annealing) delivered good predictions of soil moisture (Nash-Sutcliffe efficiency? 0.925). Then, the obtained parameterization was used to apply different scenarios of global warming. The temperature was increased step-wisely up to 4 °C. All scenarios were run (1) with present phenological conditions and (2) with phenology responding to higher temperatures. This way, we wanted to assign the effect of higher temperatures and longer growing seasons on the water dynamics of the forest stands. A warming of 1 °C corresponded roughly to an elongation of the growing season of 4.5 days, where the start of the growing season was affected more strongly than the end. Apparently, higher temperatures led to drier soils. The strongest change was observed in early summer, also amplified by an earlier start of the growing season. Rising temperatures led to lower export fluxes of liquid water, simultaneously increasing evapotranspiration (ET). The gain in ET was almost entirely assignable to increased soil evaporation. Drier soils led to a sharp depression of transpiration during summer months. This decline was compensated by the effect of elongated growing seasons. The risk of severe drought was increased by higher temperatures, but here the contribution of growing season length was negligible. Drier soils seem to hamper the stands' productivity. For all warming scenarios, the estimated increase of the gross primary production, caused by longer periods of assimilation, is nullified by the effect of soil water deficit in mid-summer.

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Project description:Height to crown base (HCB) of a tree is an important variable often included as a predictor in various forest models that serve as the fundamental tools for decision-making in forestry. We developed spatially explicit and spatially inexplicit mixed-effects HCB models using measurements from a total 19,404 trees of Norway spruce (Picea abies (L.) Karst.) and European beech (Fagus sylvatica L.) on the permanent sample plots that are located across the Czech Republic. Variables describing site quality, stand density or competition, and species mixing effects were included into the HCB model with use of dominant height (HDOM), basal area of trees larger in diameters than a subject tree (BAL- spatially inexplicit measure) or Hegyi's competition index (HCI-spatially explicit measure), and basal area proportion of a species of interest (BAPOR), respectively. The parameters describing sample plot-level random effects were included into the HCB model by applying the mixed-effects modelling approach. Among several functional forms evaluated, the logistic function was found most suited to our data. The HCB model for Norway spruce was tested against the data originated from different inventory designs, but model for European beech was tested using partitioned dataset (a part of the main dataset). The variance heteroscedasticity in the residuals was substantially reduced through inclusion of a power variance function into the HCB model. The results showed that spatially explicit model described significantly a larger part of the HCB variations [R2adj = 0.86 (spruce), 0.85 (beech)] than its spatially inexplicit counterpart [R2adj = 0.84 (spruce), 0.83 (beech)]. The HCB increased with increasing competitive interactions described by tree-centered competition measure: BAL or HCI, and species mixing effects described by BAPOR. A test of the mixed-effects HCB model with the random effects estimated using at least four trees per sample plot in the validation data confirmed that the model was precise enough for the prediction of HCB for a range of site quality, tree size, stand density, and stand structure. We therefore recommend measuring of HCB on four randomly selected trees of a species of interest on each sample plot for localizing the mixed-effects model and predicting HCB of the remaining trees on the plot. Growth simulations can be made from the data that lack the values for either crown ratio or HCB using the HCB models.

Dataset Information

A reference genome of the European beech (Fagus sylvatica L.).

Publications

A reference genome of the European beech (Fagus sylvatica L.).

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