Parallel adaptation results from the independent evolution of similar traits between closely related lineages and allows us to test to what extent evolution is repeatable. Similar gene expression changes are often detected but the identity of genes shaped by parallel selection and the causes of expression parallelism remain largely unknown. By comparing genomes and transcriptomes of four distinct foothill-alpine population pairs across four treatments, we addressed the genetic underpinnings, plasticity and functional consequences of gene expression parallelism in alpine adaptation. Seeds of eight populations of Arabidopsis arenosa were raised under four treatments that differed in temperature and irradiance, factors varying strongly with elevation. Parallelism in differential gene expression between the foothill and alpine ecotypes was quantified by RNA-seq in leaves of young plants. By manipulating temperature and irradiance, we also tested for parallelism in plasticity (i.e., gene-environment interaction, GEI). In spite of global non-parallel patterns transcriptome wide, we found significant parallelism in gene expression at the level of individual loci with an over-representation of genes involved in biotic stress response. In addition, we demonstrated significant parallelism in GEI, indicating a shared differential response of the originally foothill versus alpine populations to environmental variation across mountain regions. A fraction of genes showing expression parallelism also encompassed parallel outliers for genomic differentiation, with greater enrichment of such variants in cis-regulatory elements in some mountain regions. In summary, our results suggest frequent evolutionary repeatability in gene expression changes associated with the colonization of a challenging environment that combines constitutive expression differences and plastic interaction with the surrounding environment.

• Klíčová slova
• Arabidopsis arenosa, alpine adaptation, common garden experiment, gene expression, gene-environment interaction, parallel evolution, plasticity,
• MeSH
• Arabidopsis genetika   metabolismus   MeSH
• ekosystém MeSH
• ekotyp MeSH
• fyziologický stres genetika   fyziologie   MeSH
• sekvenování transkriptomu metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

A novel algorithm for implementing a general type of multireference coupled-cluster (MRCC) theory based on the Jeziorski-Monkhorst exponential ansatz [Jeziorski, B.; Monkhorst, H. J. Phys. Rev. A1981, 24, 1668] is introduced. The proposed algorithm utilizes processor groups to calculate the equations for the MRCC amplitudes. In the basic formulation, each processor group constructs the equations related to a specific subset of references. By flexible choice of processor groups and subset of reference-specific sufficiency conditions designated to a given group, one can ensure optimum utilization of available computing resources. The performance of this algorithm is illustrated on the examples of the Brillouin-Wigner and Mukherjee MRCC methods with singles and doubles (BW-MRCCSD and Mk-MRCCSD). A significant improvement in scalability and in reduction of time to solution is reported with respect to recently reported parallel implementation of the BW-MRCCSD formalism [Brabec, J.; van Dam, H. J. J.; Kowalski, K.; Pittner, J. Chem. Phys. Lett.2011, 514, 347].

• Publikační typ
• časopisecké články MeSH

Parallel evolution provides powerful natural experiments for studying repeatability of evolution and genomic basis of adaptation. Well-documented examples from plants are, however, still rare, as are inquiries of mechanisms driving convergence in some traits while divergence in others. Arabidopsis arenosa, a predominantly foothill species with scattered morphologically distinct alpine occurrences is a promising candidate. Yet, the hypothesis of parallelism remained untested. We sampled foothill and alpine populations in all regions known to harbor the alpine ecotype and used SNP genotyping to test for repeated alpine colonization. Then, we combined field surveys and a common garden experiment to quantify phenotypic parallelism. Genetic clustering by region but not elevation and coalescent simulations demonstrated parallel origin of alpine ecotype in four mountain regions. Alpine populations exhibited parallelism in height and floral traits which persisted after two generations in cultivation. In contrast, leaf traits were distinctive only in certain region(s), reflecting a mixture of plasticity and genetically determined non-parallelism. We demonstrate varying degrees and causes of parallelism and non-parallelism across populations and traits within a plant species. Parallel divergence along a sharp elevation gradient makes A. arenosa a promising candidate for studying genomic basis of adaptation.

• Klíčová slova
• Arabidopsis, adaptation, alpine environments, convergence, parallel evolution, phenotypic parallelism,
• Publikační typ
• časopisecké články MeSH

Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species, which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches, we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores, and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning ∼0.02 to 18 My of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection on the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species, and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.

• Klíčová slova
• Arabidopsis, alpine adaptation, evolution, genomics, parallelism,
• MeSH
• anotace sekvence MeSH
• Arabidopsis klasifikace   genetika   metabolismus   účinky záření   MeSH
• biologická evoluce * MeSH
• býložravci fyziologie   MeSH
• fyziologická adaptace genetika   MeSH
• fyziologický stres MeSH
• genetická variace * MeSH
• genetický drift MeSH
• genom rostlinný * MeSH
• genová introgrese MeSH
• genová ontologie MeSH
• ionizující záření MeSH
• modely genetické MeSH
• nízká teplota MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• rostlinné proteiny MeSH

BACKGROUND: Plant genomes can respond rapidly to environmental changes and transposable elements (TEs) arise as important drivers contributing to genome dynamics. Although some elements were reported to be induced by various abiotic or biotic factors, there is a lack of general understanding on how environment influences the activity and diversity of TEs. Here, we combined common garden experiment with short-read sequencing to investigate genomic abundance and expression of 2245 consensus TE sequences (containing retrotransposons and DNA transposons) in an alpine environment in Arabidopsis arenosa. To disentangle general trends from local differentiation, we leveraged four foothill-alpine population pairs from different mountain regions. Seeds of each of the eight populations were raised under four treatments that differed in temperature and irradiance, two factors varying with elevation. RNA-seq analysis was performed on leaves of young plants to test for the effect of elevation and subsequently of temperature and irradiance on expression of TE sequences. RESULTS: Genomic abundance of the 2245 consensus TE sequences varied greatly between the mountain regions in line with neutral divergence among the regions, representing distinct genetic lineages of A. arenosa. Accounting for intraspecific variation in abundance, we found consistent transcriptomic response for some TE sequences across the different pairs of foothill-alpine populations suggesting parallelism in TE expression. In particular expression of retrotransposon LTR Copia (e.g. Ivana and Ale clades) and LTR Gypsy (e.g. Athila and CRM clades) but also non-LTR LINE or DNA transposon TIR MuDR consistently varied with elevation of origin. TE sequences responding specifically to temperature and irradiance belonged to the same classes as well as additional TE clades containing potentially stress-responsive elements (e.g. LTR Copia Sire and Tar, LTR Gypsy Reina). CONCLUSIONS: Our study demonstrated that the A. arenosa genome harbours a considerable diversity of TE sequences whose abundance and expression response varies across its native range. Some TE clades may contain transcriptionally active elements responding to a natural environmental gradient. This may further contribute to genetic variation between populations and may ultimately provide new regulatory mechanisms to face environmental challenges.

• Klíčová slova
• Alpine environment, Arabidopsis arenosa, Common garden experiment, Parallelism, RNA-seq, Transposable elements,
• Publikační typ
• časopisecké články MeSH

• MeSH
• státní lékařství * MeSH
• zákonodárství lékařské * MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Československo MeSH
• SSSR MeSH

UNLABELLED: By invention of his forceps in 1950´s W. B. Shute introduces a new principle of parallelism, which is characterised by higher safety for the foetus. The main advantage is that the force acting on the head can be exactly controlled. Authors explain design and use of the instrument which is, by it´s indications and versatility, similar to Kjelland´s forceps. Literary review is cited and brief biografy of inventor is added. Where Shute´s instrument is available, priority shoud be given to it, as parallel forceps exceeds the Kjelland´s one by it´s safety for the foetus and moreover is easier to use and to learn too. KEYWORDS: parallel forceps, W. B Shute, obstetrical operations, obstetrical forceps.

• Publikační typ
• anglický abstrakt MeSH
• časopisecké články MeSH

Parallel evolution is common in nature and provides one of the most compelling examples of rapid environmental adaptation. In contrast to the recent burst of studies addressing genomic basis of parallel evolution, integrative studies linking genomic and phenotypic parallelism are scarce. Edaphic islands of toxic serpentine soils provide ideal systems for studying rapid parallel adaptation in plants, imposing strong, spatially replicated selection on recently diverged populations. We leveraged threefold independent serpentine adaptation of Arabidopsis arenosa and combined reciprocal transplants, ion uptake phenotyping, and available genome-wide polymorphisms to test if parallelism is manifested to a similar extent at both genomic and phenotypic levels. We found pervasive phenotypic parallelism in functional traits yet with varying magnitude of fitness differences that was congruent with neutral genetic differentiation between populations. Limited costs of serpentine adaptation suggest absence of soil-driven trade-offs. On the other hand, the genomic parallelism at the gene level was significant, although relatively minor. Therefore, the similarly modified phenotypes, for example, of ion uptake arose possibly by selection on different loci in similar functional pathways. In summary, we bring evidence for the important role of genetic redundancy in rapid adaptation involving traits with polygenic architecture.

• Klíčová slova
• Adaptation, Arabidopsis, genetic redundancy, natural selection, parallel evolution, reciprocal transplant,
• MeSH
• Arabidopsis * genetika   MeSH
• fenotyp MeSH
• fyziologická adaptace genetika   MeSH
• genomika MeSH
• půda MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• půda MeSH

BACKGROUND: Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. RESULTS: We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. CONCLUSIONS: The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.

• Klíčová slova
• Assembly, Metagenomics, NGS analysis, Parallel processing, Viral dark matter, Viromes, Virus, Visualization,
• MeSH
• genetická variace MeSH
• genomika metody   MeSH
• internet * MeSH
• lidé MeSH
• mikrobiota genetika   MeSH
• software * MeSH
• viry genetika   MeSH
• vysoce účinné nukleotidové sekvenování * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discover significant parallelism in candidate genes involved in ion homeostasis. We further model parallel selection and infer repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms.

• MeSH
• alely * MeSH
• Arabidopsis účinky léků   genetika   MeSH
• fyziologická adaptace účinky léků   genetika   MeSH
• genom rostlinný * MeSH
• jednonukleotidový polymorfismus MeSH
• mutace MeSH
• polyploidie * MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• půda chemie   MeSH
• sekologanin-tryptaminové alkaloidy metabolismus   MeSH
• vápníkové kanály metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny huseníčku MeSH
• půda MeSH
• sekologanin-tryptaminové alkaloidy MeSH
• serpentine (alkaloid) MeSH Prohlížeč
• TPC1 protein, Arabidopsis MeSH Prohlížeč
• vápníkové kanály MeSH