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2,785 results for “genotypes”
Data for: Range and niche expansion through multiple interspecific hybridization - a genotyping by sequencing analysis of Cherleria (Caryophyllaceae)
<p><b>Background:</b> <i>Cherleria</i> (Caryophyllaceae) is a circumboreal genus that also occurs in the high mountains of the northern hemisphere. In this study, we focus on a clade that diversified in the European High Mountains, which was identified using nuclear ribosomal (nrDNA) sequence data in a previous study. With the nrDNA data, all but one species was monophyletic, with little sequence variation within most species. Here, we use genotyping by sequencing (GBS) data to determine whether the nrDNA data showed the full picture of the evolution in the genomes of these species.</p> <p><b>Results:</b> The overall relationships found with the GBS data were congruent with those from the nrDNA study. Most of the species were still monophyletic and many of the same subclades were recovered, including a clade of three narrow endemic species from Greece and a clade of largely calcifuge species. The GBS data provided additional resolution within the two species with the best sampling, <i>C. langii</i> and <i>C. laricifolia</i>, with structure that was congruent with geography. In addition, the GBS data showed significant hybridization between several species, including species whose ranges did not currently overlap.</p> <p><b>Conclusions:</b> The hybridization led us to hypothesize that lineages came in contact on the Balkan Peninsula after they diverged, even when those lineages are no longer present on the Balkan Peninsula. Hybridization may also have helped lineages expand their niches to colonize new substrates and different areas. Not only do genome-wide data provide increased phylogenetic resolution of difficult nodes, they also give evidence for a more complex evolutionary history than what can be depicted by a simple, branching phylogeny.</p>
Genotypes for Iberian sows
<p>This file contains SNP genotype information for 435 sows of Iberian pigs. This is one inpute file of software developed for implementation of the Corner Algorithm</p> <p><a href="https://github.com/lgomezraya/CORNER">https://github.com/lgomezraya/CORNER</a></p>
Pinus pinaster genotypes from Sierra Espadan
<p>Data file: " Ppinaster_6100SNPs_GPScoordinates_Espadan.txt"</p> <p>species: Pinus pinaster (Pinaceae)</p> <p>data: Single Nucleotide Polymorphism (SNP) genotype data</p> <p>column "sample_ID" indicates the individual tree number and the sample plot number</p> <p>column "latitude" indicates the latitude in decimal degrees (WGS84) for each sampled tree</p> <p>column "longitude" indicates the longitude in decimal degrees (WGS84) for each sampled tree</p> <p>column "altitude" indicates the altitude above sea level in meters of each sampled tree</p> <p>row 1, column 2-6104: SNP names as in Plomion et al. 2016, doi: 10.1111/1755-0998.12464</p> <p>row 2-151, column 2-6104: genotypes of SNP loci, A= Adenine, C= Cytosine, G= Guanine, T= Thymine, -- = missing data</p>
Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping
<p>Genetic research is a key component to modern wildlife conservation, but it is contingent on the collection of reliable and high-quality genetic samples. Invasive genetic sampling techniques have potential to negatively impact individuals, which may be prohibitive when working with threatened and endangered species. Prior to sample collection, project managers must try to balance the negative impact on individuals included in the study with the demand for DNA and the difficulty of obtaining samples. Although established methods for blood and tissue collection in reptiles meet the need for high-quantity and quality DNA, they inherently require longer handling times and more skill to obtain. Thus, non-invasive DNA collection methods, such as cloacal swabs, may be preferred when animal welfare is a priority. Cloacal swabs are quicker, easier, require less training and reduce handling time. To evaluate cloacal swabbing as an alternative to collecting blood, we obtained both cloacal and blood swabs. We extracted DNA from cloacal and blood cells that were collected from 23 Timber Rattlesnakes (Crotalus horridus). We assessed DNA by purity (A260/A280), concentration, and microsatellite genotyping. Our results show high-quality DNA can be obtained from both cloacal swabs and blood samples, but quality and concentration of DNA was significantly lower from cloacal swabs. Further, degradation and contamination affects the performance of cloacal DNA when compared to blood DNA in microsatellite-based genotyping. Although we recommend collecting blood samples whenever possible to obtain the highest-quality DNA, cloacal swabs represent a viable alternative for genetic sampling when using microsatellite loci as genetic markers.</p>
Genotypic sex shapes maternal care in the African Pygmy mouse, Mus minutoides
<p><span>Sexually dimorphic behaviours, such as parental care, have long been thought to be </span><span>mainly</span><span> driven by gonadal hormones. In the past two decades, a few studies have challenged this view, highlighting the direct influence of the sex chromosome complement (XX vs XY or ZZ vs ZW). The African pygmy mouse, </span><span>Mus minutoides</span><span>, is a wild mouse species with naturally occurring XY sex reversal induced by a third, feminizing X* chromosome, leading to three female genotypes: XX, XX* and X*Y. Here, we show that sex reversal in X*Y females shapes a divergent maternal care strategy (maternal aggression, pup retrieval and nesting behaviours) from both XX and XX* females. Although neuroanatomical investigations were inconclusive, we show that the dopaminergic system in the anteroventral periventricular nucleus of the hypothalamus is worth investigating further as it may support differences in pup retrieval behaviour between females. Combining </span><span>behaviours</span><span> and neurobiology in a rodent subject to natural selection, we evaluate potential candidates for the neural basis of maternal behaviours and strengthen the underestimated role of the sex chromosomes in shaping sex differences in brain and behaviours. All things considered, we further highlight the emergence of a third sexual phenotype, challenging the binary view of phenotypic sexes.</span></p>
Structure and dynamics of enterovirus genotype networks
<p>Like all biological populations, viral populations exist as networks of genotypes connected through mutation. Mapping the topology of these networks and quantifying population dynamics across them is crucial to understanding how populations adapt to changes in their selective environment. The influence of mutational networks is especially profound in viral populations which rapidly explore their mutational neighborhoods via high mutation rates. Using a novel single-cell sequencing method, scRNAseq-Enabled Acquisition of mRNA and Consensus Haplotypes Linking Individual Genotypes and Host Transcriptomes (SEARCHLIGHT), we captured and assembled viral haplotypes from hundreds of individual infected cells to reveal the complexity of viral populations. We obtained these genotypes in parallel with host cell transcriptome information, enabling us to link host cell transcriptional phenotypes to the genetic structures underlying virus adaptation. Our examination of these structures reveals the common evolutionary dynamics of enterovirus populations and illustrates how viral populations reach through mutational 'tunnels' to span evolutionary landscapes and maintain connection with multiple adaptive genotypes simultaneously.</p>
Data described in the article "Unraveling the diversity of hyphal explorative traits among Rhizophagus irregularis genotypes"
<p>The dataset includes supplementary Figures, tables and the results of two experiments published in the study titled "Unraveling the diversity of hyphal explorative traits among Rhizophagus irregularis genotypes", available here: https://doi.org/10.1007/s00572-024-01154-8</p> <p>The study compares seven homokaryotic isolates (genotypes) of Rhizophagus irregularis, aiming to characterize the range of intraspecific variability with respect to hyphal exploration of organic nitrogen (N) resources, and N supply to plants. Two experiments (one in vitro and one in open pots) were conducted, and 15N-chitin as the isotopically labeled organic N source was used.</p> <p>Experiment 1 (in vitro), mycelium of all arbuscular mycorrhizal (AM) fungal genotypes transferred a higher amount of 15N to the plants than the passive transfer of 15N measured in the non-mycorrhizal (NM) controls. Noticeably, certain genotypes (e.g., LPA9) showed higher extraradical mycelium biomass production but not necessarily greater 15N acquisition than the others. </p> <p>Experiment 2 (in pots) highlighted that some of the AM fungal genotypes (e.g., MA2, STSI) exhibited higher rates of targeted hyphal exploration of chitin-enriched zones, indicative of distinct N exploration patterns from the other genotypes. Dataset contain photos and other recorded parameters during the experiment 1 and experiment 2.</p>
Fig. 2 in Phenotypic and Genotypic Characterization ofEimeria caviae from Guinea Pigs (Cavia porcellus)
Fig. 2. Photomicrographs of sporulated oocysts of Eimeria caviae, a coccidium species recovered from Guinea pigs Cavia porcellus: (A, B, D) sub-spherical, (C, D) ellipsoidal, and (D, E, F) ovoidal oocysts. In (D) three shapes can be observed in the same field. The arrowheads point the Stieda and parastieda bodies. Sheather's sugar solution. Scale bar: 10 µm.
Fig. 3 in Phenotypic and Genotypic Characterization ofEimeria caviae from Guinea Pigs (Cavia porcellus)
Fig. 3. Histograms of (A) length, width and (B) shape-index, and (C) linear regression of the oocysts of Eimeria caviae, a coccidium species recovered from Guinea pigs Cavia porcellus.
Fig. 1 in Phenotypic and Genotypic Characterization ofEimeria caviae from Guinea Pigs (Cavia porcellus)
Fig. 1. Line drawings of sporulated oocysts of Eimeria caviae, a coccidium species recovered from Guinea pigs Cavia porcellus: (A) subspherical, (B) ellipsoidal, and (C) ovoidal oocysts; (D–G) variations of the Stieda bodies; (H–K) variations of the parastieda bodies; (L–M) variations of roughness of the oocyst wall. Scale bar: 10 µm.
Figure 5 in Biochemical, physiological, and growth evaluation of different chickpea genotypes under varying salinity regimes
Figure 5. Effect of salinity stress on stomatal conductance (a), and transpiration rate (b) of chickpea genotypes: salinity levels=S0: 0 mM NaCl, S1: 50 mM NaCl, S2:100 mM NaCl, S3: 150 mM NaCl. Genotypes= KK-2, Bhakkar-2011, Bittle-98, Punjab-2008, CM-98. Error bar shows standard error.
Figure 2 in Biochemical, physiological, and growth evaluation of different chickpea genotypes under varying salinity regimes
Figure 2. Effect of salinity stress yield (a), and R:S (b) of chickpea genotypes: salinity levels=S0: 0 mM NaCl, S1: 50 mM NaCl, S2:100 mM NaCl, S3: 150 mM NaCl. Genotypes= KK-2, Bhakkar-2011, Bittle-98, Punjab-2008, CM-98. Data labels represnts the level of significance for multiple comparison between all combination of treatments @ 0.05 probability level. Error bar shows standard error.
Figure 4 in Biochemical, physiological, and growth evaluation of different chickpea genotypes under varying salinity regimes
Figure 4. Effect of salinity stress on crude protein content (a), Reducing sugars (b) and total carbohydrates (c) of chickpea genotypes: salinity levels=S0: 0 mM NaCl, S1: 50 mM NaCl, S2:100 mM NaCl, S3: 150 mM NaCl. Genotypes= KK-2, Bhakkar-2011, Bittle-98, Punjab-2008, CM-98. Data labels represnts the level of significance for multiple comparison between all combination of treatments @ 0.05 probability level. Error bar shows standard error.
Figure 3 in Biochemical, physiological, and growth evaluation of different chickpea genotypes under varying salinity regimes
Figure 3. Effect of salinity stress on proline content (a), lipid peroxidation (b) and H 2 O 2 (c) of chickpea genotypes: salinity levels=S0: 0 mM NaCl, S1: 50 mM NaCl, S2:100 mM NaCl, S3: 150 mM NaCl. Genotypes= KK-2, Bhakkar-2011, Bittle-98, Punjab-2008, CM-98. Data labels represnts the level of significance for multiple comparison between all combination of treatments @ 0.05 probability level. Error bar shows standard error.
Figure 1 in Biochemical, physiological, and growth evaluation of different chickpea genotypes under varying salinity regimes
Figure 1. Effect of salinity stress on SL (a) and RL (b) of chickpea genotypes: salinity levels=S0: 0 mM NaCl, S1: 50 mM NaCl, S2:100 mM NaCl, S3: 150 mM NaCl. Genotypes= KK-2, Bhakkar-2011, Bittle-98, Punjab-2008, CM-98. Data labels represnts the level of significance for multiple comparison between all combination of treatments @ 0.05 probability level. Error bar shows standard error.
Figure 4 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 4. Prevalence of six different sub-allele types of Pvmsp-3β (A1-A3, B1-B2 and C1) based on PCR-RFLP.
Figure 2 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 2. Prevalence of nine different sub-allele types of Pvmsp- 3α(A1-A4), (B1-B3), C1 and D are the nine different alleles from PCR-RFLP.
Figure 1 in Growth regulators and their reflection on different hop genotypes cultivated under in vitro conditions
Figure 1. Explants of a hop genotype, grown in different culture media (yellow, blue and pink). Each medium provided different development behavior for the number of nodal segments. The larger the number of nodal segments, the more new plants will be obtained.
Figure 2 in Growth regulators and their reflection on different hop genotypes cultivated under in vitro conditions
Figure 2. Estimates of the direct and indirect effects of the variables root length (RL), shoot height (SH) and number of shoots (NS) on the variable number of nodal segments (NNS) (main variable).
Tutorial DAPCy: the Plasmodium falciparum (Pf7) genotype dataset from MalariaGEN
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