580 Pflanzen (Botanik)
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Abstract
Natural plant populations often harbour substantial heritable variation in DNA methylation. However, a thorough understanding of the genetic and environmental drivers of this epigenetic variation requires large-scale and high-resolution data, which currently exist only for a few model species. Here, we studied 207 lines of the annual weed Thlaspi arvense (field pennycress), collected across a large latitudinal gradient in Europe and propagated in a common environment. By screening for variation in DNA sequence and DNA methylation using whole-genome (bisulfite) sequencing, we found significant epigenetic population structure across Europe. Average levels of DNA methylation were strongly context-dependent, with highest DNA methylation in CG context, particularly in transposable elements and in intergenic regions. Residual DNA methylation variation within all contexts was associated with genetic variants, which often co-localized with annotated methylation machinery genes but also with new candidates. Variation in DNA methylation was also significantly associated with climate of origin, with methylation levels being lower in colder regions and in more variable climates. Finally, we used variance decomposition to assess genetic versus environmental associations with differentially methylated regions (DMRs). We found that while genetic variation was generally the strongest predictor of DMRs, the strength of environmental associations increased from CG to CHG and CHH, with climate-of-origin as the strongest predictor in about one third of the CHH DMRs. In summary, our data show that natural epigenetic variation in Thlaspi arvense is significantly associated with both DNA sequence and environment of origin, and that the relative importance of the two factors strongly depends on the sequence context of DNA methylation. T. arvense is an emerging biofuel and winter cover crop; our results may hence be relevant for breeding efforts and agricultural practices in the context of rapidly changing environmental conditions.
Author summary
Variation within species is an important level of biodiversity, and it is key for future adaptation. Besides variation in DNA sequence, plants also harbour heritable variation in DNA methylation, and we want to understand the evolutionary significance of this epigenetic variation, in particular how much of it is under genetic control, and how much is associated with the environment. We addressed these questions in a high-resolution molecular analysis of 207 lines of the common plant field pennycress (Thlaspi arvense), which we collected across Europe, propagated under standardized conditions, and sequenced for their genetic and epigenetic variation. We found large geographic variation in DNA methylation, associated with both DNA sequence and climate of origin. Genetic variation was generally the stronger predictor of DNA methylation variation, but the strength of environmental association varied between different sequence contexts. Climate-of-origin was the strongest predictor in about one third of the differentially methylated regions in the CHH context, which suggests that epigenetic variation may play a role in the short-term climate adaptation of pennycress. As pennycress is currently being domesticated as a new biofuel and winter cover crop, our results may be relevant also for agriculture, particularly in changing environments.
Abstract
Natural plant populations often harbour substantial heritable variation in DNA methylation. However, a thorough understanding of the genetic and environmental drivers of this epigenetic variation requires large-scale and high-resolution data, which currently exist only for a few model species. Here, we studied 207 lines of the annual weed Thlaspi arvense (field pennycress), collected across a large latitudinal gradient in Europe and propagated in a common environment. By screening for variation in DNA sequence and DNA methylation using whole-genome (bisulfite) sequencing, we found significant epigenetic population structure across Europe. Average levels of DNA methylation were strongly context-dependent, with highest DNA methylation in CG context, particularly in transposable elements and in intergenic regions. Residual DNA methylation variation within all contexts was associated with genetic variants, which often co-localized with annotated methylation machinery genes but also with new candidates. Variation in DNA methylation was also significantly associated with climate of origin, with methylation levels being higher in warmer regions and lower in more variable climates. Finally, we used variance decomposition to assess genetic versus environmental associations with differentially methylation regions (DMRs). We found that while genetic variation was generally the strongest predictor of DMRs, the strength of environmental associations increased from CG to CHG and CHH, with climate-of-origin as the strongest predictor in about one third of the CHH DMRs. In summary, our data show that natural epigenetic variation in Thlaspi arvense is significantly associated with both DNA sequence and environment of origin, and that the relative importance of the two factors strongly depends on the sequence context of DNA methylation. T. arvense is an emerging biofuel and winter cover crop; our results may hence be relevant for breeding efforts and agricultural practices in the context of rapidly changing environmental conditions.
Author Summary: Variation within species is an important level of biodiversity, and it is key for future adaptation. Besides variation in DNA sequence, plants also harbour heritable variation in DNA methylation, and we want to understand the evolutionary significance of this epigenetic variation, in particular how much of it is under genetic control, and how much is associated with the environment. We addressed these questions in a high-resolution molecular analysis of 207 lines of the common plant field pennycress (Thlaspi arvense), which we collected across Europe, propagated under standardized conditions, and sequenced for their genetic and epigenetic variation. We found large geographic variation in DNA methylation, associated with both DNA sequence and climate of origin. Genetic variation was generally the stronger predictor of DNA methylation variation, but the strength of environmental association varied between different sequence contexts. Climate-of-origin was the strongest predictor in about one third of the differentially methylated regions in the CHH context, which suggests that epigenetic variation may play a role in the short-term climate adaptation of pennycress. As pennycress is currently being domesticated as a new biofuel and winter cover crop, our results may be relevant also for agriculture, particularly in changing environments.
Tilletia caries and T. laevis, which are the causal agents of common bunt, as well as T. controversa, which causes dwarf bunt of wheat, threaten especially organic wheat farming. The three closely related fungal species differ in their teliospore morphology and partially in their physiology and infection biology. The gene content as well as intraspecies variation in these species and the genetic basis of their separation is unknown. We sequenced the genome of four T. caries, five T. controversa, and two T. laevis and extended this dataset with five publicly available ones. The genomes of the three species displayed microsynteny with up to 94.3% pairwise aligned regions excluding repetitive regions. The majority of functionally characterized genes involved in pathogenicity, life cycle, and infection of corn smut, Ustilago maydis, were found to be absent or poorly conserved in the draft genomes and the biosynthetic pathway for trimethylamine in Tilletia spp. could be different from bacteria. Overall, 75% of the identified protein-coding genes comprising 84% of the total predicted carbohydrate utilizing enzymes, 72.5% putatively secreted proteins, and 47.4% of effector-like proteins were conserved and shared across all 16 isolates. We predicted nine highly identical secondary metabolite biosynthesis gene clusters comprising in total 62 genes in all species and none were species-specific. Less than 0.1% of the protein-coding genes were species-specific and their function remained mostly unknown. Tilletia controversa had the highest intraspecies genetic variation, followed by T. caries and the lowest in T. laevis. Although the genomes of the three species are very similar, employing 241 single copy genes T. controversa was phylogenetically distinct from T. caries and T. laevis, however these two could not be resolved as individual monophyletic groups. This was in line with the genome-wide number of single nucleotide polymorphisms and small insertions and deletions. Despite the conspicuously different teliospore ornamentation of T. caries and T. laevis, a high degree of genomic identity and scarcity of species-specific genes indicate that the two species could be conspecific.
Due to massive energetic investments in woody support structures, trees are subject to unique physiological, mechanical, and ecological pressures not experienced by herbaceous plants. Despite a wealth of studies exploring trait relationships across the entire plant kingdom, the dominant traits underpinning these unique aspects of tree form and function remain unclear. Here, by considering 18 functional traits, encompassing leaf, seed, bark, wood, crown, and root characteristics, we quantify the multidimensional relationships in tree trait expression. We find that nearly half of trait variation is captured by two axes: one reflecting leaf economics, the other reflecting tree size and competition for light. Yet these orthogonal axes reveal strong environmental convergence, exhibiting correlated responses to temperature, moisture, and elevation. By subsequently exploring multidimensional trait relationships, we show that the full dimensionality of trait space is captured by eight distinct clusters, each reflecting a unique aspect of tree form and function. Collectively, this work identifies a core set of traits needed to quantify global patterns in functional biodiversity, and it contributes to our fundamental understanding of the functioning of forests worldwide.
Seed dispersal is a key ecosystem function for plant regeneration, as it involves the movement of seeds away from the parental plants to particular habitats where they can germinate and transition to seedlings and ultimately adult plants. Seed dispersal is shaped by a diversity of abiotic and biotic factors, particularly by associations between plants and climate and between plants and other species. Due to the ongoing loss of biodiversity and changing global conditions, such interactions are prone to change and pose a severe threat to plant regeneration. One way to address this challenge is to study associations between plant traits and abiotic and biotic factors to understand the potential impacts of global change on plant regeneration. Plant communities have long been analyzed through the lens of vegetative traits, mainly ignoring how other traits interact and respond to the environment. For instance, while associations between vegetative traits (e.g., specific leaf area, leaf nitrogen content) and climate are well studied, there are few case studies of reproductive traits in relation to trait-environment associations in the context of global change.
Thus, the overarching aim of this dissertation is to explore how trait-environment associations, with a special focus on reproductive traits, can improve our understanding of the effect that global change may have on seed dispersal, and ultimately on plant regeneration. To this end, my research focuses on studying associations between plant traits and abiotic and biotic factors along an elevational gradient in both forests and deforested areas of tropical mountains. This dissertation addresses three principal research objectives.
First, I investigate the extent to which reproductive (seed and fruit traits) and vegetative traits (leaf traits) are related to abiotic and biotic factors for communities of fleshy-fruited plants in the Ecuadorian Andes. I used multivariate analyses to test associations between four (a)biotic factors and seven reproductive traits and five vegetative traits measured on 18 and 33 fleshy fruited plant species respectively. My analyses demonstrate that climate and soil conditions are strongly associated with the distribution of both reproductive and vegetative traits in tropical tree communities. The production of “costly” vs. “cheap” seeds, fruits and leaves, i.e., the production of few rewarding fruits and acquisitive leaves versus the production of many less-rewarding fruits and conservative leaves, is primarily limited by temperature, whereas the size of plant organs is more related to variation in precipitation and soil conditions. My findings suggest that associations between reproductive and vegetative traits and the abiotic environment follow similar principles in tropical tree communities.
Second, I assess how climate and microhabitat conditions affect the prevalence of endozoochorous plant species in the seed rain of tropical montane forests in southern Ecuador. I analyzed seed rain data for an entire year from 162 traps located across an elevational gradient spanning of 2000 m. I documented the microhabitat conditions (leaf area index and soil moisture next to each seed trap) at small spatial scale as well as the climatic conditions (mean annual temperature and rainfall in each plot) at large spatial scale. After a one-year of sampling, I counted 331,838 seeds of 323 species/morphospecies. My analyses demonstrate that the prevalence of endozoochorous plant species in the seed rain increases with temperature across elevations and with leaf area index within elevations. These results show that the prevalence of endozoochory is shaped by the interplay of both abiotic and biotic factors at large and small spatial scales.
Third, I examine the potential of seed rain to restore deforested tropical areas along an elevational gradient in southern Ecuador. For this chapter, I collected seed rain using 324 seed traps installed in 18 1-ha plots in forests (nine forest plots) and in pastures (nine deforested plots) along an elevational gradient of 2000 m. After a sampling period of three months, I collected a total of 123,039 seeds of 255 species/morphospecies from both forests and pastures along the elevational gradient. I did not find a consistent decrease in the amount and richness of seed rain between forests and pastures, but I detected a systematic change in the type of dispersed seeds, as heavier seeds and a higher proportion of endozoochorous species were found in forests compared to pastures at all elevations. This finding suggests that deforestation acts as a strong filter selecting seed traits that are vital for plant regeneration.
Understanding the role that trait-environment associations play in how plant communities regenerate today could serve as a basis for predicting changes in regeneration processes of plant communities under changing global conditions in the near future. Here, I show how informative the measurement of reproductive traits and trait environment associations are in facilitating the conservation of forest habitats and the restoration of deforested areas in the context of global change.
The lianescent genus Tinospora Miers in Singapore is revised. Four species are recognised, two of which are newly described. Tinospora krispura I.M.Turner sp. nov. is known from Christmas Island and Singapore. Tinospora singapura I.M.Turner sp. nov. is known only from Singapore. Two new lectotypifications are included, one at the second step.
Around 400 BC, pottery- and iron-producing populations immigrated into the Inner Congo Basin (ICB) and subsequently spread upstream some major tributaries of the Congo River. Until recently, their subsistence was almost completely unknown. We present an archaeobotanical study of three sites in the ICB covering parts of the Early Iron Age (ca. 400 BC-AD 650) and of the Late Iron Age (LIA) as well as subrecent times (ca. AD 1300–2000). We studied 82 flotated samples of botanical macroremains, and 68 soil phytolith samples, recovered from the terra firme sites Iyonda and Mbandaka, and the floodplain fishing camp site of Bolondo. The EIA assemblage from Iyonda yielded domesticated Cenchrus americanus (pearl millet), Vigna unguiculata (cowpea), Canarium schweinfurthii, Elaeis guineensis (oil palm), several wild plants, and parenchyma fragments tentatively attributed to Dioscorea sp. (yams). The exploitation of these plants originated in the savannas and forest-savanna ecotones of West Africa. The presence of C. americanus in LIA contexts at Bolondo and Mbandaka, dated to ca. AD 1350–1550, indicates that its cultivation is not dependent on a seasonal climate with a distinct dry season, contrary to previous views. The role of C. americanus as a staple is difficult to assess; it might have been used for special purposes, e.g. beer brewing. In spite of extensive screening, we did not detect any banana phytoliths in the EIA samples. Musa phytoliths were only present in LIA contexts after ca. AD 1400, leaving room for the possibility that the introduction and spread of Musa spp. AAB ‘Plantain’ in the ICB was a late phenomenon.
A comprehensive checklist of Habenaria from Chapada dos Veadeiros, State of Goiás, was performed alongside morphologic and molecular phylogenetic studies, revealing three new taxa endemic to this region. A total of 61 taxa (59 species and two varieties) of Habenaria are recorded for Chapada dos Veadeiros, representing a two-fold increase compared to previous lists and comprising one of the greatest diversities of the genus in Brazil. Of this total, four taxa are locally endemic. Habenaria cultellifolia, until recently known only from the type collection, was rediscovered in the region after 127 years without records and represents this species’ only known extant population. Three proposed new taxa of Habenaria (H. minuticalcar J.A.N. Bat. & Bianch. sp. nov., H. proiteana J.A.N. Bat., A.A. Vale & Bianch. sp. nov., and H. lavrensis var. xanthodactyla J.A.N. Bat. & Bianch. var. nov.) are corroborated by molecular phylogenetic analyses based on nuclear and plastid markers. They are described, illustrated, tentatively assessed as threatened, and compared to phylogenetically and morphologically related species. Since some areas of this mountain range have not yet been floristically sampled, additional taxonomic novelties and new records are still expected in the future.
Questions: Both species turnover and intraspecific trait variation can affect plant assemblage dynamics along environmental gradients. Here, we asked how community assemblage patterns in relation to species turnover and intraspecific variation differ between endemic and non-endemic species. We hypothesized that endemic species show lower intraspecific variation than non-endemic species because they tend to have high rates of in situ speciation, whereas non-endemic species are expected to have a larger gene pool and higher phenotypic plasticity.
Location: La Palma, Canary Islands.
Methods: We established 44 sampling sites along a directional gradient of precipitation, heat load, soil nitrogen, phosphorus and pH. Along this gradient, we estimated species abundances and measured three traits (plant height, leaf area and leaf thickness) on perennial endemic and non-endemic plant species. In total, we recorded traits for 1,223 plant individuals of 43 species. Subsequently, we calculated community-weighted mean traits to measure the relative contribution of species turnover, intraspecific variation and their covariation along the analysed gradient.
Results: The contribution of intraspecific variation to total variation was similar in endemic and non-endemic assemblages. For plant height, intraspecific variation explained roughly as much variation as species turnover. For leaf area and leaf thickness, intraspecific variation explained almost no variation. Species turnover effects mainly drove trait responses along the environmental gradient, but intraspecific variation was important for responses in leaf area to precipitation.
Conclusions: Despite their distinct evolutionary history, endemic and non-endemic plant assemblages show similar patterns in species turnover and intraspecific variation. Our results indicate that species turnover is the main component of trait variation in the underlying study system. However, intraspecific variation can increase individual species’ fitness in response to precipitation. Overall, our study challenges the theory that intraspecific trait variation is more important for the establishment of non-endemic species compared with endemic species.
Differential derepression of the genome of potato tuber cells can be initiated by slicing the tissue into disks. The consequence of this procedure on the cells of the wound surface is dedifferentiation and cell division followed by redifferentiation to a suberized phellem cell. The drift of glucose-, glucose-1-phosphate-, glucose-6-phosphate-, fructose-6-phosphate- and 6-phospho-gluconatelevels has been determined in the derepressed tissue. With the exception of 6-phospho-gluconate all intermediates so far investigated showed a rise in concentration after derepression.
This is interpreted as a consequence of altered enzymic activities which were estimated for phosphoglucomutase, hexokinase, phosphoglucoisomerase, gluco-6-phosphate- and 6-phosphogluconatedehydrogenase. The two dehydrogenases were activated after derepression, the activation represented a de-novo-synthesis, as was demonstrated with the inhibitors Actidione (translation) and p-Fluorophenyl-alanine (protein synthesis in general). Hexokinase and phosphoglucoisomerase were not severely affected by cutting the tissue. Phosphoglucomutase was degrated rapidly, the degradation being dependent on protein synthesis. The importance of an enhanced activity of the pentose phosphate shunt for the stressed cell is emphasized and the possibility of an alteration in the osmotic pressure within the cell and especially in the nucleus — a primary consequence of wounding — as a cause of derepression in potato tuber cells is discussed.
Positive plant–plant interactions are thought to drive vegetation patterns in harsh environments, such as semi-arid areas. According to the stress-gradient hypothesis (SGH), the role of positive interactions between species (facilitation) is expected to increase with harshness, predicting associated variation in species composition along environmental gradients. However, the relation between stress and facilitation along environmental gradients is debated. Furthermore, differentiating facilitative interactions from other underlying mechanisms, such as microtopographic heterogeneity, is not trivial. We analysed the spatial co-occurrence relationships of vascular plant species that form patchy vegetation in arid lapilli fields (tephra) from recent volcanic eruptions on La Palma, Canary Islands. Assuming a harshness gradient negatively correlated with elevation because the lower elevations are more arid and water availability is considered the most limiting resource, and that an outcome of facilitation is plants co-occurring in the same patch, from the SGH we expected a greater degree of co-occurrence at lower elevation. We tested this at both the species and the individual plant level. We analysed the species composition of 1277 shrubby vegetation patches at 64 different sampling points, ranging from the coast to around 700 m a.s.l. Patch morphology and microtopographic heterogeneity variables were also measured, to account for their potential effects on the species composition of patches. We used generalized linear models and generalized mixed-effects models to analyse species richness, number of individuals in patches and percentage of patches with positive co-occurrences, and a pairwise co-occurrence analysis combined with a graphical network analysis to reveal positive links between 13 of the species. We found that the percentage of patches with positive co-occurrences increased at higher elevations, in contrast to the predictions of the SGH, but in accordance with a refined stress-gradient hypothesis for arid sites, in which characteristics of the interacting species are incorporated.
We present a preliminary discussion about cauliflory, sexual dimorphism and biogeographic patterns in Drypetes Vahl (Putranjivaceae Endl.), focused on Africa. We also present a taxonomic treatment for two new species of cauliflorous trees of this genus from the rainforests of western Central Africa, one endemic to Gabon and known from six gatherings, D. aphanes Quintanar, D.J.Harris & Barberá sp. nov., and the other distributed in Gabon and the Republic of the Congo, D. cauta D.J.Harris, Barberá & Quintanar sp. nov., also known from another six gatherings. They are presented along with D. gabonensis Pierre ex Hutch., known from 25 gatherings made throughout western Central Africa, a species with markedly dimorphic flowers between sexes compared to the rest of the species in the genus. Specimens of these two new species have been confused with D. gabonensis due to some morphological resemblances. This treatment includes the detailed descriptions of these three species, the typification of their names, a comparative table summarizing their main morphological differences, an identification key, an illustration and information about their habitat and distribution. A provisional IUCN Red List assessment shows that D. gabonensis and D. cauta sp. nov. are ‘Vulnerable’ species, and D. aphanes sp. nov. is ‘Endangered’. After the publication of these new species, Drypetes consists of 86 species in continental Africa and the Malagasy Region and 219 species for the whole world.
Merianthera is a genus of flowering plants with up to now seven species occurring in eastern Brazil, in the states of Bahia, Espírito Santo, and Minas Gerais. It belongs to the tribe Pyramieae (Melastomataceae), and can be recognized by its shrubby or treelet habit with caducous leaves, 5-merous flowers with a strongly zygomorphic androecium, the latter with dimorphic stamens bearing complex dorsal connective appendages, as well as an inferior ovary and capsular fruits. We describe here a new species of Merianthera from two collections and a photographic record, all from the same locality, an inselberg in the Municipality of Jacinto, in northeastern Minas Gerais. Its candelabriform habit, with a fistulose stem, and solitary, axillary or cauliflorous flowers are only shared with M. burlemarxii. However, M. calyptrata R.Goldenb., Bochorny & Fraga sp. nov. has at least three characters that are absent in M. burlemarxii and all other species in the genus: the total absence of both a peduncle and bracteoles, the calyptrate calyx and the fruits developing from inferior ovaries and dehiscing through longitudinal slits. The first character appears to be unknown in other species in the family.
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 Mb and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb of the genome in which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome- wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
We provide a floristic account for the Begoniaceae of Peru. The family is represented in Peru by 76 species, which are all members of the genus Begonia and represent eighteen sections. Twelve new species are described: B. condorensis Jara & Moonlight sp. nov., B. deltoides Moonlight sp. nov., B. huancabambae Moonlight sp. nov., B. imbrexiformis Moonlight sp. nov., B. longinqua Moonlight sp. nov., B. longitepala Moonlight sp. nov., B. nunezii Moonlight sp. nov., B. occultata J.P.Allen & Moonlight sp. nov., B. pedemontana Moonlight sp. nov., B. serratistipula Moonlight sp. nov., B. vargasii Moonlight sp. nov. and B. yuracyacuensis Moonlight sp. nov. We also provide four new records for the country: B. andina Rusby, B. brandbygeana L.B.Sm. & Wassh., B. neoharlingii L.B.Sm. & Wassh. and B. unilateralis Rusby. We provide an identification key to all species. The ecology, distribution, and conservation status of all Peruvian Begonia species are discussed, including provisional IUCN threat assessments. Most species are illustrated by either historical illustrations, contemporary photographic plates, or line drawings. Twenty-six names are newly synonymised including fifteen previously accepted species, and we designate eighty-three lectotypes, four neotypes, and four epitypes.
The change in allele frequencies within a population over time represents a fundamental process of evolution. By monitoring allele frequencies, we can analyze the effects of natural selection and genetic drift on populations. To efficiently track time-resolved genetic change, large experimental or wild populations can be sequenced as pools of individuals sampled over time using high-throughput genome sequencing (called the Evolve & Resequence approach, E&R). Here, we present a set of experiments using hundreds of natural genotypes of the model plant Arabidopsis thaliana to showcase the power of this approach to study rapid evolution at large scale. First, we validate that sequencing DNA directly extracted from pools of flowers from multiple plants -- organs that are relatively consistent in size and easy to sample -- produces comparable results to other, more expensive state-of-the-art approaches such as sampling and sequencing of individual leaves. Sequencing pools of flowers from 25-50 individuals at ∼40X coverage recovers genome-wide frequencies in diverse populations with accuracy r > 0.95. Secondly, to enable analyses of evolutionary adaptation using E&R approaches of plants in highly replicated environments, we provide open source tools that streamline sequencing data curation and calculate various population genetic statistics two orders of magnitude faster than current software. To directly demonstrate the usefulness of our method, we conducted a two-year outdoor evolution experiment with A. thaliana to show signals of rapid evolution in multiple genomic regions. We demonstrate how these laboratory and computational Pool-seq-based methods can be scaled to study hundreds of populations across many climates.
In search for practical silvicultural management tools to identify alternative tree species for predicted Central European climate conditions, a cross-species survey with five evergreen, semi-evergreen, and deciduous Quercus taxa with contrasting morphological leaf traits was performed. Fast chlorophyll fluorescence induction of PSII and relative leaf chlorophyll contents were performed to assess the overall plant vitality at any point in time during two complete vegetation periods in consecutive years (2012 and 2013). Maximum photochemical efficiency of PSII and the performance index on absorption base showed a very conservative relationship to each other and a similar intra-annual progress in all deciduous species, but with a different speed of increase and decrease during leaf development and senescence and thus a different length of vegetation period. The intra-annual variability of OJIP and chlorophyll content parameters is considered with respect to the practicability of measurements in the field for management purposes.
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.