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107 results for “ploidy”
Data and code from: Effects of ploidy on relationship between outbreeding response and fitness in a plant selfing species
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Data for: Interactions between breeding system and ploidy affect niche breadth in Solanum
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Data from: Competition among native and invasive Phragmites australis populations: an experimental test of the effects of invasion status, genome size, and ploidy level.
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Data from: Interaction among ploidy, breeding system, and lineage diversification
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Data from: Host-induced genome instability rapidly generates phenotypic variation across Candida albicans strains and ploidy states
<p>Candida albicans is an opportunistic fungal pathogen of humans that is typically diploid yet has a highly labile genome tolerant of large-scale perturbations including chromosomal aneuploidy and loss-of-heterozygosity events. The ability to rapidly generate genetic variation is crucial for C. albicans to adapt to changing or stressful environments, like those encountered in the host. Genetic variation occurs via stress-induced mutagenesis or can be generated through its parasexual cycle, in which tetraploids arise via diploid mating or stress-induced mitotic defects and undergo nonmeiotic ploidy reduction. However, it remains largely unknown how genetic background contributes to C. albicans genome instability in vitro or in the host environment. Here, we tested how genetic background, ploidy, and the host environment impacts C. albicans genome stability. We found that host association induced both loss-of-heterozygosity events and genome size changes, regardless of genetic background or ploidy. However, the magnitude and types of genome changes varied across C. albicans strain background and ploidy state. We then assessed if host-induced genomic changes resulted in fitness consequences on growth rate and nonlethal virulence phenotypes and found that many host-derived isolates significantly changed relative to their parental strain. Interestingly, diploid host-associated C. albicans predominantly decreased host reproductive fitness, whereas tetraploid host-associated C. albicans increased host reproductive fitness. Together, these results are important for understanding how host-induced genomic changes in C. albicans alter its relationship with the host.</p> <p>IMPORTANCE Candida albicans is an opportunistic fungal pathogen of humans. The ability to generate genetic variation is essential for adaptation and is a strategy that C. albicans and other fungal pathogens use to change their genome size. Stressful environments, including the host, induce C. albicans genome instability. Here, we investigated how C. albicans genetic background and ploidy state impact genome instability, both in vitro and in a host environment. We show that the host environment induces genome instability, but the magnitude depends on C. albicans genetic background. Furthermore, we show that tetraploid C. albicans is highly unstable in host environments and rapidly reduces in genome size. These reductions in genome size often resulted in reduced virulence. In contrast, diploid C. albicans displayed modest host-induced genome size changes, yet these frequently resulted in increased virulence. Such studies are essential for understanding how opportunistic pathogens respond and potentially adapt to the host environment.</p> <p> </p>
Spatial, climate and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra
<p>This data set was used to assess the climate resilience of <i>Themeda triandra</i>, a foundational species and the most widespread plant in Australia, by assessing the relative contributions of spatial, environmental, and ploidy factors to contemporary genomic variation. Reduced-representation genome sequencing on 472 samples from 52 locations was used to test how the distribution of genomic variation, including ploidy polymorphism, supports adaptation to hotter and drier climates.</p>
Data from: Ploidy and domestication are associated with genome size variation in Palms
PREMISE OF THE STUDY: The genome size of a species (C-value) is associated with growth, development and adaptation to environmental changes. Angiosperm C-values range 1200-fold and frequently vary within species, although little is known about the impacts of domestication on genome size. Genome size variation among related species of palms is of evolutionary significance because changes characterize clades and may be associated with polyploidy, transposon amplifications, deletions, or rearrangements. Further knowledge of genome size will provide crucial information needed for planning of whole genome sequencing and accurate annotations. We studied the genome size of Cocos nucifera and its variation among cultivars, and compared it to values for related palms from the Attaleinae subtribe. METHODS: Flow cytometric analysis of isolated nuclei from young palm leaves was used to estimate genome sizes of 23 coconut cultivars (Talls, Dwarfs, and hybrids) worldwide and 17 Cocoseae species. Ancestral genome size was reconstructed on a maximum likelihood phylogeny of Attaleinae from seven WRKY loci. KEY RESULTS: The coconut genome is large—averaging 5.966 pg—and shows intraspecific variation associated with domestication. Variation among Tall coconuts was significantly greater than among Dwarfs. Attaleinae genomes showed moderate size variation across genera, except polyploids Jubaeopsis caffra, Voanioala gerardii, Beccariophoenix alfredii, and Allagoptera caudescens, which had larger genomes. CONCLUSIONS: Our results contribute to the understanding of the relationship between domestication and genome size in long-lived tree crops and provide a basis for whole-genome sequencing of the coconut and other domesticated plants. Polyploidy evolved independently in two clades within Attaleinae.
Data from: Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing
In recent years, new genome-wide marker systems have provided highly informative alternatives to low density marker systems for evaluating plant populations. To date, most apple germplasm collections have been genotyped using low-density markers such as simple sequence repeats (SSRs), whereas only a few have been explored using high-density genome-wide marker information. We explored the genetic diversity of the Pometum gene bank collection (University of Copenhagen, Denmark) of 349 apple accessions using over 15,000 genome-wide single nucleotide polymorphisms (SNPs) and 15 SSR markers, in order to compare the strength of the two approaches for describing population structure. We found that 119 accessions shared a clonal relationship with at least one other accession in the collection, resulting in the identification of 272 (78%) unique accessions. Of these unique accessions, over half (52%) share a first-degree relationship with at least one other accession. There is therefore a high degree of clonal and family relatedness in the Danish apple gene bank. We find significant genetic differentiation between Malus domestica and its supposed primary wild ancestor, M. sieversii, as well as between accessions of Danish origin and all others. Overall, we found strong concordance between analyses based on the genome-wide SNPs and the 15 SSR loci. However, we argue that GBS is superior to traditional SSR approaches because it allowed the estimation of ploidy levels that were in accordance with flow cytometry results, and can be further exploited in genome-wide association studies (GWAS). Finally, we compare GBS with SSR for the purposes of characterizing a diverse apple gene bank and discuss the advantages and constraints of the two approaches.
Data from: Interspecific variation in ploidy as a key plant trait outlining local extinction risks and community patterns in fragmented landscapes
1. Polyploidy is associated with a plethora of phenotypic and genetic changes yielding transformative effects on species' life-history and ecology. These biological attributes can contribute to the success of species on ecological timescales, as observed in the invasion success or rapid environmental and climatic adaptation of polyploids. However, to date there has been a distinct lack of empirical evidence linking species' local extinction risk, species distributions and community structure in fragmented landscapes with interspecific variation in ploidy. 2. We aimed to investigate the relationship between levels of habitat fragmentation and patterns in both diversity and the frequency of species with different ploidy levels. We included additional persistence- and dispersal related life-history traits, to establish the relative importance of ploidy in determining species richness and frequencies following habitat fragmentation. We therefore collected plant community presence-absence data and landscape data from grassland fragments from South-Central Sweden. 3. Community-level analysis uncovered that interspecific variation in ploidy proved the strongest predictor of plant community species richness and turn-over across grassland fragments. Local extinction risk decreased as ploidy increased, with diploids most prone to local extinction. 4. In the species-level analysis, ploidy outweighed the combined explanatory power of commonly used life-history traits such as clonality, dispersal mechanism and mating system; key predictors of plant species distributions across fragmented landscapes. 5. Ploidy appears to capture parallel variation in a series of advantageous genetic and life-history mechanisms which operate on ecological timescales, emerging as the strongest predictor of local extinction risk even after accounting for variation in other crucial life-history traits. Our results therefore highlight the importance of genomic traits such as ploidy and total chromosome number as valuable factors explaining and predicting local extinction risk in fragmented landscapes.
Data from: Solidago altissima differs with respect to ploidy frequency and clinal variation across the prairie-forest biome border in Minnesota
PREMISE OF THE STUDY: Although our awareness of ploidy diversity has expanded with the application of flow cytometry, we still know little about the extent to which cytotypes within mixed-ploidy populations are genetically differentiated across environmental gradients. METHODS: To address this issue, we reared 14 populations of Solidago altissima spanning the prairie–forest ecotone in Minnesota in a common garden with a watering treatment. We assessed ploidy frequencies and measured survival, flowering phenology, and plant architectural traits for 4 years. KEY RESULTS: All populations harbored multiple cytotypes; prairie populations were dominated by tetraploids, forest populations by hexaploids. Diploids and polyploids differed significantly for 84% of the traits. Beyond average differences, the slope of trait values covaried with latitude and longitude, but this relationship was stronger for diploids than the other two polyploid cytotypes as indicated by numerous ploidy × latitude and ploidy × longitude interactions. For example, the timing of flowering of the cytotypes overlapped in populations sampled from the northeastern hemiboreal forest but differed significantly between cytotypes sampled from populations in the southwestern prairie. The watering treatments had weak effects, and there were no ploidy differences for phenotypic plasticity. CONCLUSIONS: Our data show that diploids have diverged genetically to a greater extent than polyploids along the environmental clines sampled in this study. Moreover, different environments favor phenotypic convergence over divergence among cytotypes for some traits. Differences in ploidy frequency and phenotypic divergence among cytotypes across gradients of temperature and precipitation are important considerations for restoration in an age of climate change.
Data from: Population genomic variation reveals roles of history, adaptation, and ploidy in switchgrass
Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration, and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98,042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities, and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass.
FIGURE 1 in A naturalized diploid Fragaria sp. (Rosaceae) found in southern Chile as revealed by morphological, ploidy and cytogenetic analyses
FIGURE 1. Map of Chile with the locations of the eight accessions of Fragaria chiloensis subsp. chiloensis f. patagonica and Fragaria sp. (Fragaria-MEN) in the Araucania and Los Rios regions. CRC, Curacautin; MAL, Malalcahuello; HUE, Huerquehue; HUE2, Huerquehue 2; HUE3, Huerquehue 3; HUE4, Huerquehue 4; MEN, Menetue; MAM, Mamuil-Malal; NEL, Neltume. Modified from Oñate et al. (2018) and Mora et al. (2016, 2019). For coordinates details of each accession see Table S1.
FIGURE 3 in A naturalized diploid Fragaria sp. (Rosaceae) found in southern Chile as revealed by morphological, ploidy and cytogenetic analyses
FIGURE 3. Adaxial and abaxial leaf surfaces of Fragaria chiloensis subsp. chiloensis f. patagonica, Fragaria vesca 'Hawaii' and Fragaria-MEN. Scale = 1 cm.
FIGURE 4 in A naturalized diploid Fragaria sp. (Rosaceae) found in southern Chile as revealed by morphological, ploidy and cytogenetic analyses
FIGURE 4. Metaphasic plate of the complete set of chromosomes for the diploid Fragaria-MEN sample reported in the present research. Scale = 2 µm.
FIGURE 2. A in A naturalized diploid Fragaria sp. (Rosaceae) found in southern Chile as revealed by morphological, ploidy and cytogenetic analyses
FIGURE 2. A Fragaria-MEN specimen collected in Menetue, Araucania Region, Chile (Latitude 39º19'49'' S; Longitude 71º43'17'' W, 370 m.a.s.l.) maintained in the herbarium of the University of Talca (UTAL N° 6312). Scale = 1 cm.
Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex
<p>This contains data for the manuscript: "Illumina Whole Genome Sequencing indicates Ploidy Level Differences within the <i>Valenzuela flavidus </i>(Psocodea: Psocomorpha: Caeciliusidae) Species Complex".</p> <p><i>Valenzuela flavidus</i> is a species of bark louse which is known to have asexual parthenogenetic populations in Europe but is believed to have sexual and asexual populations in North America as well. Historically, <i>Valenzuela aurantiacus</i> was the species epithet recognized for North American members until reports of asexual reproduction surfaced in certain North American populations. Cytogenetic studies have demonstrated European all-female populations are triploid. However, males are often reported in North America suggesting diploidy for sexual populations. With the use of Illumina whole genome sequencing, genetic diversity among North American and European populations was explored with phylogenomic methods. Ploidy level was estimated by examining allele frequencies of read-mapped homologous gene regions. Results indicate divergent populations between Europe and North America. North American populations containing males are estimated to be diploid suggesting a different mechanism of genomic reproduction. These results suggest divergent population structure among European asexual and North American sexual members of <i>V. flavidus</i> providing insight for future studies to understand patterns of asexuality reported within the complex.</p> <p>The following file contains all gene alignments, concatenated supermatrix, and mitochondrial alignment for this manuscript. In addition, the BAM files used to estimate allele frequencies. Also, gene trees for coalescent analysis, resultant treefiles from IQ-tree searches, and MCMCtree result.</p>
Data from: Evolutionary patterns of ploidy and genome size variations show positive correlations with taxonomic diversity in tropical gingers (Zingiberaceae)
<p><strong>Premise: </strong>Cytogenetic traits such as an organism's chromosome number and genome size are taxonomically critical and can define angiosperm diversity. Variations in these cytogenetic traits by evolutionary processes such as polyploidization are known to be common, although underexplored in tropical plants. Zingiberaceae is a pantropical monocot family with ~1500 species where cytogenetic characters have often been used to define taxonomic boundaries, but a family-wide synthesis of cytogenetic patterns is absent.</p> <p><strong>Methods:</strong> A time-calibrated Bayesian phylogenetic tree was constructed to test for different models of chromosome number and genome size evolution in Zingiberaceae. We next tested how chromosome number and genome size variations differed with lineage-age, taxonomic diversity, and distributional range at two taxonomic ranks: within the family Zingiberaceae, and in the genus Hedychium using correlations, generalized linear models and phylogenetic least square models.</p> <p><strong>Key results:</strong> The most frequent changes in chromosome number within Zingiberaceae were demi-polyploidization and polyploidization (~57 % of the time), followed by ascending dysploidy (~27 %). The subfamily Zingiberoideae showed descending dysploidy at its base, while Alpinioideae showed polyploidization at its internal nodes. Although chromosome counts and genome sizes did not corroborate with each other, suggesting that they are not equivalent, at both taxonomic ranks, higher chromosome number variations and higher genome size variations were associated with higher taxonomic diversity and wider biogeographic distribution.</p> <p><strong>Conclusions:</strong> Within Zingiberaceae, multiple incidences of polyploidization were discovered, and these cytogenetic events appear to have impacted the morphology, decreased genome sizes, and increased taxonomic diversity, distributional range and invasiveness of plants within this family. </p>
FIGURE 8 in Synflorescence analysis in South American species of Andropogon section Leptopogon (Andropogoneae, Poaceae): a tool to identify different ploidy levels
FIGURE 8. Plot of scores by principal component axes 1 and 3 from 253 specimens of Andropogon sect. Leptopogon. Andropogon arenarius (), A. bicornis (), A. glaziovii (), A. hypogynus (), A. lateralis (), A. macrothrix (), A. leucostachyus (), A. selloanus () and A. ternatus (). PC1= 34.3 %, PC3= 10.9 %.
FIGURE 6 in Synflorescence analysis in South American species of Andropogon section Leptopogon (Andropogoneae, Poaceae): a tool to identify different ploidy levels
FIGURE 6. Diagrams of the enrichment zone in synflorescences of Andropogon sect. Leptopogon. A–B. Diploid species. A. A. macrothrix (Norrmann 115) and A. ternatus (Norrmann 74); B, A. leucostachyus (Norrmann 46) and A. selloanus (Norrmann 229). C–F. Hexaploid species. C. A. arenarius (Nagahama & Norrmann 29a); D. A. lateralis (Schinini et al. 16842); E. A. glaziovii (Norrmann 217a); F. A. bicornis (Norrmann & Quarín 91).
FIGURE 5 in Synflorescence analysis in South American species of Andropogon section Leptopogon (Andropogoneae, Poaceae): a tool to identify different ploidy levels
FIGURE 5. Variations of PcTTs in the section Leptopogon. A–B. Diploid species. A. Not ramified PcTT in A. macrothrix (Norrmann 115) and A. ternatus (Norrmann 74); B. PcTT showing a second ramification degree in A. leucostachyus (Norrmann 46) and A. selloanus (Norrmann 229); C–F. Hexaploid species. C. PcTT ramified from axillary buds of bracts and prophylls in A. arenarius (Nagahama & Norrmann 29a); D. PcTT ramified from axillary buds of bracts and prophylls in A. lateralis (Schinini et al. 16842); in this species the PcTT ramified from axillary buds of prophylls develops new PcTTs; E. PcTT showing numerous PcTTs developed from axillary buds of bracts and prophylls in A. glaziovii (Norrmann 217a); F. PcTT showing numerous PcTTs developed from axillary buds of bracts and prophylls in A. bicornis (Norrmann & Quarín 91).
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