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1,009 results for “clonal”
Single-cell repertoire and transcriptome sequencing reveals clonally expanded and transcriptionally distinct lymphocytes in aged CNS
<p>Single-cell repertoire and transcriptome sequencing reveals clonally expanded and transcriptionally distinct lymphocytes in aged CNS. Gene expression and immune receptor repertoire sequencing was performing for both B and T cells. This dataset contains the VDJ sequencing information for the four samples. Each B cell and T cell library was sequenced across four lanes. </p> <p> </p> <p>Files with _WT_ in their name correspond to the young (4-6 week B6 mice) </p> <p>Files with _12_ in their name before the BDJ or VDJ text correspond to the 12-month-old cohort.</p> <p>Files with _18_ in their name before the BDJ or VDJ text correspond to the 18-month-old cohort in which four brains were pooled.</p> <p>Files with 4_18_ in their name before the BDJ or VDJ text correspond to the 18-month-old mouse that was processed and sequenced alone. </p> <p> </p> <p>The L001 - L004 in the file names indicates the sequencing lane. Samples with BDJ correspond to the B cell repertoire library (B cell VDJ). Samples with TDJ correspond to the T cell repertoire library (T cell VDJ). </p>
Microsatellite genotypes and associated data for: The contribution of clonality to population genetic structure in the sea anemone Diadumene lineata
<p>Ecological and evolutionary processes differ depending on how genetic diversity is organized in space. For clonal organisms, the organization of both genetic and genotypic diversity can influence the fitness effects of competition, the mating system, and reproductive mode, which are key drivers of life cycle evolution. Understanding how individual reproductive behavior contributes to population genetic structure is essential for disentangling these forces, particularly in species with complex and plastic life cycles. The widespread sea anemone <i>Diadumene lineata</i> exhibits temperature-dependent fission which contributes to predictable variation in clonal rate along the Atlantic coast of the United States, part of its non-native range. Because warmer conditions lead to higher rates of clonality, we expected to find lower genotypic and genetic diversity in lower versus higher latitude populations. We developed primers for 11 microsatellite loci and genotyped 207 anemones collected from 8 sites ranging from Florida to Massachusetts. We found clonal influence at all sites, and as predicted, the largest clones were found at lower latitude sites. We also found genetic signatures of sex in the parts of the range where gametogenesis is most common. Evidence of sex outside the native range is novel for this species and provides insights into the dynamics of this successful invader. Our findings also illustrate challenges that partially clonal taxa pose for eco-evolutionary studies, such as difficulty sampling statistically robust numbers of genets and interpretating common population genetic metrics. For example, we found high among-locus variation in F<i><sub>is, </sub></i>which makes the meaning of mean multilocus F<i><sub>is</sub></i> unclear.</p>
Input data of manuscript "CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"
<p>This is the directory containing input data necessary to reproduce analyses presented in the manuscript:</p> <blockquote> <p><strong>CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells</strong><br> Shadi Darvish Shafighi, Szymon M Kiełbasa, Julieta Sepúlveda Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, Roberta Menafra, Susan Kloet, Hendrik Veelken, Cornelis A.M. van Bergen, Ewa Szczurek</p> </blockquote>
Data from: Non-clonal coloniality: genetically chimeric colonies through fusion of sexually produced polyps in the hydrozoan Ectopleura larynx
Hydrozoans typically develop colonies through asexual budding of polyps. Although colonies of Ectopleura are similar to other hydrozoans in that they consist of multiple polyps physically connected through continuous epithelia and shared gastrovascular cavity, Ectopleura larynx does not asexually bud polyps indeterminately. Instead, after an initial phase of limited budding in a young colony, E. larynx achieves its large colony size through the aggregation and fusion of sexually (non-clonally) produced polyps. The apparent chimerism within a physiologically integrated colony presents a potential source of conflict between distinct genetic lineages, which may vary in their ability to access the germline. In order to determine the extent to which the potential for genetic conflict exists, we characterized the types of genetic relationships between polyps within colonies, using a RAD-Seq approach. Our results indicate that E. larynx colonies are indeed comprised of polyps that are clones and sexually reproduced siblings and offspring, consistent with their life history. In addition, we found that colonies also contain polyps that are genetically unrelated, and that estimates of genome-wide relatedness suggests a potential for conflict within a colony. Taken together, our data suggests that there are distinct categories of relationships in colonies of E. larynx, likely achieved though a range of processes including budding, regeneration and fusion of progeny and unrelated polyps, with the possibility for a genetic conflict resolution mechanism. Together these processes contribute to the re-evolution of the ecologically important trait of coloniality in E. larynx.
Data from: Clonal evolution and genome stability in a 2,500-year-old fungal individual
Individuals of the basidiomycete fungus Armillaria are well-known for their ability to spread from woody substrate to substrate on the forest floor through the growth of rhizomoprhs. Here we made 248 collections of A. gallica in one locality in Michigan's Upper Peninsula. To identify individuals, we genotyped collections with molecular markers and somatic compatibility testing. We found several different individuals in proximity to one another, but one genetic individual stood out as exceptionally large, covering hundreds of tree root systems over approximate 75 hectares of forest floor. Based on observed growth rates of the fungus, we estimate the minimum age of the large individual as 2,500 years. With whole-genome sequencing and variant discovery, we also found that mutation had occurred within the somatic cells of the individual, reflecting its historical pattern of growth from a single point. The overall rate of mutation over the 90 mb genome, however, was extremely low. This same individual was first discovered in the late 1980s, but its full spatial extent and internal mutation dynamic was unkown at that time. The large individual of A. gallica has been remarkably resistant to genomic change as it has persisted in place.
Patterns of pollen dispersal and mating in a population of the clonal plant Sagittaria latifolia
<p>1) Increased plant size is generally expected to have negative consequences for mating by increasing pollen transfer between flowers of the same plant. Such geitonogamous self-pollination would then reduce sexual fitness through both female and male function. However, recent theoretical work has indicated that when plants grow clonally, the outward expansion of plants caused by clonal growth might have positive effects on siring without substantially increasing rates of self-pollination.</p> <p>2) We investigated patterns of pollen dispersal, selfing, and siring in a monoecious population of the clonal plant <em>Sagittaria latifolia</em>, in which clones varied in size and the extent of intermingling with other clones. A spatially-explicit statistical model based on the inferred pollen-dispersal kernel was constructed to examine the mechanisms underlying observed mating patterns.</p> <p>3) Pollen dispersal typically occurred over distances that exceeded the spatial extent of clones. There was a positive association between clone size (measured as the number of ramets per genet) and the likelihood that clones were intermingled with the shoots of other clones. Together, these patterns of pollen dispersal and clonal intermingling resulted in a weak positive association between clone size and selfing rates and a strong positive association between clone size and outcross siring success. These patterns were replicated in the spatially-explicit model, indicating that the intermingling of clones is an important determinant of mating patterns in this population.</p> <p>4) Synthesis. Our study provides the first examination of the pollen dispersal kernel for a clonal plant. It is the first study providing empirical support for model predictions that potentially negative effects of increased selfing in large clones might be offset by increased siring success. This implies that the negative consequences of becoming large do not necessarily apply to clonal plants.</p>
Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'
<p>Authors</p> <p>Zhian N. Kamvar, Jonah C. Brooks, and Niklaus J. Grünwald</p>
Clonal relationship of ESBL-producing Salmonella strains from humans and poultry in North-Eastern Algeria
<p>BVET-D-16-00240</p> <p>A study was conducted to determine antibiotic resistance levels and patterns, and to assess the relationship of avian drug-resistant Salmonella to human clinical isolates in Algéria.</p>
Exome-wide association analysis (ExWAS) of clonal haematopoiesis in 136,401 Admixed Americans and 416,118 Europeans
<p>We performed exome-wide association analysis (ExWAS) of germline genetic variants identified from whole-exome sequencing (WES) to identify novel inherited genetic determinants of clonal haematopoiesis (CH). Here, we provide the summary statistics from ExWAS CH performed on Admixed Americans recruited to the Mexico City Prospective Study (MCPS), Europeans recruited to the United Kingdom Biobank (UKB), and cross-ancestry meta-analysis of Admixed Americans and Europeans. Analyses was performed with REGENIE software (Firth's logistic regression), Fisher's exact test, and METAL software (inverse variance-weighted average method to derive effect size and <em>P</em>-value method to derive P value), respectively.</p> <p> </p> <p>In version 1 of this repository, UKB variants (*_UKB.tsv) with minor allele frequency (MAF) 1% or more were uploaded. In version 2, this is now rectified so that rare variants with MAF of 0.1% or more were uploaded. This threshold now matches the MCPS (*_MCPS.tsv) and UKB-MCPS meta-analysis summary statistics (*_MCPS-UKB_meta-analysis.tsv)</p>
NextClone and CloneDetective: An Integrated Nextflow Pipeline and R Package for Clonal Barcode Extraction and Quantification
<p>Raw FASTQ files for the DNA-seq data required to replicate the analyses presented at: https://phipsonlab.github.io/NextClone-analysis/.</p>
Sustained liver HBsAg loss and clonal T and B cell expansion upon therapeutic DNA vaccination require low HBsAg levels
<p>C57BL/6 mice samples transduced with AAV-HBV, followed by treatment with siRNA+TxTv, control siRNA+TxVx or control siRNA+empty plasmid. 10x genomics (VDJ) was performed in liver IHIC.</p><p>An rds object with the raw and normalised counts, the annotations is available.</p>
Data from: Rapid evolution of flower phenology and clonality in restored populations of multiple grassland species
<ol> <li>Restoration of terrestrial ecosystems often requires re-introduction of plants. In restored sites, the plants often face environments that differ from those of natural populations. This can affect plant traits, reduce performance and impose novel selection pressures. As a response, restored populations might rapidly evolve and adapt to the novel conditions. This may enhance population survival and contribute to restoration success but has been rarely tested so far.</li> <li>Here, we focused on populations of three grassland species restored 20 years ago (<em>Galium wirtgenii, Inula salicina </em>and<em> Centaurea jacea</em>) by the transfer of green hay, and compared them with donor populations that were the source of the hay. We measured plants both in situ and in a common garden under control and three stress conditions.</li> <li>In-situ, plants in restored sites flowered earlier than plants in donor sites in two out of the three species. In the common garden, plants from the restored populations flowered earlier (in <em>Galium</em>) or showed increased plasticity of clonal propagation in response to clipping (in <em>Inula</em>). Both these traits suggest rapid adaptation to the contrasting mowing regimes in restored in comparison to the donor sites. In <em>Centaurea</em>, we detected no differentiation, neither in situ nor in the common garden.</li> <li> <em>Synthesis and applications</em>: Grassland plants introduced into degraded habitats within the framework of ecological restoration may quite commonly evolve in response to novel selection pressures at restored sites. This rapid evolution likely increases the plant's adaptation to the new conditions of the restored grassland and thus enhances the likelihood of survival of the population and ultimately restoration success. While most practitioners do not consider evolution to be part of restoration, our finding highlights that restored populations of grassland species can be systems with considerable eco-evolutionary dynamics.</li> </ol>
Clonal hematopoiesis GWAS summary statistics
<p>Datasets linked to the pre-print titled, "Genome-wide analyses of 200,453 individuals yields new insights into the causes and consequences of clonal hematopoiesis", which is available at <a href="https://doi.org/10.1101/2022.01.06.22268846">https://doi.org/10.1101/2022.01.06.22268846</a></p> <p>To estimate odds ratios from BOLT-LMM betas and standard errors please use the formula provided <a href="https://alkesgroup.broadinstitute.org/BOLT-LMM/BOLT-LMM_manual.html#x1-5500010.2">here</a>. The formula requires the number of controls (= 173,918 for each of the five GWAS) and the numbers of cases (10,203 overall-CH, 5,185 DNMT3A-CH, 2,042 TET2-CH, 4,049 large-CH, and 6,154 small-CH).</p>
Directed endozoochorous dispersal by scavengers facilitate sexual reproduction in otherwise clonal plants at cadaver sites
<ol> <li>The regeneration niche of many plant species involves spatially and temporally unpredictable disturbances, called recruitment windows of opportunity. However, even species with clear dispersal adaptations such as fleshy berries may not successfully reach such elusive regeneration microsites. Ericaceous, berry-producing species in the northern hemisphere demonstrate this dispersal limitation. They are said to display a reproductive paradox owing to their lack of regeneration in apparently suitable microsites despite considerable investment in producing large quantities of berries.</li> <li>Cadavers generate vegetation-denuded and nutrient-rich disturbances termed cadaver decomposition islands. Cadavers attract facultative scavengers with considerable capacity for endozoochorous seed dispersal. We hypothesize that cadaver decomposition islands facilitate recruitment in berry-producing ericaceous species due to endozoochorous dispersal directed towards favorable microsites with low competition.</li> <li>We examined seedling establishment within a permanent, semi-regular 10 × 10 m grid across an ungulate mass die-off on the Hardangervidda plateau in southeastern Norway. Competing models regarding the relative importance of factors governing recruitment were evaluated, specifically cadaver location (elevated seed rain) and microsite conditions (competition).</li> <li>We found that cadaver decomposition islands did facilitate seedling establishment, as cadaver density was the best predictor of seedling distribution. Other important factors governing seedling establishment such as percentage cover of soil and vascular plants alone were inadequate to explain seedling establishment.</li> <li> <i>Synthesis:</i> This study provides a novel understanding of sexual reproduction in species with cryptic generative reproduction. The directed nature of endozoochorous dispersal combined with long-distance dispersal abilities of medium to large vertebrate scavengers towards cadavers allows plants to exploit the advantageous but ephemeral resource provided by cadaver decomposition islands.</li> </ol>
Extensive polyploid clonality was a successful strategy for seagrass to expand into a newly submerged environment
<p>Polyploidy has the potential to allow organisms to outcompete their diploid progenitor(s) and occupy new environments. Shark Bay, Western Australia, is a World Heritage Area dominated by temperate seagrass meadows including Poseidon's ribbon weed, Posidonia australis. This seagrass is at the northern extent of its natural geographic range and experiences extreme temperatures and salinities. Our genomic and cytogenetic assessments of ten meadows identified geographically restricted, diploid clones (2n = 20) in a single location, and widespread, high heterozygosity, polyploid clones (2n = 40) in all other locations. A single polyploid clone spanned at least 180 km, making it the largest known example of a clone in any environment on earth. Whole genome duplication through polyploidy, combined with clonality, may have provided the mechanism for P. australis to expand into new habitats and adapt to new environments that became increasingly stressful for its diploid progenitor(s). The new polyploid clones likely formed in the shallow waters after inundation of Shark Bay < 8,500 years ago and subsequently expanded via vegetative growth into newly submerged habitats.</p>
Polyploidization-enhanced effective clonal reproduction endows the successful invasion of Solidago canadensis
Clonality and ploidy levels are positively associated with plant invasiveness. However, there is still no consensus on whether polyploidization can promote the invasion of alien plants by enhancing clonality. Our recent long-term community succession study found that the more vigorous clone of introduced polyploid Solidago canadensis succeeded into mono-dominant community, which seems to be a positive correlationship between polyploidization and clonal reproduction. However, how polyploidization improves the clonal reproduction of S. canadensis remains unknown. Here, we compared clonal growth ability among diploids and polyploids of S. canadensis from native and introduced ranges in a common garden. Results showed that the rhizomes of S. canadensis originated from axillary buds of dense nodes at the basal stem of seedling and then produced into clonal ramets. Diploids had denser nodes and more buds, developed more rhizomes per unit mass and produced more clonal propagules at the early growth stage compared with polyploids. However, the number of juvenile and secondary rhizomes, as well as the diameter and length of rhizomes in polyploid populations was significant higher than those of diploids, and those clonal traits in introduced polyploids were significant higher than in native polyploids. Moreover, a phalanx growth form was observed in native and introduced diploid populations, which allocated about 3% and 5% of the total biomass to rhizomes, respectively, resulting in short and weak rhizomes. However, native and introduced polyploids allocated about 35% and 40%, respectively, of the total biomass to rhizomes, resulting in long and strong rhizomes, which were guerrilla growth forms. This study firstly shows that polyploidization enhanced the effective clonal reproduction of S. canadensis through pre-adaptation and rapid post-adaptation evolution, and consequently contributed to its successful invasion.
Supporting data and code for: Host plant and insecticides shape the evolution of genetic and clonal diversity in a major aphid crop pest
<p>This is the first release of the final data and code for the article accepted for publication in <em>Evolutionary Applications</em> journal. It contains the necessary scripts to produce most of the analyses and figures of the manuscript. All the necessary data can be found in the 'data' folder.</p>
Autopolyploid establishment depends on life history strategy and the mating outcomes of clonal architecture
<p><span>Polyploidy is a significant component in the evolution of many taxa, particularly plant groups. However, new polyploids face substantial fitness disadvantages due to a lack of same-cytotype mates, and the factors promoting or preventing polyploid establishment in natural populations are often unclear. We develop spatially explicit agent-based simulation models to test the hypothesis that a perennial life history and clonal propagation facilitate the early stages of polyploid establishment and persistence. Our models show that polyploids are more likely to establish when they have longer lifespans than diploids, especially when self-fertilization rates are high. Polyploids that combine sexual and clonal reproduction can establish across a wide range of life histories, but their success is moderated by clonal strategy. By tracking individuals and mating events we reveal that clonal architecture has a substantial impact on the spatial structure of the mixed diploid-polyploid population during polyploid establishment: altering patterns of mating within or between cytotypes via geitonogamous self-fertilization, the mechanisms through which polyploid establishment proceeds, and the final composition of the polyploid population. Overall, our findings provide novel insight into the role of clonal structure in modulating the complex relationship between polyploidy, perenniality, and clonality; and offer testable predictions for future empirical work. </span></p>
Clonal functional traits favor the invasive success of alien plants into native communities
<p><span>Functional traits are frequently proposed to determine the invasiveness of alien species. However, few empirical studies have directly manipulated functional traits and tested their importance in the invasion success of alien species into native plant communities, particularly under global change. We manipulated clonal integration (a key clonal functional trait) of four alien clonal plants by severing inter-ramet connections or keeping them intact, and simulated their invasion into native plant communities with two levels of species diversity, population density and nutrient availability</span><span>. High community diversity and density impeded the invasion success of the alien clonal plants. Clonal integration of the alien plants promoted their invasion success, particularly in the low-density communities associated with low species diversity or nutrient addition, which resulted in a negative correlation between performance of alien plants and native communities, as expected under global change. Thus, clonal integration can favor the invasion success of alien clonal plants into degraded resident communities with </span><span>a high degree of disturbance</span><span> and eutrophication. Our findings confirm the role of clonal</span><span> functional traits in facilitating alien plant invasions into native plant communities, and suggest that </span><span>clonal functional traits should be considered to efficiently restore degraded communities heavily invaded by alien clonal plants.</span></p>
Pollinator data from: Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs
<p>In agricultural landscapes, forest herbs live in small, spatially isolated forest patches. For their long-term survival, their populations depend on animals as genetic linkers that provide pollen- or seed-mediated gene flow among different forest patches. However, whether insect pollinators serve as genetic linkers among spatially isolated forest herb populations in agricultural landscapes remains to be shown. Here, we used population genetic methods to analyze: (A) the genetic diversity and genetic differentiation of populations of two common, slow-colonizing temperate forest herb species (<em>Polygonatum</em> <em>multiflorum</em> (L.) All. and <em>Anemone</em> <em>nemorosa</em> L.) in spatially isolated populations within three agricultural landscapes in Germany and Sweden and (B) the movement activity of their most relevant associated pollinator species, i.e., the bumblebee <em>Bombus</em> <em>pascuorum</em> (Scopoli, 1763) and the hoverfly <em>Melanostoma</em> <em>scalare</em> (Fabricus, 1794), respectively, which differ in their mobility. We tested whether the indicated pollinator movement activity affected the genetic diversity and genetic differentiation of the forest herb populations. Bumblebee movement indicators that solely indicated movement activity between the forest patches affected both genetic diversity and genetic differentiation of the associated forest herb <em>P</em>. <em>multiflorum</em> in a way that can be explained by pollen-mediated gene flow among the forest herb populations. In contrast, movement indicators reflecting the total movement activity at a forest patch (including within-forest patch movement activity) showed unexpected effects for both plant-pollinator pairs that might be explained by accelerated genetic drift due to enhanced sexual reproduction. Our integrated approach revealed that bumblebees serve as genetic linkers of associated forest herb populations, even if they are more than 2 km apart from each other. No such evidence was found for the forest-associated hoverfly species which showed significant genetic differentiation among forest patches itself. Our approach also indicated that a higher within-forest patch movement activity of both pollinator species might enhance sexual recruitment and thus diminishes the temporal buffer that clonal growth provides against habitat fragmentation effects.</p>
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