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2,785 results for “genotyping”
Data from: Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content
A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4 Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.
Data from: Genotype-by-environment interactions for cuticular hydrocarbon expression in Drosophila simulans
Genotype-by-environment interactions (G x Es) describe genetic variation for phenotypic plasticity. Recent interest in the role of these interactions in sexual selection has identified G x Es across a diverse range of species and sexual traits. Additionally, theoretical work predicts that G x Es in sexual traits could help to maintain genetic variation, but could also disrupt the reliability of these traits as signals of mate quality. However, empirical tests of these theoretical predictions are scarce. We reared iso-female lines of Drosophila simulans across two axes of environmental variation (diet and temperature) in a fully factorial design and tested for G x Es in the expression of cuticular hydrocarbons (CHCs), a multivariate sexual trait in this species. We find sex-specific environmental, genetic and G x E effects on CHC expression, with G x Es for diet in both male and female CHC profile and a G x E for temperature in females. We also find some evidence for ecological crossover in these G x Es, and by quantifying variance components, genetic correlations and heritabilities, we show the potential for these G x Es to help maintain genetic variation and cause sexual signal unreliability in D. simulans CHC profiles.
Microsatellite genotypes of Camellia oleifera for GenoDive analysis
<p><i>Camellia oleifera</i>, a hexaploid evergreen broadleaf shrub or small tree, is the dominant woody oilseed crop in China. Understanding the spatial pattern of genetic diversity in wild <i>C. oleifera</i> is essential for conservation and utilization of genetic resources. Six wild <i>C. oleifera</i> populations were sampled along a latitudinal gradient in subtropical evergreen broadleaf forests of Southern China. A new high-throughput sequencing-based microsatellite genotyping method was developed to resolve allele dosage uncertainty in hexaploid wild <i>C. oleifera </i>with 35 microsatellite markers. Finally, the dataset of mcrosatellite genotypes was generated with corrected allele dosages. In addition, another dataset of microsatellite genotypes with uncorrected allele dosages (showing only different alleles) was generated, for mimicking the situation of current microsatellite genotyping methods.</p>
Genotype and individual data for genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture
<p><b><span>Premise: </span></b><span>When divergent lineages come into secondary contact reproductive isolation may be incomplete, thus providing an opportunity to investigate how speciation is manifested in the genome. The Louisiana Irises (<i>Iris</i>, series <i>Hexagonae</i>) comprise a group of three or more ecologically and reproductively divergent lineages that can produce hybrids where they come into contact. In this study we sought to estimate standing genetic variation to understand the current distribution of population structure in the Louisiana Irises.</span></p> <p><b><span>Methods:</span></b><span> We used genotyping-by-sequencing techniques to sample the genomes of Louisiana Iris species across their ranges. Twenty populations were sampled (total n=632) across 11,249 loci. Population genetic data were assessed using ENTROPY and PCA models. </span></p> <p><b><span>Results: </span></b><span>We discovered evidence for interspecific gene flow in parts of the range and revealed patterns of population structure at odds with widely accepted nominal taxonomy. Undescribed hybrid populations were discovered that were designated as belonging to the <i>I. brevicaulis</i> lineage. <i>Iris nelsonii </i>shared significant ancestry with only one of the purported parent species, <i>I. fulva, </i>evidence inconsistent with a hybrid origin.</span></p> <p><b><span>Conclusions: </span></b><span>This study provides several key findings important to the investigation of standing genetic variation in the Louisiana Iris species complex. <i>Iris brevicaulis</i> has a large amount of genetic diversity within it relative to the other nominal species. In addition, this study has discovered a previously unknown hybrid zone between <i>I. brevicaulis </i>and <i>I. hexagona</i> along the Texas coast. Finally, <i>I. nelsonii</i> does not appear to have mixed ancestry from three parental taxa as has been the longstanding hypothesis. </span></p>
Guppy MHC and microsatellite genotypes, gyrodactylid infection trials, and analysis code
<p>Natural host populations differ in their susceptibility to infection by parasites, and these intra-population differences are still an incompletely understood component of host-parasite dynamics. In this study, we used controlled infection experiments with wild-caught guppies (<em>Poecilia reticulata</em>) and their ectoparasite <em>Gyrodactylus turnbulli</em> to investigate the roles of local adaptation and host genetic composition (immunogenetic and neutral) in explaining differences in susceptibility to infection. We found differences between our four study host populations that were consistent between two parasite source populations, with no indication of local adaptation by either host or parasite at two tested spatial scales. Greater host population genetic variability metrics broadly aligned with lower population mean infection intensity, with the best alignments associated with Major Histocompatibility Complex (MHC) 'supertypes'. Controlling for intra-population differences and potential inbreeding variance, we found a significant negative relationship between individual-level functional MHC variability and infection: fish carrying more MHC supertypes experienced infections of lower severity, with limited evidence for supertype-specific effects. We conclude that population-level differences in host infection susceptibility likely reflect variation in parasite selective pressure and/or host evolutionary potential, underpinned by functional immunogenetic variation.</p>
Genotype-by-environment interactions for precopulatory mate guarding in a lek-mating insect
In sexually reproducing species males often experience strong pre- and postcopulatory sexual selection leading to a wide variety of male adaptations. One example is mate guarding, where males prevent females from mating with other males either before or after they (will) have mated themselves. In case social conditions vary short-term and in an unpredictable manner and if there is genetic variation in plasticity of mate guarding (i.e. genotype-by-environment interaction, G x E), adaptive behavioral plasticity in mate guarding may evolve. Here, we test for genetic variation in the plasticity of precopulatory mate guarding behavior in the lek-mating lesser wax moth Achroia grisella. When offered two females in rapid succession, virgin males of this species usually copulate around 10-20 min with the first female. With the second female, however, they engage in copulation posture for many hours until they have produced another spermatophore, an unusual behavior among insects possibly functioning as precopulatory mate guarding. Previous studies showed the mating latency with the second female to be shorter under higher perceived sperm competition risk. We accordingly measured the mate guarding behavior of males from six inbred lines under either elevated perceived male-male competition risk or under control conditions allowing us to test for G x E interactions. We found significant inbred line-by-competitor treatment interactions on mating latency and copulation duration with the second female suggesting genetic variation in the degree of behavioral plasticity. However, we found no significant G x E interaction on the sum of mating latency and copulation duration. Our results suggest a potential for adaptive evolution of mate guarding plasticity in natural populations of lek-mating species. Future studies using selection experiments and experimental evolution approaches in laboratory populations, or comparisons of multiple natural populations will be helpful to study under which conditions plasticity in male mate guarding behavior evolves.
Silicon enrichment alters functional traits in legumes depending on plant genotype and symbiosis with nitrogen-fixing bacteria
<p>1. Silicon (Si) uptake and deposition (silicification) in tissues is known to alleviate stresses and generally improve plant health. This is mostly studied in Si-high accumulators, such as grasses, with comparatively less known about its effects on other plant functional groups, such as legumes. There is speculation that Si may positively impact the symbiosis between legumes and the nitrogen-fixing bacteria (rhizobia) they associate with, but this is poorly understood. This study examined the effects of Si enrichment on legume species associated with rhizobia and the potential underlying mechanism of Si impacts.</p> <p>2. We conducted a glasshouse experiment with lucerne (<i>Medicago sativa</i>) and barrel medic (<i>M. truncatula</i>) associated with a model rhizobial strain. Six genotypes (three per species) were either supplemented with Si (+Si) or untreated (-Si). We quantified 16 functional traits which could be classified as plant growth, physiology, elemental chemistry, nodule activity and nitrogen fixation.</p> <p>3. The two legume species responded to Si distinctively. For example, Si supplementation increased shoot biomass by more than 10% in lucerne but growth was unaffected in barrel medic. Conversely, nitrogen-fixing enzyme (nitrogenase) activity was promoted by more than 85% in +Si barrel medic plants but not in lucerne. Moreover, Si supplementation of lucerne increased the concentrations of Si in leaves by more than 36% but not in root nodules. Increased foliar concentrations of Si in lucerne was positively associated with increased shoot and root biomass in Sequel and Trifecta genotypes, respectively. Conversely, Si supplementation of barrel medic increased the concentration of Si in root nodules by 29% but not that in foliar tissues. Nitrogenase activity and where silicification occurred, differed between genotypes in barrel medic; nitrogenase activity was correlated with concentrations of Si in root nodules rather than that in foliar tissues in one genotype (Sephi) but the reverse was true in another (Hannaford).</p> <p>4.This study demonstrates that two closely related legume species can respond to Si in distinct ways, depending on plant genotype and symbiosis. These results present the overlooked function of Si in legume-rhizobia interactions, which could potentially enhance productivity of this important group of plants.</p>
Host genotype and genetic diversity shape the evolution of a novel bacterial infection
<p><span><span><span><span><span><span><span><span><span><span><span>Pathogens continue to emerge from increased contact with novel host species. Whilst these hosts can represent distinct environments for pathogens, the impacts of host genetic background on how a pathogen evolves post-emergence are unclear. In a novel interaction, we experimentally evolved a pathogen (<i>Staphylococcus aureus</i>) in populations of wild nematodes (<i>Caenorhabditis elegans</i>) to test whether <span><span>host genotype and genetic diversity affect pathogen evolution</span></span>. After 10 rounds of selection, we found that pathogen virulence evolved to vary across host genotypes, with differences in host metal ion acquisition detected as a possible driver of increased host exploitation. Diverse host populations selected for the highest levels of pathogen virulence, but infectivity was constrained, unlike in host monocultures. We hypothesize that population heterogeneity might pool together individuals that contribute disproportionately to the spread of infection or to enhanced virulence. The genomes of evolved populations were sequenced, and it was revealed that pathogens selected in distantly-related host genotypes diverged more than those in closely-related host genotypes. <i>S. aureus </i>nevertheless maintained a broad host range. Our study provides unique empirical insight into the evolutionary dynamics that could occur in other novel infections of wildlife and humans.</span></span></span></span></span></span></span></span></span></span></span></p>
Figure 1 from: Saitoh K, Shindo K, Fujimoto Y, Takahashi K, Shimada T (2016) Mitochondrial genotyping of an endangered bitterling Acheilognathus typus (Cyprinidae). ZooKeys 623: 131-141. https://doi.org/10.3897/zookeys.623.8981
Figure 1 - Collecting localities (1–12) and range contraction of Acheilognathus typus. Shaded areas are prefectures with past (light) and recent (dark) records. Major mountain ranges are indicated by Λ. Locality 4 contains two ponds, and 6 contains a creek and five ponds around Lake Izunuma-Uchinuma, close to each other respectively. K and T indicate locations of Lake Kasumigaura and Teganuma Lake where Acheilognathus typus was abundant in the past.
Figure 3 from: Saitoh K, Shindo K, Fujimoto Y, Takahashi K, Shimada T (2016) Mitochondrial genotyping of an endangered bitterling Acheilognathus typus (Cyprinidae). ZooKeys 623: 131-141. https://doi.org/10.3897/zookeys.623.8981
Figure 3 - NJ tree based on net nucleotide divergence showing interrelationships among localities. Long branch between #12 with Hap8 and a node of #1, 2, 5, 6-4, 11 with Hap1 only is abbreviated and the real length is 2.4687.
Figure 2 from: Saitoh K, Shindo K, Fujimoto Y, Takahashi K, Shimada T (2016) Mitochondrial genotyping of an endangered bitterling Acheilognathus typus (Cyprinidae). ZooKeys 623: 131-141. https://doi.org/10.3897/zookeys.623.8981
Figure 2 - Haplotype network of Acheilognathus typus sequenced in this research. Small circles denote missing haplotypes. Numbers below haplotype ID stand for number of individuals observed. Numbers and bases at branches show nucleotide changes at these sites.
PERVASIVE ADAPTATION OF HEPATITIS C VIRUS TO INTERFERON LAMBDA POLYMORPHISM ACROSS MULTIPLE GENOTYPES
<p>Genetic polymorphism in the interferon lambda (IFN-λ) region is associated with spontaneous clearance of hepatitis C virus (HCV) infection and with response to interferon-based antiviral treatment. Here, we evaluate the associations between IFN-λ polymorphism and HCV variation by performing a genome-to-genome analysis in 8,729 patients from diverse ancestral backgrounds infected with various HCV genotypes. We searched for associations between human rs12979860 genotype, a tag for IFN-λ haplotypes, and amino acid variants in the NS3, NS4A, NS5A and NS5B proteins of HCV. We report multiple associations between host and pathogen variants in the full cohort as well as in subgroups defined by viral genotype and human ancestry. We also assess the combined impact of human and HCV variation on pre-treatment viral load. By demonstrating that IFN-λ genetic variation leaves a large footprint in the viral genome, this study provides strong evidence of pervasive viral adaptation to host innate immune pressure during chronic HCV infection.</p>
SolCap Genotyping of approx. 400 tomato and tomato crop wild relative genotypes
<p>SOLCAP genotyping of 400 tomato and tomato crop wild relatives.</p>
SNP data for Syringa vulgaris genotypes
<p><span>Common lilac (<em>Syringa</em> <em>vulgaris</em> L.) is a popular landscaping plant. In the present study, its genotypes were investigated using genotyping-by-sequencing (GBS) methodology. Our aim was to obtain a large set of SNP markers, to reveal the precise identities of the investigated <em>S. vulgaris</em> accessions, and to discover genetic relationships among them. The studied plant material included local Finnish, previously unidentified accessions, known reference cultivars, and so-called historical accessions i.e., old shrubs growing in historic cultural landscapes. We intended to verify cultivar names for some valuable local common lilac accessions and to provide insights into the history of common lilac cultivation in Finland. In the analyses, we used a set of 15,007 SNP markers.</span> <span>First, polymorphic information contents (PIC) were calculated (mean 0.190, range 0.012–0.500 per marker). Then, to investigate genetic relationships among genotypes, a phylogenetic tree was constructed, and a principal coordinate analysis (PCoA) was conducted. A Bayesian analysis of population structure was carried out to determine the number and distribution of genetic clusters among samples. Genetic marker data combined with existing historical and phenotypic knowledge revealed novel information on the unidentified cultivars and on the genetic relationships among studied accessions, and solved the arrival and early history of common lilac in Finland. Overall, such comprehensive genomic characterization and deep understanding of genetic relationships of <em>S. vulgaris</em> can be used when utilizing present cultivars and developing new ones in future breeding programs.</span></p>
Supplementary material 1 from: Watermann LY, Rotert J, Erfmeier A (2022) Coming home: Back-introduced invasive genotypes might pose an underestimated risk in the species´ native range. NeoBiota 78: 159-183. https://doi.org/10.3897/neobiota.78.91394
Supplementary information
Low-dose pioglitazone for polycystic ovary syndrome in adolescent girls: differential fat-mass redistribution by HOTAIR rs1443512 genotype
<p>HOTAIR data</p>
Low-dose pioglitazone for polycystic ovary syndrome in adolescent girls: differential fat-mass redistribution by HOTAIR rs1443512 genotype
<p>HOTAIR data</p>
Fig. 2 in Genotype diversity, phylogenetic analysis and seasonality of isolates of Acanthamoeba spp. in swimming pools in Kafrelsheikh, Egypt
Fig. 2. The maximum-likelihood constructed phylogenetic tree of Acanthamoeba isolates inferred from the small subunit ribosomal RNA gene sequences from GenBank showing the phylogenetic position of three strains detected in the present study; T4 (blue), T9 (green) and T11 (red). The tree with the highest log likelihood (-1201.92) is shown.
Supplementary material 1 from: Jablonski D, Tzoras E, Panagiotopoulos A, Asztalos M, Fritz U (2023) Genotyping the phenotypic diversity in Aegean Natrix natrix moreotica (Bedriaga, 1882) (Reptilia, Serpentes, Natricidae). ZooKeys 1169: 87-94. https://doi.org/10.3897/zookeys.1169.104594
Supplementary information
Genotype by sequencing SNP dataset for Malus domestica x Malus sieversii F1 populations GMAL4591 and GMAL4592
<p>Fire blight, a bacterial disease caused by <em>Erwinia</em> <em>amylovora</em>, is the most devastating disease of apples and a major threat to apple production. Most commercial apple cultivars are susceptible to fire blight driving the need to develop fire blight resistant cultivars. Although several major fire blight resistance QTLs have been identified from wild species of <em>Malus</em>, the challenges of breeding apples due to long juvenile phase and heterozygosity greatly limit their use. <em>M. sieversii</em>, the primary progenitor of domesticated apples, is one of the wild <em>Malus</em> species that is sexually compatible with <em>M. domestica</em> and has some favorable fruit quality traits. In this study, we performed QTL analysis on two F1 apple populations of <em>M. domestica</em> cv. 'Royal Gala' × <em>M. sieversi</em>i (GMAL4591 and GMAL4592) to identify fire blight resistance QTL. Parental linkage maps were constructed for each family using marker sets of approximately 20K GBS-SNPs. Phenotype data was collected from parents and progeny through controlled fire blight inoculations in the greenhouse for two subsequent years. A significant (P < 0.0001) moderate-effect fire blight resistance QTL on linkage group 7 of GMAL4591 was identified from the paternal parent<em> M. sieversii</em> 'KAZ 95 17-14' (<em>Msv_FB7</em>). <em>Msv_FB7</em> explains about 48–53% of the phenotyping variance across multiple years and time points. Additionally, a significant (P < 0.001) minor effect QTL explaining 18% of the phenotypic variance was identified in population GMAL4592 on LG10 from 'Royal Gala'. We developed diagnostic SSR markers flanking the Msv_FB7 QTL to use in apple breeding. These findings have the potential to accelerate the development of fire-blight-resistant cultivars.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.