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169 results for “haploid”
Data from: Complex population structure and haplotype patterns in Western Europe honey bee from sequencing a large panel of haploid drones
<p>This vcf file contains 7.023.689 SNPs and 870 honey bee samples, as described in the paper "Complex population structure and haplotype patterns in Western Europe honey bee from sequencing a large panel of haploid drones" by Wragg et al., available at https://doi.org/10.1101/2021.09.20.460798 as preprint.</p> <p>Eight hundred and seventy haploid drone samples from several honey bee subspecies hybrids were sequenced and aligned to the HAv3.1 reference genome. Sequence read alignment and genotyping quality filters were used to obtain a selection of 7.023.689 high-quality SNPs. The file Diversity_Study_629_Samples.txt corresponds to the 629 unique samples that were used for the diversity study described in the paper and can be used to recreate the restricted diversity dataset using bcftools or an equivalent software.</p> <p>Having sequenced haploid drones, heterozygous SNPs resulting from duplicated regions could be filtered out and the data is phased.</p>
An ultra-dense haploid genetic map for evaluating the highly fragmented genome assembly of Norway spruce (Picea abies)
<p>Data files for construction of the haploid genetic map for Norway spruce (<em>Picea abies</em>). Available at <a href="https://doi.org/10.1101/292151">https://doi.org/10.1101/292151</a></p>
Data and code for: Realized genetic gains via recurrent selection in a tropical maize haploid inducer population and optimizing simultaneous selection for the next cycles
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Data from: Parental effects of male alternative reproductive tactics (ARTs) on ARTs of haploid sons
1. Alternative reproductive tactics (ARTs) represent distinct behavioral phenotypes to maximize reproductive success within the same sex, primarily males, and may be genetically and/or conditionally determined. Across animals, intragenerational determinants of conditional ARTs are relatively well understood but transgenerational (non-genetic) effects of parental ARTs on filial ARTs are largely unknown. 2. Here, we assessed parental effects of conditional male ARTs on sons' ARTs in arrhenotokous spider mites Tetranychus urticae. Arrhenotoky, i.e. males arising from unfertilized and females from fertilized eggs, sets the stage for sexual and transgenerational conflicts between male mates and females and their sons. Male ARTs of T. urticae are dichotomous, fighting and sneaking, and apparent in male-male combat and pre-copulatory guarding behavior. Due to haplodiploidy, male ARTs can only exert non-genetic effects on sons of their mates. 3. We hypothesized that parental ART effects are likely to occur in T. urticae because maternal ART mating status (unmated, sneaker- or fighter-mated) is indicative of the offspring' social environment and ART flexibility rather prevails in younger than older males. 4. Fighter-mated mothers produced more offspring than unmated mothers and had a more daughter-biased offspring sex ratio than sneaker-mated mothers. Sons of fighter-mated mothers were more likely to guard and did so earlier than sons of unmated and sneaker-mated mothers. Unmated and sneaker-mated, but not fighter-mated, mothers produced sneaker sons that were quicker to start guarding than were fighter sons. 5. Proximately, parental ART effects on sons' ARTs were most likely mediated by differences in seminal fluids. Ultimately, observed alterations of sons' ARTs represent adaptive maternal responses to ART phenotypes rather than manipulation by male mates. 6. Fighter-mated mothers tuned filial ARTs to male-competitive environments whereas unmated and sneaker-mated mothers tuned them to benign environments. Observed alterations in reproductive traits of fighter-mated mothers suggest adaptive manipulation by the fighter phenotype or aligned male and female interests. 7. Overall, our study documents previously unknown transgenerational ART effects on haploid sons' ARTs.
The weakest link: Haploid honey bees are more susceptible to neonicotinoid insecticides
<p><span>Neonicotinoid insecticides are currently of major concern for the health of wild and managed insects that provide key ecosystem services like pollination. Even though sublethal effects of neonicotinoids are well known, there is surprisingly little information on how they possibly impact developmental stability, and to what extent genetics are involved. This holds especially true for haploid individuals because they are hemizygous at detoxification loci and may be more susceptible. Here we take advantage of haplodiploidy in Western honey bees, <i>Apis mellifera</i>, to show for the first time that neonicotinoids affect developmental stability in diploid females (workers), and that haploid males (drones) are even more susceptible. Phenotypic fore wing venation abnormalities and fluctuating wing asymmetry, as measures of developmental instability, were significantly increased under field-realistic neonicotinoid-exposure of colonies. The higher susceptibility of haploid drones suggests that heterozygosity can play a key role in the ability to buffer the sublethal effects of neonicotinoids. Aiming to improve conservation efforts, our findings highlight the urgent need to better understand the role that genetics plays at enabling non-target organisms to cope with insecticide exposure.</span></p>
Haploid Diploid optimization data from eCS (EVONANO)
<p>Data-set produced by and depicted in https://arxiv.org/abs/1911.07302</p>
Fig. 1 in Effectiveness Of Doubled Haploids Production By Anther Culture From Selected Winter Wheat Hybrids
Fig. 1. Efficiency of formation of embryos and plants-regenerants.
Three sex phenotypes in a haploid algal species give insights into the evolutionary transition to a self-compatible mating system
<p>Mating systems of haploid species such as fungi, algae, and bryophytes are either heterothallic (self-incompatible) with two sex phenotypes (male and female, or mating type <i>minus</i> and <i>plus</i> in isogamous species) or homothallic (self-compatible) with only a bisexual phenotype producing zygotes within a clone. The anisogamous volvocine green alga <i>Pleodorina starrii</i> is a haploid species previously reported to have a heterothallic mating system. Here, we found that two additional culture strains originating from the same water system of <i>P. starrii</i> were taxonomically identified as <i>P. starrii</i> and produced male and female gametes and zygotes within a clone (bisexual). Sequences of rapidly evolving plastid genome regions were identical between the bisexual and unisexual (male or female) <i>P. starrii</i> strains. Intercrossings between the bisexual and unisexual strains demonstrated normal thick-walled zygotes and high survivability of F1 strains. Thus, these strains belong to the same biological species. <i>P. starrii</i> has a new haploid mating system that is unique in having three sex phenotypes; namely, male, female, and bisexual. Genetic analyses suggested the existence of autosomal "bisexual factor" locus independent of volvocine male and female determining regions. The present findings increase our understanding of the initial evolutionary step of transition from heterothallism to homothallism.</p>
Data from: Parental effects of male alternative reproductive tactics (ARTs) on ARTs of haploid sons
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Data from: Estimating the number of sexual events per generation in a facultatively sexual haploid population
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The weakest link: Haploid honey bees are more susceptible to neonicotinoid insecticides
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Three sex phenotypes in a haploid algal species give insights into the evolutionary transition to a self-compatible mating system
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Unveiling an asymmetric plant–fungal symbiosis: morphological, cytogenetic, and molecular characterization of a haploid <em>Epichloë festucae</em> strain associated with three polyploid cytotypes of the Iberian endemic grass <em>Festuca rothmaleri</em>
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Data from: Haploid gynogens facilitate disomic marker development in paleotetraploid sturgeons
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Data from: Morphological, cellular and molecular evidences of chromosome random elimination in vivo upon haploid induction in maize
The mechanism of maternal in vivo haploid induction is not fully understood. In this study, the young embryos were identified by morphology, cytology and simple sequence repeat (SSR) markers at different developmental stages in the cross HZ514 (sweet corn) × HZI1 (inducer). The results indicated that the low seed setting rate was determined by the inducer pollen during the process of fertilization. The mosaic endosperm kernels and the different percentages of aneuploidy, mixploidy, lagged chromosome, micronuclei, chromosomal bridge and ring chromosome were found in the cross; 7.37% of the haploid embryos carried chromosome segments from HZI1. About 1% twin seedlings resulted from the cross and were analyzed by cytology and SSR markers. Four pairs of twin seedlings had different chromosome numbers (2n = 20 and 2n = 10–20) and there were some chromosome fragments from HZI1. Aneuploidy, mixploidy and the abnormal chromosomes occurred in the in vivo haploid induction by HZI1, which is the cytological basis for haploid induction and indicates that the inducer's chromosomes are prone to be lost during mitotic and meiotic divisions. Morphological, cellular and molecular evidences reveal that complete or partial chromosome elimination from inducer HZI1 controls the maize in vivo haploid induction.
Data from: Haploid selection within a single ejaculate increases offspring fitness
An inescapable consequence of sex in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid phases. The occurrence of selection during the haploid phase can have far-reaching consequences for fundamental evolutionary processes including the rate of adaptation, the extent of inbreeding depression, and the load of deleterious mutations, as well as for applied research into fertilization technology. Although haploid selection is well established in plants, current dogma assumes that in animals, intact fertile sperm within a single ejaculate are equivalent at siring viable offspring. Using the zebrafish Danio rerio, we show that selection on phenotypic variation among intact fertile sperm within an ejaculate affects offspring fitness. Longer-lived sperm sired embryos with increased survival and a reduced number of apoptotic cells, and adult male offspring exhibited higher fitness. The effect on embryo viability was carried over into the second generation without further selection and was equally strong in both sexes. Sperm pools selected by motile phenotypes differed genetically at numerous sites throughout the genome. Our findings clearly link within-ejaculate variation in sperm phenotype to offspring fitness and sperm genotype in a vertebrate and have major implications for adaptive evolution.
Data from: The effects of quantitative fecundity in the haploid stage on reproductive success and diploid fitness in the aquatic peat moss Sphagnum macrophyllum
A major question in evolutionary biology is how mating patterns affect the fitness of offspring. However, in animals and seed plants it is virtually impossible to investigate the effects of specific gamete genotypes. In bryophytes, haploid gametophytes grow via clonal propagation and produce millions of genetically identical gametes throughout a population. The main goal of this research was to test whether gamete identity has an effect on the fitness of their diploid offspring in a population of the aquatic peat moss Sphagnum macrophyllum. We observed a heavily male-biased sex ratio in gametophyte plants (ramets) and in multilocus microsatellite genotypes (genets). There was a steeper relationship between mating success (number of different haploid mates) and fecundity (number of diploid offspring) for male genets compared with female genets. At the sporophyte level, we observed a weak effect of inbreeding on offspring fitness, but no effect of brood size (number of sporophytes per maternal ramet). Instead, the identities of the haploid male and haploid female parents were significant contributors to variance in fitness of sporophyte offspring in the population. Our results suggest that intrasexual gametophyte/gamete competition may play a role in determining mating success in this population.
Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species
<p>Despite their suitability for studying evolution, many conifer species have large and repetitive giga-genomes (16-31Gbp) that create hurdles to producing high coverage SNP datasets that capture diversity from across the entirety of the genome. Due in part to multiple ancient whole genome duplication events, gene family expansion and subsequent evolution within <i>Pinaceae</i>, false diversity from the misalignment of paralog copies creates further challenges in accurately and reproducibly inferring evolutionary history from sequence data. Here, we leverage the cost-saving benefits of pool-seq and exome-capture to discover SNPs in two conifer species, Douglas-fir (<i>Pseudotsuga menziesii</i> var. <i>menziesii </i>(Mirb.) Franco, <i>Pinaceae</i>) and jack pine (<i>Pinus banksiana</i> Lamb., <i>Pinaceae</i>). We show, using minimal baseline filtering, that allele frequencies estimated from pooled individuals show a strong positive correlation with those estimated by sequencing the same population as individuals (r > 0.948), on par with such comparisons made in model organisms. Further, we highlight the utility of haploid megagametophyte tissue for identifying sites that are likely due to misaligned paralogs. Together with additional minor filtering, we show that it is possible to remove many of the loci with large frequency estimate discrepancies between individual and pooled sequencing approaches, improving the correlation further (r > 0.973). Our work addresses bioinformatic challenges in non-model organisms with large and complex genomes, highlights the use of megagametophyte tissue for the identification of paralog sites, and suggests the combination of pool-seq and exome capture to be robust for further evolutionary hypothesis testing in these systems.</p>
Atypical flagella assembly and haploid genome coiling during male gamete formation in Plasmodium
<p>Movies of Plasmodium berghei SBF-SEM and serial tomogram datasets including 3D models used in publication 'Atypical flagella assembly and haploid genome coiling during male gamete formation in <em>Plasmodium</em>. Molly Hair, Flavia Moreira-Leite, David Ferguson, Mohammed Zeeshan, Rita Tewari, Sue Vaughan. bioRxiv 2023.05.17.540968; doi: https://doi.org/10.1101/2023.05.17.540968'</p> <p><strong>Movie 1.</strong> Serial block face scanning electron microscopy datasets used in this work. The section thickness (Z resolution) is 100 nm, and each dataset consist of 197 images (pixel dimension and X-Y resolution). </p> <p><strong>Movie 2.</strong> SBF-SEM data and segmentation of a single microgametocyte post-activation showing 8 axonemes coiling around the nucleus in two orientations. Organelles are modelled on the following colours: plasma membrane (white), nucleus (blue), basal body (red), axonemes (yellow/blue – two colours to highlight different directions of coiling). </p> <p><strong>Movie 3.</strong> SBF-SEM imaging and 3D model of a microgamete cell undergoing exflagellation. Structures are modelled on the following colours: plasma membrane (white), nucleus (blue), basal body (red), flagella (pink). </p> <p><strong>Movie 4.</strong> Serial tomogram of a microgamete highlighting the coiling of the nucleus around the axoneme. </p> <p><strong>Movie 5.</strong> Serial tomogram of a microgametocyte showing a nuclear projection surrounding the axoneme, with the 3D reconstruction of the nuceloplasm (cyan), which forms a coil within the nuclear projection. </p>
Data from: Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability
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