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660 results for “Genome assemblies”
Jaminaea angkorensis draft genome assembly
<p>A draft assembly of the genome of yeast Jaminaea angkorensis produced by SPAdes assembler from Illumina reads, The main purpose is to serve as a reference for analyzing DNA methylation in nanopore sequencing data produced with in vitro methylation. The nanopore data can be downloaded from ENA bioproject <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB64246">PRJEB64246</a>.</p>
Chromosome-scale thraustochytrid genome assembly
<p><span>We used long-read sequencing to produce a telomere-to-telomere genome assembly for the osmoheterotrophic stramenopile protist <em>Aurantiochytrium limacinum</em> MYA-1381. Its ~62 Mb genome is mainly organized in 26 linear chromosomes with a novel configuration: subtelomeric rDNAs are interspersed with long repeated sequence elements denoted as LOng REpeated - TElomere And Rdna Spacers (LORE-TEARS). These repeats may play a role in chromosome end maintenance. A putative circular mirusvirus genome is present at a high copy number (called circular element 1; CE1). The presence of another mirusvirus genome at the end of chromosome 15 in superposition between two complete sets of rRNA and LORE-TEAR elements suggests a dynamic process at the chromosome ends.</span></p>
Quast outputs for "When do longer reads matter? A benchmark of long read de novo assembly tools for eukaryotic genomes"
<p>Quast outputs for "When do longer reads matter? A benchmark of long read de novo assembly tools for eukaryotic genomes"</p>
Six genome assemblies of Drosophila species for: Identification and genetic analysis of a pervasive "needle-eye" sperm phenotype in Drosophila sterile hybrid males
<p>Interspecies hybrid sterility has been extensively studied, especially in the genus <em>Drosophila</em>. Hybrid sterility is more often found in the heterogametic (XX or ZW) sex, a trend called Haldane's rule. Although this phenomenon is pervasive, identification of a common genetic mechanism remains elusive, with modest support found for a range of potential theories. Here, we identify a single precise morphological phenotype, which we call "needle-eye sperm," that is associated with hybrid sterility in three separate species pairs that span the <em>Drosophila</em> genus. The nature of the phenotype indicates a common point of meiotic failure in sterile hybrid males. We used ten generations of backcross selection paired with whole-genome pooled sequencing to genetically map the regions underlying the needle-eye sperm phenotype. Surprisingly, the sterility phenotype was present in ~50% of males even after ten generations of backcrossing, yet the genetic map showed multiple regions associated with sterility, indicating multiple regions may have the capacity to be sufficient to induce sterility in the F1. Due to the common phenotype among sterile male hybrids and the strong effect of individual loci, further exploration of the genes uncovered here may identify a universal mechanism for the evolution of hybrid sterility. </p>
Genome assemblies for Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in mice.
<p>Genome scaffolds, annotations, and CAZy prediction for Gellman et al., 2023.</p>
Atypical flagella assembly and haploid genome coiling during male gamete formation in Plasmodium
<p>Movies of Plasmodium berghei SBF-SEM and serial tomogram datasets including 3D models used in publication 'Atypical flagella assembly and haploid genome coiling during male gamete formation in <em>Plasmodium</em>. Molly Hair, Flavia Moreira-Leite, David Ferguson, Mohammed Zeeshan, Rita Tewari, Sue Vaughan. bioRxiv 2023.05.17.540968; doi: https://doi.org/10.1101/2023.05.17.540968'</p> <p><strong>Movie 1.</strong> Serial block face scanning electron microscopy datasets used in this work. The section thickness (Z resolution) is 100 nm, and each dataset consist of 197 images (pixel dimension and X-Y resolution). </p> <p><strong>Movie 2.</strong> SBF-SEM data and segmentation of a single microgametocyte post-activation showing 8 axonemes coiling around the nucleus in two orientations. Organelles are modelled on the following colours: plasma membrane (white), nucleus (blue), basal body (red), axonemes (yellow/blue – two colours to highlight different directions of coiling). </p> <p><strong>Movie 3.</strong> SBF-SEM imaging and 3D model of a microgamete cell undergoing exflagellation. Structures are modelled on the following colours: plasma membrane (white), nucleus (blue), basal body (red), flagella (pink). </p> <p><strong>Movie 4.</strong> Serial tomogram of a microgamete highlighting the coiling of the nucleus around the axoneme. </p> <p><strong>Movie 5.</strong> Serial tomogram of a microgametocyte showing a nuclear projection surrounding the axoneme, with the 3D reconstruction of the nuceloplasm (cyan), which forms a coil within the nuclear projection. </p>
Figure 3 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 3. Phylogenetic analysis of Romerolagus diazi and related species in the family Leporidae. Totalevidence phylogenetic tree obtained from ML analysis based on a concatenated alignment of amino acids of the 13 protein-coding genes present in the mitochondrial genome of representatives of the family Leporidae. In the analysis, two species of the family Ochotonidae were used as the outgroup. Numbers above or below the branches represent bootstrap values. Photo credit: J.A. Guerrero.
Figure 2 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 2. Relative codon usage analysis for protein coding genes (PCGs) in the mitochondrial genome of Romerolagus diazi assembled from eDNA (field collected droppings, sample SRR14209493 [top] and SRR14209494 [bottom]).
Figure 1 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 1. Circular DNA mitochondrial genome map of Romerolagus diazi assembled from eDNA (field collected droppings, sample SRR14209493). The annotated map depicts 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS: 12S ribosomal RNA and rrnL: 16S ribosomal RNA), 22 transfer RNA (tRNA) genes, and the putative control region (not annotated). Photo credit: J.A. Guerrero.
Sample data for Galaxy genome assembly tutorials
<p>Datasets for assembly tutotorials.</p>
Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia
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Genome assembly and population sequencing reveal three populations and signatures of insecticide resistance of Tuta absoluta in Latin America
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Data from: Genome assembly of Chiococca alba uncovers key enzymes involved in the biosynthesis of unusual terpenoids
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Marasmius oreades genome assembly v2: Linkage map & repeat library
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Data from: "De novo transcriptome assembly of the mountain fly Drosophila nigrosparsa using short RNA-seq reads" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014
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Data from: The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome
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Chromosome-scale thraustochytrid genome assembly
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Data from: "De novo transcriptome assembly and polymorphism detection in ecological important widely distributed Neotropical toads from the Rhinella marina species complex (Anura: Bufonidade)" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014
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Data from: Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution
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Sequencing and assembly of the Mexican lime genome
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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)
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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.