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Article ; Online: Signatures of local adaptation to current and future climate in phenology-related genes in natural populations of Quercus robur.

Meger, Joanna / Ulaszewski, Bartosz / Chmura, Daniel J / Burczyk, Jarosław

2024 Volume 25, Issue 1, Page(s) 78

Abstract: Background: Local adaptation is a key evolutionary process that enhances the growth of plants in their native habitat compared to non-native habitats, resulting in patterns of adaptive genetic variation across the entire geographic range of the species. ...

Abstract	Background: Local adaptation is a key evolutionary process that enhances the growth of plants in their native habitat compared to non-native habitats, resulting in patterns of adaptive genetic variation across the entire geographic range of the species. The study of population adaptation to local environments and predicting their response to future climate change is important because of climate change. Results: Here, we explored the genetic diversity of candidate genes associated with bud burst in pedunculate oak individuals sampled from 6 populations in Poland. Single nucleotide polymorphism (SNP) diversity was assessed in 720 candidate genes using the sequence capture technique, yielding 18,799 SNPs. Using landscape genomic approaches, we identified 8 F Conclusions: The model revealed that pedunculate oak populations in the eastern part of the analyzed geographical region are the most sensitive to climate change. Our results might offer an initial evaluation of a potential management strategy for preserving the genetic diversity of pedunculate oak.
MeSH term(s)	Humans ; Quercus/genetics ; Biological Evolution ; Genomics ; Forests ; Poland ; Adaptation, Physiological/genetics
Language	English
Publishing date	2024-01-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-023-09897-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Genomic prediction of resistance to

Meger, Joanna / Ulaszewski, Bartosz / Pałucka, Małgorzata / Kozioł, Czesław / Burczyk, Jarosław

Evolutionary applications

2024 Volume 17, Issue 5, Page(s) e13694

Abstract: The increase in introduced insect pests and pathogens due to anthropogenic environmental changes has become a major concern for tree species worldwide. Common ash ( ...

Abstract	The increase in introduced insect pests and pathogens due to anthropogenic environmental changes has become a major concern for tree species worldwide. Common ash (
Language	English
Publishing date	2024-05-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2405496-3
ISSN	1752-4563 ; 1752-4571
ISSN (online)	1752-4563
ISSN	1752-4571
DOI	10.1111/eva.13694
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Article: A reference genome of the European beech (Fagus sylvatica L.)

Pfenninger, Markus / Hickler, Thomas / Langer, Ewald / Paule, Juraj / SHARMA, RAHUL / Ulaszewski, Bartosz / Warmbier, Joanna / Burczyk, Jaroslaw / Thines, Marco

GigaScience, 7(6):giy063

2018

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 ... ...

Institution	Senckenberg Biodiversität und Klima Forschungszentrum
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.
Keywords	genomics ; forest tree ; fungi ; hardwood ; hybrid assembly ; transcriptomics
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article ; Online: Genetic resources of common ash (Fraxinus excelsior L.) in Poland.

Meger, Joanna / Kozioł, Czesław / Pałucka, Małgorzata / Burczyk, Jarosław / Chybicki, Igor J

BMC plant biology

2024 Volume 24, Issue 1, Page(s) 186

Abstract: Background: Knowledge of genetic structure and the factors that shape it has an impact on forest management practices. European ash (Fraxinus excelsior L.) has declined dramatically throughout its range as a result of a disease caused by the fungus ... ...

Abstract	Background: Knowledge of genetic structure and the factors that shape it has an impact on forest management practices. European ash (Fraxinus excelsior L.) has declined dramatically throughout its range as a result of a disease caused by the fungus Hymenoscyphus fraxineus. Despite the need for conservation and restoration of the species, genetic data required to guide these efforts at the country level are scarce. Thereofore, we studied the chloroplast and nuclear genetic diversity of 26 natural common ash populations (1269 trees) in Poland. Results: Chloroplast polymorphisms grouped the populations into two geographically structured phylogenetic lineages ascribed to different glacial refugia (the Balkans and the Eastern Alps). However, the populations demonstrated high genetic diversity (mean A Conclusions: Genetic diversity was not homogeneously distributed among populations within phylogenetic gene pools, indicating that ash populations are not equal as potential sources of reproductive material. Genetic differences among populations could be related to their histories, including founder effects or gene flow between evolutionary lineages (admixture). Our results suggest that ash stands across Poland could be treated as two main management units (seed zones). Therefore, despite the homogenizing effect of pollen gene flow known for this species, the genetic structure should be taken into account in the management of the genetic resources of the common ash. Although ash dieback poses an additional challenge for the management of genetic resources, efforts should be directed towards protecting populations with high genetic diversity within defined phylogenetic units, as they may be an important source of adaptive variation for future stands.
MeSH term(s)	Humans ; Fraxinus/genetics ; Fraxinus/microbiology ; Poland ; Phylogeny ; Ascomycota ; Forests ; Genetic Variation
Language	English
Publishing date	2024-03-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2059868-3
ISSN	1471-2229 ; 1471-2229
ISSN (online)	1471-2229
ISSN	1471-2229
DOI	10.1186/s12870-024-04886-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A novel synthesis of two decades of microsatellite studies on European beech reveals decreasing genetic diversity from glacial refugia [Correction: Feb. 2023, 19(1), p. 6]

Stefanini, Camilla / Csilléry, Katalin / Ulaszewski, Bartosz / Burczyk, Jarosław / Schaepman, Michael E. / Schuman, Meredith C.

Tree Genetics & Genomes. 2023 Feb., v. 19, no. 1, p. 3

2023 , Page(s) 3

Abstract: Genetic diversity influences the evolutionary potential of forest trees under changing environmental conditions, thus indirectly the ecosystem services that forests provide. European beech (Fagus sylvatica L.) is a dominant European forest tree species ... ...

Abstract	Genetic diversity influences the evolutionary potential of forest trees under changing environmental conditions, thus indirectly the ecosystem services that forests provide. European beech (Fagus sylvatica L.) is a dominant European forest tree species that increasingly suffers from climate change-related die-back. Here, we conducted a systematic literature review of neutral genetic diversity in European beech and created a meta-data set of expected heterozygosity (He) from all past studies providing nuclear microsatellite data. We propose a novel approach, based on population genetic theory and a min–max scaling to make past studies comparable. Using a new microsatellite data set with unprecedented geographic coverage and various re-sampling schemes to mimic common sampling biases, we show the potential and limitations of the scaling approach. The scaled meta-dataset reveals the expected trend of decreasing genetic diversity from glacial refugia across the species range and also supports the hypothesis that different lineages met and admixed north of the European mountain ranges. As a result, we present a map of genetic diversity across the range of European beech which could help to identify seed source populations harboring greater diversity and guide sampling strategies for future genome-wide and functional investigations of genetic variation. Our approach illustrates how to combine information from several nuclear microsatellite data sets to describe patterns of genetic diversity extending beyond the geographic scale or mean number of loci used in each individual study, and thus is a proof-of-concept for synthesizing knowledge from existing studies also in other species.
Keywords	Fagus sylvatica subsp. sylvatica ; climate ; data collection ; dieback ; ecosystems ; forest trees ; forests ; genetic variation ; genome ; heterozygosity ; metadata ; microsatellite repeats ; plant genetics ; population genetics ; refuge habitats
Language	English
Dates of publication	2023-02
Size	p. 3
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
Note	Review
ZDB-ID	2180926-4
ISSN	1614-2950 ; 1614-2942
ISSN (online)	1614-2950
ISSN	1614-2942
DOI	10.1007/s11295-022-01577-4
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L.

Meger, Joanna / Ulaszewski, Bartosz / Burczyk, Jaroslaw

BMC genomics

2021 Volume 22, Issue 1, Page(s) 583

Abstract: Background: Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as forest trees. European beech (Fagus ... ...

Abstract	Background: Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as forest trees. European beech (Fagus sylvatica L.) is widespread, and is one of the most important broadleaved tree species in Europe; however, its potential for adaptation to climate change is a matter of uncertainty, and little is known about the molecular basis of climate change-relevant traits like bud burst. Results: We explored single nucleotide polymorphisms (SNP) at candidate genes related to bud burst in beech individuals sampled across 47 populations from Europe. SNP diversity was monitored for 380 candidate genes using a sequence capture approach, providing 2909 unlinked SNP loci. We used two complementary analytical methods to find loci significantly associated with geographic variables, climatic variables (expressed as principal components), or phenotypic variables (spring and autumn phenology, height, survival). Redundancy analysis (RDA) was used to detect candidate markers across two spatial scales (entire study area and within subregions). We revealed 201 candidate SNPs at the broadest scale, 53.2% of which were associated with phenotypic variables. Additive polygenic scores, which provide a measure of the cumulative signal across significant candidate SNPs, were correlated with a climate variable (first principal component, PC1) related to temperature and precipitation availability, and spring phenology. However, different genotype-environment associations were identified within Southeastern Europe as compared to the entire geographic range of European beech. Conclusions: Environmental conditions play important roles as drivers of genetic diversity of phenology-related genes that could influence local adaptation in European beech. Selection in beech favors genotypes with earlier bud burst under warmer and wetter habitats within its range; however, selection pressures may differ across spatial scales.
MeSH term(s)	Europe ; Fagus/genetics ; Genomics ; Humans ; Selection, Genetic ; Trees/genetics
Language	English
Publishing date	2021-07-31
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-021-07907-5
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Article: Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of

Ulaszewski, Bartosz / Jankowska-Wróblewska, Sandra / Świło, Katarzyna / Burczyk, Jarosław

Plants (Basel, Switzerland)

2021 Volume 10, Issue 11

Abstract: Several genera formerly contained within the ... ...

Abstract	Several genera formerly contained within the genus
Language	English
Publishing date	2021-11-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants10112534
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Article ; Online: Complete Chloroplast Genomes of

Ulaszewski, Bartosz / Meger, Joanna / Mishra, Bagdevi / Thines, Marco / Burczyk, Jarosław

Genes

2021 Volume 12, Issue 9

Abstract: Growing amounts of genomic data and more efficient assembly tools advance organelle genomics at an unprecedented scale. Genomic resources are increasingly used for phylogenetic analyses of many plant species, but are less frequently used to investigate ... ...

Abstract	Growing amounts of genomic data and more efficient assembly tools advance organelle genomics at an unprecedented scale. Genomic resources are increasingly used for phylogenetic analyses of many plant species, but are less frequently used to investigate within-species variability and phylogeography. In this study, we investigated genetic diversity of
MeSH term(s)	Base Sequence ; Conserved Sequence ; Europe ; Fagus/genetics ; Genetic Variation ; Genome Size ; Genome, Chloroplast/genetics ; Genomics/methods ; Inverted Repeat Sequences ; Microsatellite Repeats ; Phylogeny ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2021-08-29
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12091357
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A novel synthesis of two decades of microsatellite studies on European beech reveals decreasing genetic diversity from glacial refugia.

Stefanini, Camilla / Csilléry, Katalin / Ulaszewski, Bartosz / Burczyk, Jarosław / Schaepman, Michael E / Schuman, Meredith C

Tree genetics & genomes

2022 Volume 19, Issue 1, Page(s) 3

Abstract: Genetic diversity influences the evolutionary potential of forest trees under changing environmental conditions, thus indirectly the ecosystem services that forests provide. European beech (: Supplementary information: The online version contains ... ...

Abstract	Genetic diversity influences the evolutionary potential of forest trees under changing environmental conditions, thus indirectly the ecosystem services that forests provide. European beech ( Supplementary information: The online version contains supplementary material available at 10.1007/s11295-022-01577-4.
Language	English
Publishing date	2022-12-12
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2180926-4
ISSN	1614-2950 ; 1614-2942
ISSN (online)	1614-2950
ISSN	1614-2942
DOI	10.1007/s11295-022-01577-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A Comparison of Three Circular Mitochondrial Genomes of Fagus sylvatica from Germany and Poland Reveals Low Variation and Complete Identity of the Gene Space

Mishra, Bagdevi / Ulaszewski, Bartosz / Meger, Joanna / Ploch, Sebastian / Burczyk, Jaroslaw / Thines, Marco

Forests. 2021 May 01, v. 12, no. 5

2021

Abstract: Similar to chloroplast loci, mitochondrial markers are frequently used for genotyping, phylogenetic studies, and population genetics, as they are easily amplified due to their multiple copies per cell. In a recent study, it was revealed that the ... ...

Abstract	Similar to chloroplast loci, mitochondrial markers are frequently used for genotyping, phylogenetic studies, and population genetics, as they are easily amplified due to their multiple copies per cell. In a recent study, it was revealed that the chloroplast offers little variation for this purpose in central European populations of beech. Thus, it was the aim of this study to elucidate, if mitochondrial sequences might offer an alternative, or whether they are similarly conserved in central Europe. For this purpose, a circular mitochondrial genome sequence from the more than 300-year-old beech reference individual Bhaga from the German National Park Kellerwald-Edersee was assembled using long and short reads and compared to an individual from the Jamy Nature Reserve in Poland and a recently published mitochondrial genome from eastern Germany. The mitochondrial genome of Bhaga was 504,730 bp, while the mitochondrial genomes of the other two individuals were 15 bases shorter, due to seven indel locations, with four having more bases in Bhaga and three locations having one base less in Bhaga. In addition, 19 SNP locations were found, none of which were inside genes. In these SNP locations, 17 bases were different in Bhaga, as compared to the other two genomes, while 2 SNP locations had the same base in Bhaga and the Polish individual. While these figures are slightly higher than for the chloroplast genome, the comparison confirms the low degree of genetic divergence in organelle DNA of beech in central Europe, suggesting the colonisation from a common gene pool after the Weichsel Glaciation. The mitochondrial genome might have limited use for population studies in central Europe, but once mitochondrial genomes from glacial refugia become available, it might be suitable to pinpoint the origin of migration for the re-colonising beech population.
Keywords	DNA ; Fagus sylvatica ; chloroplast genome ; chloroplasts ; conservation areas ; gene pool ; genes ; genetic variation ; genotyping ; glaciation ; mitochondria ; mitochondrial genome ; national parks ; nucleotide sequences ; phylogeny ; refuge habitats ; Central European region ; Germany ; Poland
Language	English
Dates of publication	2021-0501
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2527081-3
ISSN	1999-4907
ISSN	1999-4907
DOI	10.3390/f12050571
Database	NAL-Catalogue (AGRICOLA)

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