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83 results for “diploid data”
Supporting data: HiFi chromosome-scale diploid assemblies of the grape rootstocks 110R, Kober 5BB, and 101-14 Mgt
<p>Repository for supporting data to the paper: HiFi chromosome-scale diploid assemblies of the grape rootstocks 110R, Kober 5BB, and 101-14 Mgt</p>
Data of: Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts
<p>These files are results obtained in<br><span><span><span><span>Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts</span></span></span></span><br>by Yoshito Hirata, Arisa H. Oda, Chie Motono, Masanori Shiro & Kunihiro Ohta.</p> <p>There are 33 files for the corresponding each reconstruction of three-dimensional chromosomone structures<br>for each cell.<br>There are 3D structures for 15 GM cells and 18 PBMC cells, which are obtained from the single cell Hi-C data of Tan et al. Science (2018).</p> <p>For each file, there are 6 columns:<br>The first column corresponds to the allele (0: maternal, 1: paternal)<br>The second column corresponds to the chromosome (1-22: chromosome's number, 23: X, 24: Y)<br>The third column corrsponds to the base point.<br>The fourth column, the fifth column and the sixth column correspond to x-, y-, and z-axes of our reconstruction.</p>
Data of: Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts
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Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species
<ul> <li>Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors.</li> <li> We quantified soil properties and light availability of habitats of an allotetraploid <i>Cardamine flexuosa</i> and its diploid progenitors <i>C. amara</i> and <i>C. hirsuta</i> in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA-seq.</li> <li>We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in <i>C. flexuosa</i> varied spatially and temporally. </li> <li>These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.</li> </ul>
Data from: Are acute and acclimated thermal effects on metabolic rate modulated by cell size? A comparison between diploid and triploid zebrafish larvae
Being composed of small cells may carry energetic costs related to maintaining ionic gradients across cell membranes as well as benefits related to diffusive oxygen uptake. Here we test the hypothesis that these costs and benefits of cell size in ectotherms are temperature dependent. To study the consequences of cell size for whole-organism metabolic rate we compared diploid and triploid zebrafish larvae differing in cell size. A fully factorial design was applied combining three different rearing and test temperatures that allowed us to distinguish acute from acclimated thermal effects. Individual oxygen consumption rates of diploid and triploid larvae across declining levels of oxygen availability were measured. We found that both acute and acclimated thermal effects affected the metabolic response. In comparison to triploids, diploids responded more strongly to acute temperatures, especially when reared at the highest temperature. These observations support the hypothesis that animals composed of smaller cells (i.e. diploids) are less vulnerable to oxygen limitation in warm aquatic habitats. Furthermore, we found slightly improved hypoxia tolerance in diploids. By contrast, warm-reared triploids had higher metabolic rates when they were tested at acute cold temperature, suggesting that being composed of larger cells may provide metabolic advantages in the cold. We offer two mechanisms as a potential explanation of this result, related to homeoviscous adaptation of membrane function and the mitigation of developmental noise. Our results suggest that being composed of larger cells provides metabolic advantages in cold water, while being composed of smaller cells provides metabolic advantages in warm water.
Data for genetic characterization and curation of diploid a-genome wheat species
<p>Diploid A-genome relatives of wheat comprises <i>T</i>. <i>urartu</i>, <i>T</i>. <i>monococcum</i> subsp. <i>monococcum</i> (domesticated einkorn) and <i>T</i>. <i>monococcum</i> subsp. <i>aegilopoides</i> (wild einkorn). About 930 accessions of A-genome diploid wheat species preserved in the gene bank of the Wheat Genetics Resource Center (WGRC) at Kansas State University were genotyped using genotyping-by-sequencing (GBS). We constructed four pooled GBS libraries (384- and 288-plex) using restriction enzymes (Pst1-Msp1) combinations and the libraries were sequenced on the Illumina platform. The sequence data was processed using Tassel 5 GBS v2 pipeline and identified thousands of single nucleotide polymorphisms (SNPs) for downstream genetic and genomic dissections of the tested population. We have used <i>T</i>. <i>urartu</i> pseudomolecule (Tu2.0) as a reference genome to detect the genetic markers. Four fastq files with raw sequence reads information can be obtained at the National Center for Biotechnology Information (NCBI) SRA database with the BioProject accession PRJNA744683 (<a href="https://www.ncbi.nlm.nih.gov/sra/PRJNA744683" rel="noopener noreferrer">https://www.ncbi.nlm.nih.gov/sra/PRJNA744683</a>). Provided key file has information for demultiplexing including flowcell, lane number, barcodes and sample names to replicate the analysis. This experiment led us to curate the gene bank through identification of genetically duplicated accessions, miss-classified accessions and miss-classified non-diploid accessions. We were able to observe the unique genetic and evolutionary relationships among the diploid A-genome wheat species along with the unique population structures per species and sub-species. </p>
Haploid Diploid optimization data from eCS (EVONANO)
<p>Data-set produced by and depicted in https://arxiv.org/abs/1911.07302</p>
Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)
Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: 1) Tocantinia and Hippeastrum with 2n = 22, and 2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n = 12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade.
Soil composition, phenotypic and genetic data to: Adaptive differentiation on serpentine soil in diploid versus autotetraploid populations of Biscutella laevigata (Brassicaceae)
<p><span>Serpentine soils exhibit extreme properties (e.g. high magnesium content) influencing plant growth and survival and have been repeatedly documented to promote adaptive edaphic differentiation in plants. Individuals from four pairs of nearby diploid and autotetraploid populations of <em>Biscutella laevigata</em> sampled on serpentine vs non-serpentine soils in a factorial design are used to assess the genetic and phenotypic changes associated with edaphic origin and ploidy level. Individual samples from natural populations were subjected to soil elemental analysis and genotyping using restriction site-associated DNA sequences (RAD-seq) to link genetic variation with contrasting soils and ploidy levels. In diploids, genetic variation was consistent with demographic contraction and a pattern of isolation by environment with respect to the ratio of calcium / magnesium concentrations, whereas tetraploids presented evidence of expansion with limited edaphic differentiation. The genetic basis of tolerance and adaptation to serpentine was further assessed experimentally on seed-grown individuals from all populations subjected to high (serpentine-like) vs low (control) concentrations of magnesium in hydropony. Fitness-related phenotypic traits under experimental cultivation were consistent with adaptive differentiation among diploid ecotypes but not among the tetraploids that similarly grow in both habitats and consistently present higher investment in roots. Further work comparing experimentally resynthesized polyploids to natural diploids and polyploids has to tease the role of whole genome duplication apart from the impact of post-polyploidy evolution.</span></p>
Data from: Are acute and acclimated thermal effects on metabolic rate modulated by cell size? A comparison between diploid and triploid zebrafish larvae
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Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species
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Data for genetic characterization and curation of diploid a-genome wheat species
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Soil composition, phenotypic and genetic data to: Adaptive differentiation on serpentine soil in diploid versus autotetraploid populations of Biscutella laevigata (Brassicaceae)
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Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)
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Data from: The structure and allelic diversity of the self-incompatibility locus (S-locus) in diploid potatoes inferred from genome sequences and transcriptome data from styles and pollen
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Data from: Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe
Polyploidization is a rare yet sometimes successful way for animals to rapidly create geno- and phenotypes that may colonize new habitats and quickly adapt to environmental changes. In this study, we use water frogs of the Pelophylax esculentus complex, comprising two species (Pelophylax lessonae, genotype LL; Pelophylax ridibundus, RR) and various diploid (LR) and triploid (LLR, LRR) hybrid forms, summarized as P. esculentus, as a model for studying recent hybridization and polyploidization in the context of speciation. Specifically, we compared the geographic distribution and genetic diversity of diploid and triploid hybrids across Europe to understand their origin, maintenance and potential role in hybrid speciation. We found that different hybrid and parental genotypes are not evenly distributed across Europe. Rather, their genetic diversity is structured by latitude and longitude and the presence/absence of parental species but not of triploids. Highest genetic diversity was observed in central and eastern Europe, the lowest in the northwestern parts of Europe. This gradient can be explained by the decrease in genetic diversity during postglacial expansion from southeastern glacial refuge areas. Genealogical relationships calculated on the basis of microsatellite data clearly indicate that hybrids are of multiple origin and include a huge variety of parental genomes. Water frogs in mixed-ploidy populations without any parental species (i.e. all-hybrid populations) can be viewed as evolutionary units that may be on their way towards hybrid speciation. Maintenance of such all-hybrid populations requires a continuous exchange of genomes between diploids and triploids, but scenarios for alternative evolutionary trajectories are discussed.
Data from: Conservation genetics of Neotropical pollinators revisited: microsatellite analysis suggests that diploid males are rare in orchid bees
Allozyme analyses have suggested that Neotropical orchid bee (Euglossini) pollinators are vulnerable because of putative high frequencies of diploid males, a result of loss of sex allele diversity in small hymenopteran populations with single locus complementary sex determination. Our analysis of 1010 males from 27 species of euglossine bees sampled across the Neotropics at 2-11 polymorphic microsatellite loci revealed only 5 diploid males at an overall frequency of 0.005 (95% CIs 0.002-0.010); errors through genetic non-detection of diploid males were likely small. In contrast to allozyme-based studies, we detected very weak or insignificant population genetic structure, even for a pair of populations >500 km apart, possibly accounting for low diploid male frequencies. Technical flaws in previous allozyme-based analyses have probably led to considerable overestimation of diploid male production in orchid bees. Other factors may have a more immediate impact on population persistence than the genetic load imposed by diploid males on these important Neotropical pollinators.
Data from: Unidirectional diploid–tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers
Hybridization may lead to introgression of genes among species. Introgression may be bidirectional or unidirectional, depending on factors such as the demography of the hybridizing species, or the nature of reproductive barriers between them. Previous microsatellite studies suggested bidirectional introgression between diploid Betula nana (dwarf birch) and tetraploid B. pubescens (downy birch) and also between B. pubescens and diploid B. pendula (silver birch) in Britain. Here, we analyse introgression among these species using 51 237 variants in restriction site-associated (RAD) markers in 194 individuals, called with allele dosages in the tetraploids. In contrast to the microsatellite study, we found unidirectional introgression into B. pubescens from both of the diploid species. This pattern fits better with the expected nature of the reproductive barrier between diploids and tetraploids. As in the microsatellite study, introgression into B. pubescens showed clear clines with increasing introgression from B. nana in the north and from B. pendula in the south. Unlike B. pendula alleles, introgression of B. nana alleles was found far from the current area of sympatry or allopatry between B. nana and B. pubescens. This pattern fits a shifting zone of hybridization due to Holocene reduction in the range of B. nana and expansion in the range of B. pubescens.
Data from: Adaptation of diploid and tetraploid Chamerion angustifolium to elevation but not local environment
Polyploid organisms often have different geographic ranges than their diploid relatives. However, it is unclear whether this divergence is maintained by adaptation or results from historical differences in colonization. Here we conducted a reciprocal transplant experiment with diploid and autotetraploid Chamerion angustifolium to test for adaptation at the ploidy and population level. In the Rocky Mountains, pure diploid populations occur at high elevations and pure autotetraploid populations occur at low elevations with mixed-ploidy populations between. We planted 3134 seedlings in 2004 and 3890 juveniles (bolting) in 2005 among nine plots, three in each of the diploid, mixed-ploidy and tetraploid zones, and monitored survival until 2008. For both seedlings and juvenile plants, elevation significantly influenced survival. The juvenile plants also showed a significant ploidy by elevation interaction, indicating that diploids and tetraploids survived best at their native elevations. In contrast, we found no evidence of local adaptation to plot within elevation. This suggests that the current distribution of diploids and tetraploids across elevations is the result of adaptation and that genome duplication may have facilitated the invasion of lower elevation habitats by limiting the movement of maladapted alleles from diploid populations at higher elevations.
Data from: Fitness of an allopolyploid rupicolous fern compared to its diploid progenitors: From sporogenesis to sporophyte formation
PREMISE OF THE STUDY: When two populations of related cytotypes grow in sympatry, the rarer cytotype tends to be excluded due to a frequency-dependent mating disadvantage. Evolutionary models predict that polyploids, which are typically the rarer cytotype upon first formation, should have higher relative fitness and/or higher selfing rates to establish and then coexist with diploid parents. METHODS: We compared performance in early recruitment among three co-occurring rupicolous fern species: the allotetraploid Cheilanthes tinaei and its diploid ancestors, C. hispanica and C. maderensis. We made culture experiments with fresh spores and samples of soil spore banks to test for variation among cytotypes in germination, survival, growth and fecundity, and mating system of gametophytes. KEY RESULTS: Compared to its diploid parents, C. tinaei fresh spores had: higher abortion percentages, worselower dispersal ability due to larger spores, and similar vigor at germination. As for gametophytes from soil spore banks, C. tinaei showed high survival as C. maderensis, but its , similar germination percentage and similar time taken to germinate at each incubation temperature. Regarding soil spore banks, C. tinaei showed more abundant germination than both diploids, which supports greater spore deposition under sporophytes of the allotetraploid. Its gender expression resembles that of C. hispanica, with a high proportion of males. Patterns of sporophyte formation by females and bisexuals indicate that the polyploid does not have increased intragametophytic selfing rates. Gametophytes were larger in C. tinaei, but its reproductive success (sporophyte formation) was intermediate relative to diploids. CONCLUSIONS: Our results indicate that the allopolyploid show similar or even lower fitness than diploid progenitors show no evidence of higher selfing or fitness advantage of the allopolyploid over both diploid parents at any stage of early recruitment. In addition, all three species may have similar selfing rates. These two unexpected findings suggest that further factors, such as niche differentiation, play a more important role in cytotype coexistence.
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