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3,584 results for “genomic analysis”
Figure 16 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 16. Genomic tree of Anthoptina, Falgina and relatives. See Fig. 1 legend for notations.
Supplementary Materials from the article Characterization and molecular evolution analysis of Periploca forrestii inferred from its complete chloroplast genome sequence
<p>Table S1. Base composition of chloroplast genome in <em>P. forrestii</em>, Table S2. The lengths of introns and exons for the splitting genes, Table S3. The GC content of the codons from <em>P. forrestii </em>chloroplast genome, Table S4. Preferred codons in chloroplast genome of <em>P. forrestii</em>, Table S5. Long repeat sequences in the <em>P. forrestii </em>chloroplast genome, Figure S1. Codon bias analysis of P. forrestii chloroplast genome. (A) Neutrality plot analysis; (B) Analysis of PR2 bias plot; (C) Analysis on ENC and GC3 relationship.</p>
Epigenomic analysis on the HPRC genome graphs
<p>Processed data, analysis and figure code for the epigenomic analysis on the HPRC genome graph.</p>
Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae
<p>The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. Results The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. Conclusions The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.</p>
Genome assemblies of 118 Pisum accessions used for Pisum pan-genome analysis
<p>This repository stores genome assemblies of 118 <em>Pisum</em> accessions used for <em>Pisum</em> pan-genome anaylsis.</p> <p>Please refer to the supplementary data in publication and NCBI BioSamples for details.</p> <p>Associated NCBI BioProject : <strong>PRJNA730094</strong></p> <p>Correspondance : gaoshh@im.ac.cn</p>
Genome content flat files for comparative genomic analysis of seadragons and relatives
<p>Seadragons are widely recognized for their derived and novel traits. Research and conservation efforts involving these unique fish species and their relatives have been hindered by a lack of genomic resources. From this project we present full, annotated genomes of leafy and weedy seadragons, which help uncover surprising features of gene family and genome architecture evolution that likely relate to extreme phenotypic traits in seadragons, pipefishes, and seahorses. These genomes are important research resources for the Syngnathidae, a diverse, morphologically exceptional group of vertebrates, and for comparative genomic study of vertebrates in general.</p>
VCF datasets and analysis scripts for: The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability
<p>Global warming is increasingly exacerbating biodiversity loss. Populations locally adapted to spatially heterogeneous environments may respond differentially to climate change, but this intraspecific variation has only recently been considered when modelling vulnerability under climate change. Here, we incorporate intraspecific variation in genomic offset and ecological niche modelling to estimate climate change-driven vulnerability in two bird species in the Sino-Himalayan Mountains. We found that the cold-tolerant populations show higher genomic offset but risk less challenge for niche suitability decline under future climate than the warm-tolerant populations. Based on a genome-niche index estimated by combining genomic offset and niche suitability change, we identified the populations with the least genome-niche interruption as potential donors for evolutionary rescue, i.e., the populations tolerant to climate change. We evaluated potential rescue routes via a landscape genetic analysis. Overall, we demonstrate that the integration of genomic offset, niche suitability modelling, and landscape connectivity can improve climate change-driven vulnerability assessments and facilitate effective conservation management.</p>
A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component
<p>Over the last six decades, populations of the bumblebees <em>Bombus sylvicola</em> and <em>Bombus balteatus</em> in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations.</p> <p>We analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as <em>B</em>. <em>sylvicola</em>, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species ("incognitus"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis.</p> <p>This archive contains genetic variation data derived from genome sequencing of 580 bumblebee samples collected from high-elevation locations in Colorado. The species are Bombus sylvicola (n=214), Bombus balteatus (n=299) and "incognitus" (n=67).</p>
Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating
<pre class="js_message_plain ng-binding"><em>Sanguisorba</em> is a small genus, which consists of about 15 species widely distributed in North America and Eurasia. Previous studies on <em>Sanguisorba</em> are useful for understanding of phylogeny and chloroplast (cp) genome evolution of <em>Sanguisorba</em>. However, the cp genome resources of <em>Sanguisorba</em> are still limited, and the phylogeny and molecular dating for <em>Sanguisorba</em> and its relatives still need further explored. Here, we reported four cp genomes of <em>Sanguisorba</em> and conducted comparative analysis of the four <em>Sanguisorba</em> cp genomes plus five previously published ones. The nine cp genomes of <em>Sanguisorba</em> have typical tetrad quadripartite structure, with a total length of 154 282 to 155 730 bp, and their gene content, gene structure, and gene order are relatively conservative. The analysis of single copy (SC)/inverted repeat (IR) boundaries shows very slight boundary differences in <em>Sanguisorba</em> cp genomes. Eight variation hotspots were screened as excellent candidate markers of <em>Sanguisorba</em>. Phylogenetic analysis indicated <em>Sanguisorba</em> was monophyletic and was a member of tribe Agrimonieae subtribe Sanguisorbinae. Within <em>Sanguisorba</em>, <em>S. filiformis</em> is a sister group of six other taxa in the present sampling. Estimation of the divergence times indicated that subtribes Agrimoniinae and Sanguisorbinae diverged at the transition between the Oligocene and the Miocene, and divergent times of Agrimonieae genera ranged from the late Miocene to the Middle Pleistocene. This study enriches the available cp genome resources of <em>Sanguisorba</em>, and it is of great significance to further study the phylogeny and evolution of <em>Sanguisorba</em> and its relatives.</pre>
Supplementary information for: Redundancy analysis, genome-wide association studies, and the pigmentation of brown trout (Salmo trutta L.)
<p><span>The association of molecular variants to phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multi-trait GWAS to explore the molecular basis of pigmentation variation in brown trout (<em>Salmo</em> <em>trutta</em>) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multi-trait GWAS allowed us to extract 337 independent "colour patterning loci" (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (<em>i</em>) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (<em>ii</em>) were found associated with</span><span> 218 </span><span>candidate genes, including 197 genes </span><span>formerly mentioned in the literature dealing with skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (<em>Onchorhynchus</em> <em>mykiss</em>)</span><span>, and (<em>iii</em>) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.</span></p>
Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds
<p><strong>Summary</strong></p> <p>Uganda is endowed with a large population of goats from predominantly indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture of the exotic breed Boer is still limited. Using a medium density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six Ugandan goat breeds. Samples from five indigenous Ugandan goat breeds including Mubende (n=29), Kigezi (n=29), Small East African (n=29), Sebei (n=29) and Karamojong (n=15), and the exotic breed Boer (n=13) from different agro-ecological regions of Uganda were genotyped using the GoatSNP50 BeadChip. Analysis of genotype data revealed high levels of polymorphism with the proportion of polymorphic SNPs ranging from 0.885 in Kigezi to 0.928 in Sebei. The overall mean genetic diversity indices across breeds for <em>H<sub>O</sub></em> and <em>H<sub>E</sub></em> was 0.355±0.147 and 0.384±0.143 respectively. Principle components, genetic distances and ADMIXTURE analyses revealed weak population sub-structuring among the breeds. Principle components separate Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong are tightly entangled together while Mubende occupies a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. ADMIXTURE and four population test analyses further revealed gene-flow from Boer to Ugandan indigenous goat breeds and varying levels of admixture among the Ugandan indigenous breeds. Generally, moderate to high levels of genetic variability were observed in the Ugandan goat breeds. Our findings provide useful insight to devise strategies to maintain genetic diversity in local goat breeds from Uganda and to design appropriate breeding programs to exploit within breed diversity and heterozygote advantage in cross-breeding schemes.</p>
Pergola: boosting visualization and analysis of longitudinal data by unlocking genomic analysis tools - C. elegans unc-16 and N2 motion behavior dataset
<p>Dataset contains <em>Caenorhabditis</em> <em>elegans </em>motor behaviors originally used in this publication <a href="https://www.nature.com/articles/nmeth.2560">10.1038/nmeth.2560</a> and downloaded from the available <a href="http://wormbehavior.mrc-lmb.cam.ac.uk/">DB</a> which points to Zenodo. The dataset consists in two worm strains, 20 individuals from a mutant unc-16 strain with reduced mobility and 40 individuals from a control N2 strain. The behavioral measures derived from each individual worm trajectory were available in a HDF5-formatted file (Hierarchical Data Format Version 5) that has been included in this dataset.</p> <p>The data set consist in:</p> <p>- a "mappings" folder containing all the mappings used by the pergola in the pipeline to convert data.</p> <p>- a "N2" folder containing the 40 HDF5 files with the measures derived from the N2 worms.</p> <p>- a "N2" folder containing the 20 HDF5 files with the measures derived from the unc-16 worms.</p>
Hard edges, soft edges, and species range evolution: A genomic analysis of the Cumberland Plateau salamander
<p>Aim: Gene flow from central to edge populations is thought to limit population growth at range edges by constraining local adaptation. In this study, we explore the thesis that range edges can differ in their dynamics and be either "hard" (e.g. a river) or "soft" (e.g. ecological gradients). We hypothesize that soft edge populations will have smaller effective population sizes than central populations and that gene flow will be greater from the center to the edge than vice versa. Conversely, we hypothesize that hard edge populations should have similar effective population sizes to central populations and that gene flow will be equal between the two.</p> <p>Location: Kentucky, West Virginia, and Virginia, USA. Taxon: <em>Plethodon kentucki </em>(Caudata: Plethodontidae).</p> <p>Methods: We evaluated landscape suitability using an ecological niche model, then we compared gene flow and effective population sizes between edge and central populations and quantified gene flow between populations. Finally, we characterized landscape genetic variation, testing for isolation by distance and isolation by environment. Results: We found continuously decreasing habitat quality along soft edges, with hard edges more variable. Additionally, we found that soft edges had lower effective population sizes than central populations and that gene flow was greater from the center of the range to the soft edges than the reverse. In hard edges, by contrast, we found effective population sizes in edge populations were similar to central populations, with relatively equal gene flow in both directions.</p> <p>Main conclusions: Understanding why species have range limits is central to investigations of the structure of biodiversity, yet the evolutionary dynamics of range edges remain poorly understood. We show that within a single species with a small range, the evolutionary dynamics operating at range boundaries may depend on the nature of the boundary.</p>
Selection pressure analysis of dengue virus complete genome and E gene nucleotide sequences from Pakistan
<p>This dataset comprises 43 E gene and 44 complete genome nucleotide sequences of the dengue virus from serotypes DENV-1 to DENV-4, representing all documented sequences in Pakistan to date, sourced from the Virus Pathogen Resource (ViPR) database and NCBI. The E gene is critical as it is involved in serotype changes of the dengue virus, making it a pivotal target for understanding shifts in viral pathogenicity and immune escape mechanisms. The aim of compiling this dataset is to facilitate comprehensive genetic analysis and enhance understanding of the evolutionary dynamics of the dengue virus within the region. To assess the evolutionary pressures acting on these sequences, we conducted a selection pressure analysis utilizing computational methods. These methods include the Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), adaptive Branch Site Random Effects Likelihood (aBSREL), Mixed Effects Model of Evolution (MEME), and the Genetic Algorithm for Recombination Detection (GARD), all implemented in the HyPhy software package. Our analysis focused on identifying genomic sites under both positive and negative selection pressures, providing insights into the adaptive evolutionary processes affecting the E gene of the dengue virus in Pakistan. Understanding the molecular evolution of this gene is crucial for predicting serotype evolution, potentially aiding in the development of effective vaccines and therapeutic strategies.</p>
Baraminology of Cucurbitaceae based on chloroplast genome analysis
<p>The gourd family (Cucurbitaceae) is an economically important and diverse group of plants, with approximately 1000 species. Previous analysis of hybridization data and nuclear ITS regions in 70 species of 14 genera of the family Cucurbitaceae identified seven putative holobaramins.</p><p>The present study expands upon this previous analysis by analyzing the sequence similarity of the chloroplast genome between 30 species from Cucurbitaceae. The clustering analysis showed six putative holobaramins: <i>Gynostemma</i>, <i>Gomphogyne</i>+<i>Hemsleya</i>,<i> Cucurbita</i>, <i>Cucumis</i>, <i>Citrullus</i>, <i>Coccinia grandis</i>+<i>Hodgsonia macrocarpa</i>+<i>Lagenaria siceraria</i>+<i>Momordica charantia</i>+<i>Siraitia grosvernorii</i>+<i>Trichosanthes kirilowii</i>. All six groups had a significant p-value except <i>Gomphogyne</i>+<i>Hemsleya</i>. Of these, Gynostemma and <i>Gomphogyne</i>+<i>Hemsleya</i> are two new putative holobaramins. </p><p>The present study is the second of its kind, after an analysis of chloroplast genomes in Liliales. This study used both hybridization data and chloroplast genome sequences that supported each other's results. Future chloroplast genome studies could be performed on plant groups that have enough species with mitochondrial genomes.</p>
Genomic analysis of hyperparasitic viruses associated with entomopoxviruses; supplemental data
<p>This data set includes newick files and pdb files used to generate figures in the publication 'Genomic analysis of hyperparasitic viruses associated with entomopoxviruses'.</p>
An unsupervised deep learning framework with variational autoencoders for genome-wide DNA methylation analysis and biologic feature extraction applied to breast cancer
<p>Supplemental data for the paper titled "An unsupervised deep learning framework with variational autoencoders for genome-wide DNA methylation analysis and biologic feature extraction applied to breast cancer"</p>
Comparative genome analysis of Lactococcus lactis indicates niche adaptation and resolves genotype/phenotype disparity
<p>This publication describes the comparative genome analysis of 43 L. lactis strains</p> <p>The data stored here are individual alignments (alignments.zip) and the output files from gene trait matching (GTM_output.zip) used in this study.</p>
PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity
<p><strong>Introduction</strong></p> <p>These are the <em>Summary Level-data</em> as presented in:</p> <p>"PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity". <em>Nature Communications </em>volume 9, Article number: 2904 (2018) doi: 10.1038/s41467-018-04766-9 </p> <p>If you use these data please cite the corresponding manuscript, which can be downloaded here: https://www.nature.com/articles/s41467-018-04766-9. When you have any questions or comments regarding this study or these files, please contact me via:</p> <p>Jessica van Setten, PhD | <em>Department of Cardiology, University Medical Center Utrecht, Utrecht University</em> | j.vansetten [at] umcutrecht [dot] nl</p> <p> </p> <p><strong>Files and description</strong></p> <p>The file PR_interval_July2018_summary_results.txt is gzipped and contains the PR interval GWAS meta-analysis summary results of 92,000 European samples. The imputation reference panel used for most studies was HapMap2 (please note: hg18, build36). </p> <ul> <li><em>SNP</em> - variantID (rsID).</li> <li><em>CHR</em> - chromosome numbers [1-22 and X].</li> <li><em>POS</em> - base pair position, hg18 / build36.</li> <li><em>CODED_ALLELE</em> - coded allele, <em>i.e.</em> the effect allele, as represented (and harmonized) across cohorts. Note that this is not necessarily the minor allele.</li> <li><em>NON_CODED_ALLELE</em> - the other allele, <em>i.e.</em> the non-effect allele.</li> <li><em>CODED_ALLELE_FREQ</em> - coded allele frequency, <em>i.e.</em> the effect allele frequency. Note that this is not necessarily the minor allele frequency.</li> <li><em>BETA_FIXED</em> - beta from the fixed-effects model.</li> <li><em>SE_FIXED </em>- standard error from the fixed-effects model.</li> <li><em>P_FIXED </em>- P-value from the fixed-effects model.</li> </ul>
Lemonade Creek, Yellowstone National Park, USA - Microbial Community Analysis - Cyanidiophyceae genome data for HGT analysis
<p>This dataset consists of 12 metagenome samples that were collected from one of three environments in Yellowstone National Park:</p> <ul> <li>4 samples (numbered 1, 2, 3, 4) are from the "CreekBiofilm" environment.</li> <li>4 samples (1, 2, 3, 4) are from the "Endolithic" environment.</li> <li>4 samples (1, 2, 3, 4) are from the "Soil" environment.</li> </ul> <p>We have found that there are two species of cyanidiophyceae present in these samples: one *Galdieria sulphuraria* (the `*Gsulp*` files) and one *Cyanidioschyzon merolae* (the `*Cmer*` files). For each of these species I extracted their contigs from the metagenome assembly if they had >=10% of their lengths covered by hits with >90% ID to the respective reference genome (i.e., contigs with >10% coverage of hits with >90% ID to a given reference genome). The majority of contigs have >90% hit coverage however, to prevent removal of contigs with novel sequences (arising via HGT or other processes), I used a lenient threshold of 10%. The naming of the files indicate which sample the contigs are from and which of the two cyanidiophyceae species they are putatively from. NOTE: that there are very few predicted proteins in the `YNP_CreekBiofilm_*_Gsulp*` files. This is because this environment is completely dominated by the other algal species and so we recovered very few contigs from this species from these environments.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.