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3,584 results for “genomic analysis”
Putative mutations associated with tetracycline resistance detected in Treponema spp.- an analysis of 4,355 Spirochaetales genomes
<p>Supplementary Table 1–4, , as well as multiple sequence alignment files for 16S rRNA, rpsC, and rpsJ loci, have been deposited.</p> <p>Additionally, the archive contains a <code>scripts.txt</code> file that includes all custom Bash scripts used for:</p> <ul> <li> <p>rRNA gene detection and quantification using <em>Barrnap</em></p> </li> <li> <p>Genome quality assessment using <em>CheckM</em></p> </li> <li> <p>Gene-by-gene schema creation, allele calling, and cgMLST extraction using <em>chewBBACA</em></p> </li> <li> <p>GFF merging and wide-format transformation for summarizing rRNA copy number per genome</p> </li> </ul> <p>These materials are provided to ensure reproducibility of the analyses and to support further investigations into antimicrobial resistance in <em>Spirochaetales</em>.</p>
Supplementary material Comparative Genomic Analysis of Antimicrobial-Resistant Escherichia coli from South American Camelids in Central Germany
<p>Supplementary material for publication González-Santamarina, B.; Weber, M.; Menge, C.; Berens, C. Comparative Genomic Analysis of Antimicrobial-Resistant <i>Escherichia coli</i> from South American Camelids in Central Germany. <i>Microorganisms</i> <strong>2022</strong>, <i>10</i>, 1697. https://doi.org/10.3390/microorganisms10091697 </p>
Complete genome analysis of a novel narnavirus in sweet viburnum (Viburnum odoratissimum)
<p>genome.fasta is Vo narna-like virus complete genomo file.</p><p>JPSH_1.fq.gz and JPSH_1.fq.gz are transcriptome sequencing raw data.</p><p>JPSH.fq.gz is siRNA sequencing raw data.</p><p>trinity.JPSH.Trinity.fasta is Trinity assembly result.</p><p>trinity.nr.JPSH is DIAMOND-BLASTX result</p><p> </p>
FIG. 1 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 1.—Map of the Hawaiian Islands with collection sitesfor Hawaiian hoary bat tissues used inthis study. Sites with n> 1 are denoted with an asterisk.
FIG. 2 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 2.—PCA result plot showing clustering of individual bats from four Hawaiian Islands using 21,808,031 SNPs. Sample information included in supplementary table S4, Supplementary Material online.
FIG. 4 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 4.—SNAPP-based phylogenetic tree inference. (A) The maximum clade credibility or consensus tree, showing approximate divergence of hoary bats across the Hawaiian archipelago. The axis on the bottom of the figure corresponds to million years before present (Ma), using the emergence of Hawai'i (~0.43 Ma) as a calibration point (95% confidence intervals were given in square brackets). (B) The drawing of all sampled trees showing all ingroup nodes were supported by maximum posterior probabilities (1.00).
Genomic Analysis of Public Klebsiella Reference Strains
<p>A genomic resource of <em>Klebsiella </em>reference strains from ATCC, NCTC and BEI Resources MRSN Diversity Panel.</p>
Corallorhiza maculata genomic and transcriptomic analysis
<p>Novoplasty assemblies of plastid genomes from two different Corallorhiza maculata plants (Circularized_assembly_1_CM_1A.fasta and Circularized_assembly_1_CM_2A.fasta).</p> <p>Spades assembly of total cellular genomic DNA from one Corallorhiza maculata plant (scaffolds.fasta.gz). This assembly includes scaffolds of mitochondrial origin (as well as plastid and nuclear).</p> <p>Trinity assembly of rRNA-depleted RNA-seq reads from one Corallorhiza maculata plant (trinity_out_dir.Trinity.fasta.gz).</p>
Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds
<p>The current study was conducted from 2009 to 2019 in three hot and dry agroecological zones in Egypt: Western Desert coastal zone, New Valley desert oasis, and hot-dry Upper Egypt. Within these zones, three local sheep breeds were studied: Barki (83 ewes), Wahati (55 ewes) and Saidi (68 ewes). During the study period, the animals exercised under natural heat stress (simulating summer grazing on poor pasture). Meteorological and physiological parameters were measured and recorded. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on the animals' response to the five main physiological parameters (scale from 0 to 5). DNA samples were extracted for genomic analysis. The genetic diversity measurements showed a significant influence of breed and location on the populations. The influence of breed is more significant than that of location. The inbreeding analysis shows that the desert breeds (Wahati and Barki) have lower values than the urban breed (Saidi). The high rate of sub-clustering indicates the process of sub-population through inbreeding pressure. Wahati and Barki are very distinct breeds with strong identification, while Saidi breed has crosses with other breeds. The most significant SNPs associated with heat tolerance were found in MYO5A, PRKG1, GSTCD, and RTN1 genes (P < 0.0001). MYO5A had an effect of 0.74 on the trait heat tolerance in the studied population. It produces a protein that is widely distributed in the melanin-producing neural crest of the skin. Genetic association between genetic and phenotypic variations showed that OAR1 18300122.1, located in ST3GAL3, had the greatest positive effect on heat tolerance. GWAS analysis identified SNPs associated with heat tolerance in the PLCB1, STEAP3, KSR2, UNC13C , PEBP4, and GPAT2 genes.</p>
Figure 8 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 8. Genomic tree of Heteropterinae Aurivillius, 1925, some Old World Hesperiinae and relatives. See Fig. 1 legend for notations.
Figure 17 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 17. Genomic tree of Carystina, Pericharini, Megathymini and relatives. Clades corresponding to new subtribes described in this work are highlighted in green. See Fig. 1 legend for other notations.
Figure 2 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 2. Holotypes of the Eudaminae species described in this work: a) Ornilius rotundus Grishin, gen. n., sp. n. dorsal; b) ibid. ventral; c) Dyscophellus australis Grishin, sp. n. dorsal; d) Salantoia metallica Grishin, sp. n. dorsal; e) ibid. ventral; f) ibid. left antennal club in ventro-anterior view, nudum facing up, 1 mm scale above; g) ibid. sterigma and ovipositor in ventral view, 1 mm scale below; h) Telegonus subflavus Grishin, sp. n. dorsal; i) ibid. ventral; j) Dyscophellus basialbus Grishin, sp. n. dorsal; k) ibid. ventral. Specimen images are to scale (shown under image a) and data are in the text. Photograph c (by N.V.G.) is © of the Trustees of the Natural History Museum London and is made available under Creative Commons License 4.0 (https://creativecommons.org/ licenses/by/4.0/).
Figure 1 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 1. Genomic tree of Eudaminae. The tree is constructed from protein-coding regions. The tree is rooted with Pterourus glaucus (Linnaeus, 1758) (NVG-1670), not shown. Statistical support values are shown on nodes. For each specimen, its name adopted in this work is given first, and a previously used name is listed in square brackets (if different), supplemented with the DNA sample number, type status (see Table 2 caption for abbreviations) and general locality. See Table S1 in the Supplemental file for additional data about these specimens. Synonyms are given in parentheses preceded by "=", and in addition by "‡" for unavailable names. The type status refers to this synonym, if the synonym name is provided. Clades corresponding to new genera, subgenera and species are colored in red, orange and green, respectively, and the names of new taxa are highlighted accordingly. Names of selected tribes, subtribes, genera, and subgenera are labeled at their clades. Clades corresponding to some genera are highlighted in yellow to compare their genetic diversifications (length of the highlight in horizontal dimension) with each other. Groups of similar genetic diversification would ideally correspond to genera. The
Figure 9 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 9. Genomic trees of representative Hesperiidae to illustrate their classification into subfamilies, and for the subfamily Hesperiinae into tribes. Names of species placed in the new tribes described in this work are highlighted in yellow, their clades are colored in red and highlighted in green. Sequenced specimens of the type species of the type genera of the new tribes are illustrated in dorsal (left or above) and ventral (right or below) views and indicated by blue arrows. Some images are left-right inverted and digitally edited to correct wing damage and scale loss by removing imperfections and combining segments of left and right wings. See Fig. 1 legend for other notations.
Figure 12 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 12. Specimens of Hesperiinae. a) Decinea colombiana Grishin, sp. n. holotype dorsal; b) ibid. ventral; c) Cynea rope Grishin, sp. n. holotype dorsal; d) ibid. ventral; e) Hesperia dido Plötz, 1882 neotype dorsal; f) ibid. ventral; g) Godman's copy of an unpublished Plötz's illustration of H. dido, left/right dorsal/ventral, no. 577; h) ibid. no. 577a; i) Lerema lucius Grishin, sp. n. holotype dorsal; j) ibid. ventral; k) Godman's copy of an unpublished Plötz's illustration of Hesperia lochius Plötz, 1882, left/right dorsal/ventral, no. 576; l) H. lochius illustration (left-right inverted for comparison) from the plate 187c[5] in Draudt (1921-1924), ventral; m) Cymaenes laureolus (Schaus, 1913) ventral, Panama: Cocoli, 4-Oct-1962, leg. G. B. Small, NVG-7250 [USNM]; n) ibid. Mexico: Veracruz, Coatepec, Jun-1917, NVG-15111G01 [AMNH]; o) Lerodea sonex Grishin, sp. n. holotype dorsal; p) ibid. ventral; q) Metiscus goth Grishin, sp. n. holotype dorsal; r) Godman's copy of an unpublished Plötz's illustration of Apaustus vicinus Plötz, 1884, left/right dorsal/ventral, no. 764; s) specimen of Corticea from the Staudinger and Bang-Haas collection bearing an old identification label "Padraona vicinus", NVG-18096C08, dorsal; t) ibid. ventral. Specimen images are to scale and missing data are in the text. Photographs a–d (by Bernard Hermier) and g, h, k, r (by N.V.G.) are © of the Trustees of the Natural History Museum London and are made available under Creative Commons License 4.0 (https://creativecommons.org/licenses/by/4.0/), and photographs o, p are © of Jim Brock, used with permission.
REPIN population analysis in 49 Stenotrophomonas maltophilia genomes
<p>This dataset contains the genome sequences of 49 S. maltophilia strains (input.zip) and the processed data from four individual RAREFAN runs. RAREFAN identifies RAYTs REPINS for each supplied genome and a reference genome. Four different strains where used as a reference genome: AA1, AB550 FDARGOOS_649, ISMMS3, and Sm53. The data were processed with default RAREFAN job parameters. Links to the original RAREFAN jobs are given below.</p>
Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges
<p>The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, e.g., when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species <em>Formica polyctena</em> and <em>F. aquilonia</em>. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent-based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (ca. 500 kya) and occurred with continuous asymmetrical gene flow from <em>F. aquilonia</em> to <em>F. polyctena</em> until a recent time, when migration became negligible (2-19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.</p>
Phylogenetic analysis of policistronic amino-acid sequences encoded by 116 flavivirus genomes
<p><span>Recently, Genome Biology and Evolution (11:3341-3352) published three statistical tests for testing whether alignments of sequence data violate the phylogenetic assumption of evolution under homogeneous conditions. The tests extend the matched-pairs tests of symmetry, marginal symmetry, and internal symmetry for pairs of aligned homologous sequences to the case where a whole alignment is considered. Here we reveal that the new tests are misleading. We explain why this is so, reveal how the tests of whole alignments may be done, and release new bioinformatics tools that implement statistically sound methods of dealing with multiple comparisons (i.e., by controlling the family-wise error rate or the false discovery rate). Using the new software to analyse an alignment of amino acids encoded by 116 flavivirus genomes, we reveal, for the first time, that these genomes are unlikely to have evolved under stationary, reversible, and homogeneous Markovian conditions.</span></p>
Spanish melon landraces: revealing useful diversity by genomic, morphologic, and metabolomic analysis. Supplementary data.
<p>Original data linked to the publication Spanish melon landraces: revealing useful diversity by genomic, morphologic, and metabolomic analysis. It includes, Supp. Table 1: Genomic data; Supp. Table 2: Characterization data; Supp. Table 3: sugar and acids data; Supp Table Supp. Table 4: Voaltile organic compounds data; Supp Table 5: Germplasm details; Supp. table 6: Cromatographic parameters</p>
Genome-wide analysis resolves the radiation of New Zealand's freshwater Galaxias vulgaris complex and reveals a candidate species obscured by mitochondrial capture
<p>Aim: Freshwater fish radiations are often characterized by multiple closely-related species in close proximity, which can lead to introgression and associated discordance of mitochondrial and nuclear characterizations of species diversity. As a case in point, single locus nuclear versus mitochondrial analyses of New Zealand's stream-resident <em>Galaxias vulgaris</em> complex have yielded conflicting phylogenies. Our goal is to use genome-wide divergence patterns among these fishes to evaluate the potential role of mitochondrial capture in obscuring species diversity and to understand how ancient and anthropogenic drainage modification explains this diversity.</p> <p>Location: Freshwater ecosystems of New Zealand. Methods: We generate and analyze a genome-wide data set comprising 52,352 SNPs across 187 <em>Galaxias</em> specimens to resolve the phylogeny of this recent fish radiation. We conduct phylogenetic, PCA, STRUCTURE, and ABBA-BABA analyses to evaluate the evolutionary relationships of lineages in the context of natural and anthropogenic river drainage alterations.</p> <p>Results: In addition to the 11 previously recognized stream-resident lineages, genome-wide data reveal a twelfth candidate species (<em>G</em>. 'Pomahaka'), apparently obscured by introgressive mitochondrial capture. We identify additional examples of mito-nuclear discordance and putative mitochondrial capture, likely mediated by geological and anthropogenic modification of drainage boundaries.</p> <p>Main conclusions: Our study highlights the need for genome-wide approaches for delimiting freshwater biodiversity. Genetic data also reveal the influence of drainage history on freshwater biodiversity, including the rapid divergence of recently fragmented fish populations, and the conservation genetic risks of anthropogenic translocations events.</p>
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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.