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168 results for “chromosomal assembly”
Date for: The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into melanic pigmentation of anemonefish
<p><span>Anemonefish are an emerging group of model organisms due to interesting biological traits such as sequential hermaphroditism, social control of size, symbiosis with anemones, and varying pigmentation patterns. In addition to genus-specific traits, the anemonefish <em>Amphiprion</em> <em>clarkii</em> possesses species-specific characteristics such as interspecies co-habitation, high intraspecies color variation, no anemone specificity, and a broad distribution, that have the potential to further our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. However, despite its position as an emerging model species, the genome of <em>A. clarkii </em>is yet to be published. Here, using PacBio long-read, Illumina short-read and Hi-C chromatin capture technology we generated a high-quality chromosome-scale genome for the anemonefish <em>A. clarkii</em>. The initial assembly consisted of 1840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and then annotated with 25,050 </span>protein-coding gene models. With the chromosome-scale assembly encompassing 98.7% of conserved actinopterygian genes and the annotation containing 97.0%, the quality and completeness of this <em>A. clarkii</em> genome is the highest amongst all published anemonefish genomes. The publication of this high-quality genome, along with <em>A. clarkii'</em>s many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.</p>
Repeat annotation of a chromosomal-level assembly of the Callosobruchus maculatus genome
<p>A curated repeat library <c.mac_HiC_plus_beetle_library.lib> was constructed by manually curating the most abundant interspersed repeats identified using RepeatModeler (Smit et al., 2010). The curated library was combined with a beetle-specific library, constructed using RepeatMasker’s queryRepeatDatabase.pl script (-species coleoptera). The genome repeat annotation was generated with RepeatMasker (Smit and Hubley, 2010).</p>
Chromosome-level Genome Assembly of Euphorbia peplus
<p>Code used in genome assembly and annotation: https://github.com/ariellerjohnson/Euphorbia-peplus-genome-project Raw data is available in NCBI PRJNA837952 Euphorbia peplus Genome sequencing and assembly. Also check out our interactive genome browser: https://euphorbgenomes.biohpc.cornell.edu/ And our interactive expression browser: https://bar.utoronto.ca/efp_euphorbia/cgi-bin/efpWeb.cgi</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>
Rockfish chromosome reference assemblies (Kolora et al 2021)
<p>Rockfish chromosome reference assemblies from Kolora et al 2021. These are also uploaded on NCBI however NCBI renamed the contigs making them incompatible with the annotation GFFs. These references have the original contig names and are thus compatible with the annotation GFFs found here https://doi.org/10.5281/zenodo.5534983.</p>
Chromosome-scale thraustochytrid genome assembly
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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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Data from: Genome resources of <em>Xanthomonas vasicola</em> strains from various hosts: Reference-guided chromosome and plasmid assemblies for enhanced pathogen genomics
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Chromosome assembly and preliminary gene and repeat annotations for Myzomela tristrami reference genome
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Assembly of Aegilops umbellulata chromosomes
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A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus
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Data from: Chromosome-level reference genome assembly and gene editing of the dead-leaf butterfly Kallima inachus
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Generation of a chromosome-scale genome assembly of the insect-repellant terpenoid-producing Lamiaceae species, Callicarpa americana
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The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding the origin of domestic goat
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A chromosome-level genome assembly of the orange wheat blossom midge, Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae)
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Date for: The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into melanic pigmentation of anemonefish
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Construction of a chromosome-scale long-read reference genome assembly for potato
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Data from: Chromosome-level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs
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Data from: Chromosome scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus and Juncus inflexus
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Data from: Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome
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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.