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34 results for “ploidy level”
Data files for Competitive ability depends on mating system and ploidy level across Capsella species
<p>The three data files associated with the article:</p> <p>Competitive ability depends on mating system and ploidy level across Capsella species. Annals Of Botany 2022: doi.org/10.1093/aob/mcac044</p> <p>See README for details on each files</p>
Differentiation of rhizosphere fungal assemblages by host ploidy level in mixed-ploidy Larrea tridentata populations
<p class="MsoNormal">Polyploidy—whole genome duplication—is common in plants. Studies over the last several decades have documented numerous mixed-ploidy populations. Whether arising via recurrent whole genome duplication events within a population, or from secondary contact, the persistence of mixed populations is possible by niche differentiation. Specifically, one mechanism facilitating ploidy co-occurrence is microbially-mediated niche differentiation (MMND), wherein cytotypes occupy different niches via interactions with different sets of microbes. Inherently cryptic, MMND is underexplored in polyploid plant populations. Here, we search for evidence of MMND in creosotebush (<em>Larrea tridentata</em>), a dominant desert shrub of the southwestern U.S. and northern Mexico. We sequenced root-associated fungal taxa in soil diploid, autotetraploid, and autohexaploid plants growing in two naturally-occurring mixed-cytotype populations. Within populations, we found substantial fungal assemblage overlap across host plant cytotypes. However, using indicator species analysis, we identified some fungi that are differentiated by host plant cytotype, satisfying a precondition for MMND. Future study is needed to determine the degree of niche differentiation conferred, if any, and whether the identified fungi play a role in the long-term persistence of multiple cytotypes within populations.</p>
Differentiation of rhizosphere fungal assemblages by host ploidy level in mixed-ploidy Larrea tridentata populations
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Differentially methylated genes involved in reproduction and ploidy levels in recent diploidized and tetraploidized Eragrostis curvula genotypes
<p>Epigenetics studies changes in gene activity without changes in the DNA sequence. Methylation is an epigenetic mechanism important in many pathways, such as biotic and abiotic stresses, cell division, and reproduction. <em>Eragrostis curvula</em> is a grass species reproducing by apomixis, a clonal reproduction by seeds. This work employed the MCSeEd technique to identify deferentially methylated positions, regions, and genes in the CG, CHG, and CHH contexts in <em>E</em>. <em>curvula</em> genotypes with similar genomic backgrounds but with different reproductive modes and ploidy levels. In this way, we focused the analysis on the cvs. Tanganyika INTA (4x, apomictic), Victoria (2x, sexual), and Bahiense (4x, apomictic). Victoria was obtained from the diploidization of Tanganyika INTA, while Bahiense was produced from the tetraploidization of Victoria. This study showed that polyploid/apomictic genotypes had more differentially methylated positions and regions than the diploid sexual ones. Interestingly, it was possible to observe fewer differentially methylated positions and regions in CG than in the other contexts, meaning CG methylation is conserved across the genotypes regardless of the ploidy level and reproductive mode. In the comparisons between sexual and apomictic genotypes, we identified differentially methylated genes involved in the reproductive pathways, specifically in meiosis, cell division, and fertilization. Another interesting observation was that several differentially methylated genes between the diploid and the original tetraploid genotype recovered their methylation status after tetraploidization, suggesting that methylation is an important mechanism involved in reproduction and ploidy changes.</p>
Global ploidy levels of Phragmites australis
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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: 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.
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>
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).
FIGURE 7 in Synflorescence analysis in South American species of Andropogon section Leptopogon (Andropogoneae, Poaceae): a tool to identify different ploidy levels
FIGURE 7. Principal component analysis. Plot of scores by principal component axes 1 and 2 from 253 specimens of Andropogon sect. Leptopogon. Andropogon arenarius (), A. bicornis (), A. glaziovii (), A. hypogynus (), A. lateralis (), A. macrothrix (
FIGURE 2 in Synflorescence analysis in South American species of Andropogon section Leptopogon (Andropogoneae, Poaceae): a tool to identify different ploidy levels
FIGURE 2. Diagram of the synflorescence of Andropogon lateralis (Norrmann 71). Figure abbreviations: TT: trophotagma; UIF: unit of inflorescence; SIZ: short internodes zone; LIZ: long internodes zone; IZ: Innovation zone; HZ: Inhibition zone; EZ: Enrichment zone; b: bract; p: prophyll.
FIGURE 3 in Synflorescence analysis in South American species of Andropogon section Leptopogon (Andropogoneae, Poaceae): a tool to identify different ploidy levels
FIGURE 3. Andropogon bicornis (Norrmann & Quarín 91). A. synflorescence structure; B. basal axillary paracladium (PcTT1) (1 in A); C. cross-section (level 4 in E); D. distal zone of the synflorescence (3 in A); E. PcTT of middle zone of the synflorescence (2 in A). Figure abbreviations: TT: trophotagma; UIF: unit of inflorescence; SIZ: short internodes zone; LIZ: long internodes zone; IZ: Innovation zone; HZ: Inhibition zone; EZ: Enrichment zone; PcTT: paracladium of the trophotagma of first degree; PcTT´: paracladium of the trophotagma of second degree; PcTT´´: paracladium of the trophotagma of third degree; PcTT´´´: paracladium of the trophotagma of fourth degree; MA: main axis; pf: prophyll. Crosses represent units of inflorescence.
FIGURE 4 in Synflorescence analysis in South American species of Andropogon section Leptopogon (Andropogoneae, Poaceae): a tool to identify different ploidy levels
FIGURE 4. Diagram of the distal region of the EZ main axis and PcTTs in A. hypogynus (Krapovickas 12081). Figure abbreviations: EZ: enrichment zone; UIF: Unit of inflorescence; lPZ: long paracladia of the unit of inflorescences subzone; sPZ: short paracladia subzone; TsP: terminal short paracladium; st: sterile distal leaf (= spatheole); PcTT: paracladium of the trophotagma; b: bract; p: prophyll; filled ellipses: sessile spikelets; open ellipses: pedicellate spikelets.
FIGURE 1 in Synflorescence analysis in South American species of Andropogon section Leptopogon (Andropogoneae, Poaceae): a tool to identify different ploidy levels
FIGURE 1. Diagram of the synflorescence of Andropogon selloanus (Norrmann 73). Figure abbreviations: TT: trophotagma; UIF: unit of inflorescence; SIZ: short internodes zone; LIZ: long internodes zone; IZ: Innovation zone; HZ: Inhibition zone; EZ: Enrichment zone; PcTT1: first paracladium of the trophotagma; PcTT2: second paracladium of the trophotagma; PcTT2´: paracladium of the trophotagma of second degree in the PcTT2; b: bract; p: prophyll.
Pollination and plant reproductive success of two ploidy levels in red clover (Trifolium pratense L.)
<p>This dataset includes hand pollination, honey bee pollination and pollen germination experiments described in the article "Pollination and plant reproductive success of two ploidy levels in red clover (<em>Trifolium pratense</em> L.)", published in Frontiers in Plant Science (DOI: 10.3389/fpls.2021.720069). </p> <p>In a series of hand pollination experiments, the influence of visitation rate (10, 20, 40, 80 pollinated florets per flower head) on the seed number per pollinated floret and seed number per flower head were investigated, respectively. The influence of flowering stage (early, middle, and full flowering) on the seed number per pollinated floret was also investigated. Self-incompatibility was studied by comparing the seed number per flower head under self-pollination and interploidy pollination treatments. In order to study the autonomous pollination, we compared the seed number per flower head between self-pollination and control treatment.</p> <p>In the honey bee pollination experiments, we investigated the overall seed number per floret and compare the number of one-seeded and two-seeded florets in the studied red clover cultivars. Further, we investigated the pollen germination rate of each red clover cultivar. </p> <p>The main findings of this article include: </p> <p>(1) In hand pollination, increasing the visitation rates increased the seed number per flower head, but reduced the seed number per pollinated floret;</p> <p>(2) In hand pollination, different flowering stages did not influence the seed number per pollinated floret significantly;</p> <p>(3) In honey bee pollination, diploid red clover cultivars had more two-seeded florets compared to tetraploids.</p>
Supplementary material 1 from: de Andrade ARM, Cardoso DC, Cristiano MP (2023) Assessing ploidy levels and karyotype structure of the fire ant Solenopsis saevissima Smith, 1855 (Hymenoptera, Formicidae, Myrmicinae). Comparative Cytogenetics 17: 59-73. https://doi.org/10.3897/compcytogen.17.100945
Results from the karyomorphometrical analyses of Solenopsis saevissima and Chromosome counts frequency by individual and colony of Solenopsis saevissima
Is the AMH Intrafollicular Level a Predictor of the Ploidy Status of the Blastocyst?
ClinicalTrials.gov study NCT05837325. IPD Sharing: UNDECIDED. Countries: 1. Publications: 7.
Pollination and plant reproductive success of two ploidy levels in red clover (Trifolium pratense L.)
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