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3,584 results for “genomic analysis”
Data from: Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees
<p>The <em>Asian honeybee</em>, <em>Apis cerana</em>, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories, and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger-scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group of<em> A. cerana</em>. Integrating this with 525 resequencing datasets, we constructed the first pan-genome of <em>A. cerana</em>, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions, however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novel <em>A. cerana</em> ecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in the Atpalpha gene, indicated that this SV may promote the cold adaptation of <em>A. cerana</em> by altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation of <em>A. cerana</em>.</p>
Genome-wide meta-analysis of short-tandem repeats for Parkinson's disease risk
<p>Idiopathic Parkinson's disease (PD) is the second most common neurodegenerative disease after Alzheimer's disease and is determined by a combination of genetic and environmental risk factors. The to date largest genome-wide association study (GWAS) on single nucleotide polymorphisms (SNPs) by Nalls at al., 2019, reported 90 SNPs that were independently associated with PD risk. However, common SNPs account only for 16-36% of the total genetic heritability of the disease suggesting that other genetic variants play a role in PD susceptibility. One example of previously understudied genetic variants are short-tandem repeats (STR, also known as microsatellites), i.e., repeating sequence motifs in the human genome of 1-6 nucleotides in length. Thus, in this study, we performed a GWAS on imputed STRs in a large PD case-control dataset (n=4,757), and meta-analyzed these data with those from a previous study of the International PD Genetics Consortium (Bustos et al., 2023) resulting in a total sample size of 43,844 PD cases and controls. Thus, in this study, we performed a GWAS on imputed STRs in a large PD case-control dataset (n=4,757) from the US (the PEG and a GHC-based study) and Denmark (PASIDA).</p>
Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation
<p>Summary statistics for "Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation" </p><p>Files are organized in the following directory structure:</p><p><strong>G2G/</strong> - Summary statistics of G2G associations (SNPs, HLA, and gene-level analysis). </p><p><strong>HLA/ </strong>- Peptide binding prediction results</p><p><strong>preS1_haplotypes/ - </strong>Resolved intra-host haplotypes of the preS1 binding region. </p><p><strong>DnDs/</strong> - Calculation of intra-host positive selection, within the preS1 binding region. </p><p> </p>
Population Genomics Analysis of 30 Samples from Each of Multiple Populations Reveals Signatures of Selection from Breeding for Rapid Growth and Apical Dominance in Paulownia fortunei
<p><i>Paulownia fortunei</i> is an ecologically and economically valuable tree cultivated for its rapid growth and high-quality timber. To enhance <i>Paulownia</i> germplasm, we have developed the elite variety QingT with patented advantages in growth rate and apical dominance. To illuminate the genetic basis of QingT's superior traits, here we harness comparative population genomics to analyze genomic variation patterns between QingT and common <i>Paulownia</i>. We performed whole-genome re-sequencing of 30 QingT and 30 common samples, detecting 15.6 million SNPs and 2.6 million indels. Phylogeny and population structure analyses robustly partitioned common and QingT into distinct groups which indicate robust genome stabilization. QingT exhibited reduced heterozygosity and linkage disequilibrium decay compared to common <i>Paulownia</i>, reflecting high recombination, indicating hybridizing effects with common white-flowered string is the source of its patented advantages. Genome selection scans uncovered 25 regions of 169 genes with elevated nucleotide diversity, indicating selection sweeps among groups. Functional analysis of sweep genes revealed upregulation of ribosomal, biosynthesis and growth pathways in QingT, implicating enhanced protein production and developmental processes in its rapid growth phenotype. This study's insights comprehensively chart genomic variation during <i>Paulownia</i> breeding, localizing candidate loci governing agronomic traits, and underpinnings of future molecular breeding efforts to boost productivity. </p>
Reassessment of Amblyscirtes hegon (Hesperiidae) as a complex of four distinct species revealed by genomic analysis
<p>After the discovery of a unique phenotype in the southern United States with a different ventral ground color than nominotypical <i>Amblyscirtes hegon</i> (Scudder, 1863), which occurs in the northeastern United States, genomic analysis revealed that <i>A. hegon</i> is a species complex. Phenotypic, genitalic, and genomic differences of the complex are presented here. Four species are identified: <i>A. hegon; A. nemoris</i> (W. H. Edwards, 1864), stat. rest.; <i>A. matheri</i> Patterson, Pavulaan & Grishin, sp. n. (TL: USA, Mississippi, Warren Co.); and <i>A. gelidus</i> Grishin, Patterson & Pavulaan, sp. n. (TL: USA, Michigan, Van Buren Co.).</p>
Genomic analysis of population history for Hawaiian monk seals
<p>The Hawaiian monk seal, one of the world's most endangered pinnipeds, has faced decades of declines and been the focus of intensive conservation efforts. A myriad of conservation threats has led to range-wide population declines, but population trends among islands can vary widely in response to heterogeneous threats. Populations in the Northwestern Hawaiian Islands have been declining whereas Main Hawaiian Islands numbers are expanding. Molecular data can provide information to disentangle population structure and dynamics; however, previous studies have yielded insufficient resolution in such a genetically depauperate species. Advances in genomic technology and affordability offer a novel opportunity to revisit questions about Hawaiian monk seal trends with high resolution markers that provide better discrimination ability in low diversity species. Here, we investigated region- and island-level population structuring and connectivity. We used BestRAD sequencing on 169 seals from 14 islands that span the archipelago to estimate genetic diversity, genetic differentiation, population structure, and migration rates. We did not find robust evidence for island-level population structure. For the first time, our dataset provided resolution to differentiate regional populations with low but significant genetic differentiation. Further, DAPC analyses illustrated population structure with evidence for connectivity, which mirrored our migration rate estimates. Future conservation decisions will need to consider the balance of maintaining connectivity between regions while not homogenizing and losing valuable yet rare, regional unique variation.</p>
Data from: the great tit HapMap project: a continental-scale analysis of genomic variation in a songbird
<p>A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (<em>Parus major</em>) HapMap project. We screened <em>ca</em> 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographic range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugiam, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear "islands of differentiation", even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (F<sub>ST</sub>), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.</p>
Identification and expression analysis of transcription factors in the Carallia brachiata genome
<p>Rhizophoraceae has 2 terrestrial genera and 4 marine genera. The intertidal zone in which marine mangroves are located is known for its low oxygen and high salinity. Marine and terrestrial genera have evolved distinct adaptive characteristics, among which viviparous reproduction is the most unique. To investigate the genetic foundations difference underlying the adaptive mechanisms of marine–terrestrial genera, we selected two species from Rhizophoraceae. <em>Kandelia obovata</em> is marine and viviparous, and <em>Carallia brachiata</em> is terrestrial and non-viviparous.<em> </em>We compared their transcriptome of 8 tissues (root, stem, leaf, flower, ovule, fruit, seed, embryo) and found that the mature reproductive organs (fruit, seed, embryo) of <em>K. obovata </em>did not reduce metabolic activity compared to <em>C. brachiata</em>. The reproductive organs of <em>K. obovata</em> were regulated by the same gene set as vegetative organs. This contrasted with <em>C. brachiata</em>. Eight kinds of hormone transduction genes were up-regulated in the seed of <em>K. obovata</em>. Finally, and most importantly, the transcriptional factors AP2 and ARF families were significantly more expressed in the reproductive organs of <em>K. obovata</em> than in those of <em>C. brachiata</em>. At the same time, the ERF family was more expressed in its roots. The findings suggested that the hormone transduction may contribute to viviparous initiation. Transcriptional factors were quite crucial for mangroves' adaptation to wetlands.</p>
Summary Statistics from "Genome-wide meta-analysis of phytosterols reveals five novel loci and a detrimental effect on coronary atherosclerosis"
<p>Summary statistics of meta GWAS of phytosterols.</p>
Nanopore MinION Run Metrics and genomic DNA fragment size analysis data from automated phenol-chloroform extractions (RBI LabDroid Maholo)
<p>Nanopore MinION run MinKNOW statistical metrics output, Agilent Femto Pulse and Tape Station gDNA fragment size analysis reports of genomic DNA isolated from automated RBI LabDroid Maholo organic extractions.</p>
Freshwater viral metagenome assembled genomes (vMAGs) used for vContact2 analysis in publication Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments
<p>This dataset contains all freshwater viruses that were mined from publicly available data in an effort to provide biogeographical context to viral communities identified from the Columbia River. These two files include data from:</p> <p>1) East River, CO (PRJNA579838)</p> <p>2) A previous study from the Columbia River, WA (PRJNA375338)</p> <p>3) Prairie Potholes, ND (PRJNA365086)</p> <p>4) Amazon River (PRJNA237344)</p> <p> </p> <p>Manuscript title Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments</p>
Figure 15 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 15. Genomic tree of Moncina, part 3. See Fig. 1 legend for notations.
Figure 14 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 14. Genomic tree of Moncina, part 2. See Fig. 1 legend for notations.
Figure 13 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 13. Genomic tree of Moncina, part 1, and relatives. See Fig. 1 legend for notations.
Figure 10 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 10. Genomic tree of Ceratrichiini and Astictopterini. See Fig. 1 legend for notations.
Figure 7 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 7. Genomic tree of Erynnini. See Fig. 1 legend for notations.
Figure 11 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 11. Genomic tree of Hesperiina and relatives. See Fig. 1 legend for notations.
Figure 5 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 5. Genomic tree of Carcharodini and relatives. See Fig. 1 legend for notations.
Figure 4 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 4. Genomic tree of Tagiades. See Fig. 1 legend for notations.
Figure 6 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 6. Genomic trees of Pyrgini and relatives. See Fig. 1 legend for notations.
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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.