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314 results for “genome architecture”
Data from: Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dub and Tetraselmis sp. CCMP 881
The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction.
Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer (Cervus elaphus)
<p>Sexually-selected traits show large variation and rapid evolution across the animal kingdom, yet genetic variation often persists within populations despite apparent directional selection. A key step in solving this long-standing paradox is to determine the genetic architecture of sexually-selected traits to understand evolutionary drivers and constraints at the genomic level. Antlers are a form of sexual weaponry in male red deer. On the island of Rum, Scotland, males with larger antlers have increased breeding success, yet there has been no evidence of any response to selection at the genetic level. To try and understand the mechanisms underlying this observation, we investigate the genetic architecture of ten antler traits and their principal components using genomic data from >38,000 SNPs. We estimate the heritabilities and genetic correlations of the antler traits using a genomic relatedness approach. We then use genome-wide association and haplotype-based regional heritability to identify regions of the genome underlying antler morphology, and an Empirical Bayes approach to estimate the underlying distributions of allele effect sizes. We show that antler morphology is highly repeatable over an individual's lifetime, heritable, and has a polygenic architecture, and that almost all antler traits are positively genetically correlated with some loci identified as having pleiotropic effects. Our findings suggest that a large mutational target and genetic covariances among antler traits, in part maintained by pleiotropy, are likely to contribute to the maintenance of genetic variation in antler morphology in this population.</p>
Data from: Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes
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Data from: Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dub and Tetraselmis sp. CCMP 881
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Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer (Cervus elaphus)
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Data from: Genomic collinearity and the genetic architecture of floral differences between the homoploid hybrid species I. nelsonii and one of its progenitors, I. hexagona
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Data from: Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines
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Data from: Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice
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Data from: Integrating nonadditive genomic relationship matrices into the study of genetic architecture of complex traits
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Data from: Theoretical models of the influence of genomic architecture on the dynamics of speciation
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Data from: Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula
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Data from: Inference of genetic architecture from chromosome partitioning analyses is sensitive to genome variation, sample size, heritability and effect size distribution
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Genome-wide architecture of adaptation in experimentally evolved Drosophila dataset
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Comparative 3D Genome Architecture in Vertebrates
GEO Series GSE167581. Gallus gallus; Sus scrofa; Oryctolagus cuniculus; Macaca mulatta; Homo sapiens; Canis lupus familiaris; Bos taurus; Ovis aries; Mus musculus; Rattus norvegicus; Danio rerio; Felis catus. 54 samples. Type: Expression profiling by high throughput sequencing; Other.
SATB2 organizes the 3D genome architecture of cognition in cortical neurons [ATAC-seq]
GEO Series GSE222607. Mus musculus. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Phenotypic plasticity shapes genome architecture in the honeybee Apis mellifera
GEO Series GSE120563. Apis mellifera. 15 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
An EGR1-dependent cascade modulates genome architecture at the CSF1R locus [RNA-Seq]
GEO Series GSE283663. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
3D genomics across the tree of life reveals condensin II as a determinant of architecture type [Hi-C]
GEO Series GSE163625. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Reorganization of 3D chromatin architecture of rice genomes during heat stress (HiC)
GEO Series GSE144565. Oryza sativa. 8 samples. Type: Other.
Integration of 3D genome architecture and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects
GEO Series GSE185255. Mus musculus. 24 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
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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.