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3,457 results for “chromosomes”
Data for: Three amphioxus reference genomes reveal gene and chromosome evolution of chordates
<p><span>The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding into vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole genome duplications (WGDs), which gave rise to the extant microchromosomes that likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its 3D chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the <em>Hox</em> gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.</span></p>
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>
All chromosome variation graphs (AllChr)
<p>All chromosomes variation graph used in the experiments of GraphChainer's experiments (<a href="https://doi.org/10.1101/2022.01.07.475257">https://doi.org/10.1101/2022.01.07.475257</a>).</p> <p>The graphs were built with vg, using (<a href="https://doi.org/10.5281/zenodo.6587237">https://doi.org/10.5281/zenodo.6587237</a>) as the reference and <a>ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5c.20130502.sites.vcf.gz as the variants</a>.</p> <p>The rest of the graphs can be found at <a href="https://doi.org/10.5281/zenodo.6875064">https://doi.org/10.5281/zenodo.6875064</a> and <a href="https://doi.org/10.5281/zenodo.6587252">https://doi.org/10.5281/zenodo.6587252</a></p>
FIG. 5 in First Report of B Chromosomes in Caecilians (Amphibia: Gymnophiona)
FIG. 5. Female (BUB1227) mitotic karyotype constructed by pairing the homologous chromosomes together and arranged in their decreasing order. The lone supernumerary chromosome (designated as B) is placed at the end of the karyotype. Scale bar: 10 lm.
FIG. 2 in First Report of B Chromosomes in Caecilians (Amphibia: Gymnophiona)
FIG. 2. Somatic male (BUB1202) metaphase karyotype with the karyotypic formula 2n ¼ 42þ1B and FN ¼ 62. The lone B chromosome is the darkest in the karyotype and is placed at the end of the karyotype. Scale bar: 10 lm.
FIG. 6. C in First Report of B Chromosomes in Caecilians (Amphibia: Gymnophiona)
FIG. 6. C-banded somatic metaphase complement. The darkest chromosome (arrowhead) in the complement corresponds to the B chromosome. Scale bar: 10 lm.
FIG. 1 in First Report of B Chromosomes in Caecilians (Amphibia: Gymnophiona)
FIG. 1. Mitotic male (BUB1202) metaphase complement obtained from intestinal epithelial cells depicting a diploid number (2n) of 42 chromosomes along with a B (arrow) chromosome. Scale bar: 10 lm.
FIG. 3 in First Report of B Chromosomes in Caecilians (Amphibia: Gymnophiona)
FIG. 3. Male (BUB1202) meiotic diplotene karyotype with 21 bivalents and a B chromosome. Scale bar: 10 lm.
FIG. 4 in First Report of B Chromosomes in Caecilians (Amphibia: Gymnophiona)
FIG. 4. Female (BUB1227) somatic metaphase chromosomal complement prepared from liver cells with 2n ¼ 42 and a B chromosome (indicated by arrow). Scale bar: 10 lm.
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>
Repeatome turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets
<p>The present repository provides zipped archives containing the results of the RepeatExplorer2 runs of individual as well as comparative repeat analyses in beet genomes.</p> <p> </p> <p>Sugar beet (<em>Beta vulgaris</em> subsp. <em>vulgaris</em>) and its crop wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNA sequences represent the fastest evolving parts of the genome, they likely impact genomic variability and contribute to the separation of beet gene pools. Hence, we investigated if innovations and losses in the repeatome can be linked to chromosomal differentiation and speciation.</p> <p>We traced genome- and chromosome-wide evolution across sugar beet and twelve wild beets comprising all sections of the beet genera <em>Beta </em>and <em>Patellifolia</em>. For this, we combined data from short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive data framework for our beet panel that spans the complete scale from DNA sequence to chromosome up to the genome. Genome sizes and repeat profiles reflect the separation of the beet species into three gene pools. These gene pools harbor repeats with contrasting evolutionary patterns: We identified section- and species-specific repeat emergences and losses, e.g. of the retrotransposons causal for genome expansions in the section <em>Corollinae</em>/<em>Nanae</em>. Since most genomic variability was found in the satellite DNAs, we focused on tracing the 19 beetSat families across the three beet sections/genera. These taxa harbor evidence for contrasting strategies in repeat evolution, leading to contrasting satellite DNA profiles and fundamentally different centromere architectures, ranging from chromosomal uniformity in <em>Beta</em> and <em>Patellifolia</em> species to the formation of patchwork chromosomes in <em>Corollinae/Nanae</em> species. </p> <p>We show that repetitive DNA sequences are causal for genome size expansion and contraction across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably among beet taxa, leading to the evolution of distinct chromosomal setups. These differences likely contribute to the barriers in beet breeding between the three gene pools. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genome variability, and chromosomal differentiation/evolution and provide a theoretical basis for understanding barriers in crop breeding.</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>
Radotinib Versus Imatinib in Newly Diagnosed Philadelphia Chromosome and Chronic Myeloid Leukemia Chronic Phase Patients
ClinicalTrials.gov study NCT01511289. IPD Sharing: Not stated. Countries: 4. Publications: 1.
Ultra-early Identification of Fetal Chromosomal Characteristics From Extravillous-trophoblast Cells
ClinicalTrials.gov study NCT06523543. IPD Sharing: Not stated. Countries: 1. Publications: 9.
A Study to Investigate Tolerability and Efficacy of Asciminib (Oral) Versus Nilotinib (Oral) in Adult Participants (≥18 Years of Age) With Newly Diagnosed Philadelphia Chromosome Positive Chronic Myel
ClinicalTrials.gov study NCT05456191. IPD Sharing: YES. Countries: 24. Publications: 0.
Chromosome 18 Clinical Research Center
ClinicalTrials.gov study NCT00227253. IPD Sharing: Not stated. Countries: 1. Publications: 24.
Determining the Maximum Tolerated Dose of Low Dose Interferon-alpha in Conjunction With Nilotinib in Pretreated Philadelphia Chromosome Positive (Ph+) Chronic Myeloid Leukemia Patients in Chronic Phas
ClinicalTrials.gov study NCT01220648. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Clinicopathological Features of NSCLC Patients Associated With the Chromosome 2p (EML4-ALK)
ClinicalTrials.gov study NCT01662635. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
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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.