Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
669
datasets available to search
ShareScore release 0.9.0
Dataset results
669 results for “comparative genomics”
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>
Genome-wide association results from Phase 1 data comparing uveitis-JIA cases to non-uveitis JIA samples
<p>Summary-level GWAS results for Phase 1 data affiliated with the manuscript "An amino acid motif in HLA-DRβ1 distinguishes patients with uveitis in juvenile idiopathic arthritis."</p> <p>Columns are:</p> <p> 1. CHR: chromosome</p> <p> 2. SNP: SNP identifier</p> <p> 3. BP: basepair position (hg19)</p> <p> 4. A1: minor allele and tested allele</p> <p> 5. A2: the other allele (major allele)</p> <p> 6. FRQ: frequency of the A1 allele</p> <p> 7. INFO: imputation info score</p> <p> 8. EFFECT: beta/effect size of the SNP</p> <p> 9. SE: standard error of the SNP</p> <p> 10. P: p-value at that SNP</p> <p> </p>
Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians
<p>The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while most annelids have maintained the conserved bilaterian genome structure, a group containing leeches and earthworms possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show leeches and earthworms to have the most highly rearranged genomes of any currently sampled bilaterian. We further show that bilaterian genomes can be classified into two distinct categories—high and low rearrangement—largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion or as rapid, all-encompassing changes over short evolutionary timescales.</p>
Data from: Comparing phylogeographies to reveal incompatible geographical histories within genomes
<p>Modern phylogeography aims at reconstructing the geographic movement of organisms based on their genomic sequences and spatial information. Phylogeographic approaches are often applied to pathogen sequences and therefore tend to neglect the possibility of recombination, which decouples the evolutionary and geographic histories of different parts of the genome. Genomic regions of recombining or reassorting pathogens often originate and evolve at different times and locations, which characterise their unique spatial histories. Measuring the extent of these differences requires new methods to compare geographic information on phylogenetic trees reconstructed from different parts of the genome. Here we develop for the first time a set of measures of phylogeographic incompatibility, aimed at detecting differences between geographical histories in terms of distances between phylogeographies. We study the effect of varying demography and recombination on phylogeographic incompatibilities using coalescent simulations. We further apply these measures to the evolutionary history of human and livestock pathogens, either reassorting or recombining, such as the Victoria and Yamagata lineages of influenza B and the O/ME-SA/Ind-2001 foot-and-mouth disease virus strain. Our results reveal diverse geographical paths of migration that characterise the origins and evolutionary histories of different viral genes and genomic segments. These incompatibility measures can be applied to any phylogeography, and more generally to any phylogeny where each tip has been assigned either a continuous or discrete "trait" independent of the sequence. We illustrate this flexibility with an analysis of the interplay between the phylogeography and phylolinguistics of Uralic-speaking human populations, hinting at patrilinear language transmission.</p>
Aphids comparative genomic
<p>Chemosensory genes from 13 species (olfactory and gustatory receptors): sequences (fasta) and annotation (gff) on genomes</p> <p>TE enriched in regions surrounding these chemosensory genes (10 kb)</p>
Detection of genetic alterations in gastric cancer patients from Saudi Arabia using comparative genomic hybridization (CGH)
<p>Abstract</p> <p>Background: The present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population. </p> <p>Methods: Formalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip. </p> <p>Results: Copy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages.</p>
Comparative genomics of ten new Caenorhabditis species
<p><strong>Phylogenomic analysis</strong></p> <p><code>ASTRAL_species_tree.ASTRAL_branch_lengths.nwk</code>: Species tree generated by ASTRAL-III with branch lengths in coalescent units</p> <p><code>ASTRAL_species_tree.RAxML_branch_lengths.nwk</code>: Species tree generated by ASTRAL-III with branch lengths in substitutions per site as estimated by RAxML (GTR+Γ)</p> <p><code>Caenorhabditis_33species_1988loci_supermatrix.fas</code>: Supermatrix composed of 1988 single-copy loci 27 of 33 species analysed</p> <p><code>Orthogroups.txt</code>: Original orthology clustering file</p> <p><code>PhyloBayes_species_tree.nwk</code>: Species tree generated by PhyloBayes MPI (CAT-GTR+Γ)</p> <p><code>RAxML_species_tree.nwk</code>: Species tree generated by RAxML (GTR+Γ)</p> <p><code>singlecopy_orthologues_redundantseqs_removed.txt</code>: Orthogroups used in analysis, after removing redundant sequences</p> <p><strong>Intron analysis</strong></p> <p><code>Orthogroups_990_0missing_5hetero_paraloguesremoved_withCDSalignments.txt</code>: Single copy orthogroups.txt file (note: this is after removing redundant sequences arising from uncollapsed heterozygosity and removing orthogroups containing paralogues)</p> <p><code>genome_gene_structure_stats.tsv</code>: File containing gene structure and genome size statistics</p> <p><strong>Notch-like receptor analysis</strong></p> <p><code>OG0000658.below700removed.fa</code>: FASTA file of all sequences in orthogroup that were 700 amino acids or longer.</p> <p><code>OG0000658.below700removed.fa.aln</code>: alignment of the above FASTA file</p> <p><code>OG0000658.below700removed.fa_ProSiteProfiles.tsv</code>: InterProScan search results of the above FASTA file using the ProSiteProfiles database (release 2017_09)</p> <p><code>OG0000658.txt</code>: Line from orthology clustering with all (including those below 700 amino acid) sequence IDs</p> <p><code>RAxML_bipartitions.OG0000658.below700removed.nwk</code>: RAxML ML tree of the above alignment file with bootstrap support values</p> <p><code>extract_branch_lengths.py</code>: Python script used to extract branch lengths</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>
Comparative whole genome phylogeny of animal, environmental and human strains confirms the genogroups organization and the diversity of Stenotrophomonas maltophilia
<p>Reannotation of Smc genomes from Refseq (Prokka v1.13) and gene presence and absence spreadsheet from Roary.</p>
Comparative genomics of Helotiales (Leotiomycetes) and in silico analysis of temperature adaptations of plant-associated genes
<p><span>Table S1: Genome assembly size and quality for every species in this study; </span></p> <p><span>Table S2: Genome annotation counts for P450, virulence factors, effectors, and CAZy genes and their temperature adaptation.</span></p>
Data from: Remarkably conserved plastid genomes of Quercus Group Cerris in China: comparative and phylogenetic analyses
Quercus is one of the most important genera for considering its economic and ecological values, with approximately 500 species worldwide. Quercus group Cerris is endemic to Eurasia (including 11 species), and three species (Quercus acutissima, Quercus chenii and Quercus variabilis) are widely distributed in China. Here, we sequenced the complete plastid genomes of Q. acutissima and Q. chenii by Illumina pair-end sequencing, and obtained an additional plastome of Q. variabilis from GenBank. Although geographically distant sampling, the three plastomes in group Cerris were remarkably conserved with regard to genome size, gene organization, GC content, and IR/SC boundary regions. The phylogenetic analysis showed that group Cerris nested in group Ilex, forming a Cerris-Ilex clade. The current study provided plastid genomic-scale data for the less intensively studied group Cerris, which would be useful for studying speciation processes, geographical structure and phylogeny within the group Cerris in the future.
Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals
<p><span>Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within primates, with a special focus on the small-bodied nocturnal mouse and dwarf lemurs of Madagascar (genera <i>Microcebus</i> and <i>Cheirogaleus</i>, respectively). By doubling the existing genomic resources for strepsirrhine primates (i.e., the lemurs and lorises), we find that the highly speciose and morphologically cryptic mouse lemurs have experienced an elaborate proliferation of V1Rs that we argue is functionally related to their capacity for rapid lineage diversification. Contrary to a previous study that found equivalent degrees of V1R diversity in diurnal and nocturnal lemurs, our study finds a strong correlation between nocturnality and V1R elaboration, with nocturnal lemurs showing elaborate V1R repertoires and diurnal lemurs showing less diverse repertoires. Recognized subfamilies among V1Rs show unique signatures of diversifying positive selection, </span>as might be expected if they have each evolved to respond to specific stimuli<span>. Further, a detailed syntenic comparison of mouse lemurs with mouse (genus <i>Mus</i>) and other mammalian outgroups shows that orthologous mammalian subfamilies, predicted to be of ancient origin, tend to cluster in a densely populated region across syntenic chromosomes that we refer to as a V1R "hotspot."</span></p>
Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a geographic survey of genomic variation across four sites where apple and hawthorn flies co-occur from north to south in the Midwestern USA. The results demonstrated that the majority of the genome showing significant geographic and host-related variation can be accounted for by initial diapause intensity and eclosion time. Local genomic differences between sympatric apple and hawthorn flies were subsumed within broader geographic clines; allele frequency differences within the races across the Midwest were 2 to 3-fold greater than those between the races in sympatry. As a result, sympatric apple and hawthorn populations displayed more limited genomic clustering compared to geographic populations within the races. The findings suggest that with reduced gene flow and increased selection on diapause equivalent to that seen between geographic sites, the host races may be recognized as different genotypic entities in sympatry, and perhaps species, a hypothesis requiring future genomic analysis of related sibling species to R. pomonella to test. Our findings concerning the way selection and geography interplay could be of broad significance for many cases of earlier stages of divergence-with-gene flow, including (1) where only modest increases in geographic isolation and the strength of selection may greatly impact genetic coupling and (2) the dynamics of how spatial and temporal standing variation is extracted by selection to generate differences between new and discrete units of biodiversity.
Figure 5 in The complete mitochondrial genome of Lemyra melli (Daniel) (Lepidoptera: Erebidae) and a comparative analysis within the Noctuoidea
Figure 5. The potential stem-loop structure with "GAAT" and "TATA" in the flanking region.
Compare Analysis with a High-quality Genome of Weedy Rice Reveals the Evolutionary Game of De-domestication
<p>A02.SV.vcf is the SV information between the A02 genome and Nipponbare genome.</p> <p>All.population.SV.vcf is the data of the SV genotyping information based on the super pan-genome.</p>
Comparative Mitochondrial Genomics of selected Noctuoid Moths (Lepidoptera: Noctuoidea) with implications for their Phylogeny
<p>In this study, I sequenced and annotated the complete mitochondrial genome sequences of 19 species that belong to the superfamily Noctuoidea viz. <em>Actinotia polyodon, Episparis tortuosalis, Ercheia cyllaria, Eudocima salaminia, Hulodes caranea, Hypospila bolinoides, Ischyja manlia, Lygephila dorsigera, Mecodina praecipua, Mocis undata, Odontodes seranensis, Ophiusa tirhaca, Oraesia emarginata, Pandesma quenavadi, Polydesma boarmoides, Psimada quadripennis, Rusicada privata, Trigonodes hyppasia </em>and<em> Xanthodes albago</em>. In addition to this, I performed the analysis of their genetic compositions as well as their molecular characterization in order to provide molecular insights into their taxonomic and phylogenetic implications. Based on the data and those obtained from the NCBI database, I examined the phylogenetic relationships among the species of the superfamily Noctuoidea.</p>
Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops
<p><em>Vaccinium</em> is a large genus of shrubs that includes a handful of economically important berry crops. Given the numerous hybridizations and polyploidization events, the taxonomy of this genus has remained the subject of long debate. In addition, berries and berry-based products are liable to adulteration, either fraudulent or unintentional due to misidentification of species. The availability of more genomic information could help achieve higher phylogenetic resolution for the genus, provide molecular markers for berry crop identification, and a framework for efficient genetic engineering of chloroplasts. Therefore, in this study, we assembled five <em>Vaccinium</em> chloroplast sequences representing the economically relevant berry types: northern highbush blueberry (<em>V. corymbosum</em>), southern highbush blueberry (<em>V. corymbosum</em> hybrids), rabbiteye blueberry (<em>V. virgatum</em>), lowbush blueberry (<em>V. angustifolium</em>), and bilberry (<em>V. myrtillus</em>). Comparative analyses showed that the <em>Vaccinium</em> chloroplast genomes exhibited an overall highly conserved synteny and sequence identity among them. Polymorphic regions included the expansion/contraction of inverted repeats, gene copy number variation, simple sequence repeats, indels, and single nucleotide polymorphisms. Based on their in silico discrimination power, we suggested variants that could be developed into molecular markers for berry crop identification. Phylogenetic analysis revealed multiple origins of highbush blueberry plastomes, likely due to the hybridization events that occurred during northern and southern highbush blueberry domestication.</p>
Supplemental data for: Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma
<p><em>Trichoderma</em> is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like <em>Trichoderma</em>, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight <em>Trichoderma</em> genomes representing the full breadth of environmental <em>Trichoderma</em>'s diverse lifestyles and nutritional modes. We generated four new <em>Trichoderma endophyticum</em> genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic <em>Trichoderma</em> genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken into consideration, no particular class of metabolic gene cluster was independently associated with the <em>Trichoderma</em> endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic <em>Trichoderma</em> genomes. Most genomic differences between <em>Trichoderma</em> lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that <em>Trichoderma</em> genomes may be particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to <em>Trichoderma</em>.</p>
Key files for: Comparative genomic analysis of Microcystis strain diversity using conserved marker genes
<p>Key data outputs to accompany the manuscript "Comparative genomic analysis of Microcystis strain diversity using conserved marker genes"</p>
Genomic tools for comparative conservation genetics among three recently diverged stag beetles (Lucanus, Lucanidae)
<p>We are witnessing a rapid decline in global biodiversity. International protocols and local conservation laws have been installed to counter such an unprecedented rate of decline. However, quantitatively evaluating how much biodiversity has been lost due to climatic and anthropogenic effects and how much biodiversity has been restored due to conservation efforts remain challenging. We applied a comparative conservation genomic approach to statistically and quantitatively address these questions using three geographical taxa from a stag beetle species complex. We found that the three sky-island taxa formed three independently evolving units without detectable post-divergence gene flow; furthermore, the three taxa, which have been divergent from each other since the mid-Pleistocene, have experienced episodes of demographic decline in the past. More importantly, even though idiosyncratic anthropogenic exploitations have been hypothesized to impact the recent demographic history (< 100 years) differently, we found a shared pattern of continuous decline in effective population size among the three geographical taxa. We argue that future empirical studies should include more taxa, in addition to the focal species, that may or may not be affected by the focal historical events to avoid making biased conservation plans.</p>
ScienceDex guides
Understand access before you commit
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.