A reference genome of the European beech (<i>Fagus sylvatica</i> L.)

Mishra, Bagdevi; Gupta, Deepak Kumar; Pfenninger, Markus; Hickler, Thomas; Langer, Ewald; Nam, Bora; Paule, Juraj; Sharma, Rahul; Ulaszewski, Bartosz; Warmbier, Joanna; Burczyk, Jarosław; Thines, Marco

doi:10.1093/gigascience/giy063

Cited by 64 publications

(85 citation statements)

References 49 publications

(48 reference statements)

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“…We demultiplexed the sequences with the program stacks (Catchen, Hohenlohe, Bassham, Amores, & Cresko, 2013) using a Phred score of 10 for reads filtering ( process_radtags function). We mapped the reads against the newly assembled beech genome (Mishra et al, 2018) using bwa software (Li & Durbin, 2009) and the BWA‐MEM algorithm. We processed the mapped sequences with the gstacks function of stacks pipeline using a minimum mapping quality of 20.…”

Section: Methodsmentioning

confidence: 99%

Climate‐associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

Capblancq

Morin

Guéguen

et al. 2020

J of Evolutionary Biology

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Local adaptation patterns have been found in many plants and animals, highlighting the genetic heterogeneity of species along their range of distribution. In the next decades, global warming is predicted to induce a change in the selective pressures that drive this adaptive variation, forcing a reshuffling of the underlying adaptive allele distributions. For species with low dispersion capacity and long generation time such as trees, the rapidity of the change could impede the migration of beneficial alleles and lower their capacity to track the changing environment. Identifying the main selective pressures driving the adaptive genetic variation is thus necessary when investigating species capacity to respond to global warming. In this study, we investigate the adaptive landscape of Fagus sylvatica along a gradient of populations in the French Alps. Using a double‐digest restriction‐site‐associated DNA (ddRAD) sequencing approach, we identified 7,000 SNPs from 570 individuals across 36 different sites. A redundancy analysis (RDA)‐derived method allowed us to identify several SNPs that were strongly associated with climatic gradients; moreover, we defined the primary selective gradients along the natural populations of F. sylvatica in the Alps. Strong effects of elevation and humidity, which contrast north‐western and south‐eastern site, were found and were believed to be important drivers of genetic adaptation. Finally, simulations of future genetic landscapes that used these findings allowed identifying populations at risk for F. sylvatica in the Alps, which could be helpful for future management plans.

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Section: Methodsmentioning

confidence: 99%

Climate‐associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

Capblancq

Morin

Guéguen

et al. 2020

J of Evolutionary Biology

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“…Mishra et al [ 3 ] published a 542 Mb nuclear draft genome sequence of an up to 300-year-old F. sylvatica individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in Central Germany. The assembly comprised 6451 scaffolds that are not yet assigned to any chromosomes.…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

Mäder¹,

Schroeder²,

Schott³

et al. 2020

Plants

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European beech, Fagus sylvatica L., is one of the most important and widespread deciduous tree species in Central Europe and is widely managed for its hard wood. The complete DNA sequence of the mitochondrial genome of Fagus sylvatica L. was assembled and annotated based on Illumina MiSeq reads and validated using long reads from nanopore MinION sequencing. The genome assembled into a single DNA sequence of 504,715 bp in length containing 58 genes with predicted function, including 35 protein-coding, 20 tRNA and three rRNA genes. Additionally, 23 putative protein-coding genes were predicted supported by RNA-Seq data. Aiming at the development of taxon-specific mitochondrial genetic markers, the tool SNPtax was developed and applied to select genic SNPs potentially specific for different taxa within the Fagales. Further validation of a small SNP set resulted in the development of four CAPS markers specific for Fagus, Fagaceae, or Fagales, respectively, when considering over 100 individuals from a total of 69 species of deciduous trees and conifers from up to 15 families included in the marker validation. The CAPS marker set is suitable to identify the genus Fagus in DNA samples from tree tissues or wood products, including wood composite products.

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“…Genetic microsatellite markers can be derived from EST libraries and are located either in coding regions or in the 5' or 3' untranslated regions (UTRs) (Ellis and Burke, 2007). Despite growing genetic and genomic resources for European beech (Lalagüe et al, 2014;Lesur et al, 2015;Müller et al, 2015;Dounavi et al, 2016;Müller et al, 2017;Mishra et al, 2018) the number of available SSR markers for this species is still limited. Especially, only a few gene-based EST-SSRs that were originally developed in other species are available for F. sylvatica (e.g., Ueno et al, 2009;Dounavi et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Characterization of EST-SSRs for European beech (Fagus sylvatica L.) and their transferability to Fagus orientalis Lipsky, Castanea dentata Bork., and Quercus rubra L.

2018

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Due to ongoing climate change, forests are exposed to changing environmental conditions, such as increasing temperatures and lower precipitation, to which trees have to adapt. Successful adaptation to changing and variable environments requires sufficient genetic variation within tree populations. Knowledge of the genetic variation of trees is therefore essential, as it provides information for the long-term conservation, stability and productivity of forests. The genetic variation of a species can be analysed with molecular markers. Despite growing genomic and genetic resources for European beech (Fagus sylvatica L.), which is one of the economically and ecologically most important forest tree species in Central Europe, the number of molecular markers for population genetic analyses is still limited. Therefore, the aim of the work is the development of new EST-SSR markers for this species. A total of 72 DNA samples of European beech from three widely separated regions in Germany were used to test 41 primers for variation and polymorphism, 35 of which were originally developed for American beech (Fagus grandifolia Ehrh.) and 6 for red oak (Quercus rubra L.). Fifteen of the primers were polymorphic, 13 monomorphic and 13 did not amplify. In addition, the transferability of the markers was successfully tested in the related species Castanea dentata Bork., Fagus orientalis Lipsky and Q. rubra. The EST-SSR markers tested in this study will be useful for future population genetic analyses and extend the set of available markers in European beech.

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

Cited by 64 publications

References 49 publications

Climate‐associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

Climate‐associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

Characterization of EST-SSRs for European beech (Fagus sylvatica L.) and their transferability to Fagus orientalis Lipsky, Castanea dentata Bork., and Quercus rubra L.

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