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3,457 results for “chromosomes”
Mitonuclear interactions alter sex-specific longevity in a species without sex chromosomes
<p>Data submission accompanies a manuscript submitted to Proceedings of the Royal Society B entitled "Mitonuclear interactions alter sex-specific longevity in a species without sex chromosomes" by Flanagan, Li, and Edmands. Data files include longevity, mtDNA content, DNA damage, and sample information. All analyses are performed in a single R Markdown file.</p>
Figure 7 in Nearctic-Palaearctic relationships of black flies (Diptera: Simuliidae): chromosomal and morphological evidence for the Prosimulium magnum species group in Japan
Figure 7. Chromosome arm IIIL of male larva of Prosimulium yezoense from Shikoku Island, Japan, 5 April 2009. Section numbers refer to the Prosimulium standard map of Ottonen (1966). Relative to the standard sequence, fixed inversion IIIL-14 is present. Breakpoints of sex-linked inversions IIIL-15 and IIIL-16 are shown. Arrow in section 83 indicates extra band in one homologue, marking the X chromosome (X1). C, centromere (thick in X chromosome, thin in Y chromosome); S, shield marker; T, triad marker; ∗, additional heterochromatin.
Figure 5 in Nearctic-Palaearctic relationships of black flies (Diptera: Simuliidae): chromosomal and morphological evidence for the Prosimulium magnum species group in Japan
Figure 5. Chromosome arm IIL of male larva of Prosimulium yezoense from Shikoku Island, Japan, 5 April 2009. Section numbers refer to the Prosimulium standard map of Ottonen (1966). Relative to the standard sequence, fixed inversion IIL-14 is present. Breakpoints of floating inversion IIL-15 are shown. C, centromere; Pb, parabalbiani; '3' and '5', groups of 3 and 5 bands, respectively; ∗, enhanced bands.
Figure 4 in Nearctic-Palaearctic relationships of black flies (Diptera: Simuliidae): chromosomal and morphological evidence for the Prosimulium magnum species group in Japan
Figure 4. Chromosome arm IIS of male larva of Prosimulium yezoense from Shikoku Island, Japan, 5 April 2009. Section numbers refer to the Prosimulium standard map of Ottonen (1966). C, centromere; rB, ring of Balbiani.
Figure 6 in Nearctic-Palaearctic relationships of black flies (Diptera: Simuliidae): chromosomal and morphological evidence for the Prosimulium magnum species group in Japan
Figure 6. Chromosome arm IIIS of male larva of Prosimulium yezoense from Shikoku Island, Japan, 5 April 2009. Section numbers refer to the Prosimulium standard map of Ottonen (1966). Relative to the standard sequence, fixed inversion IIIS-1 is present. Bl, blister.
Figure 2 in Nearctic-Palaearctic relationships of black flies (Diptera: Simuliidae): chromosomal and morphological evidence for the Prosimulium magnum species group in Japan
Figure 2. Chromosome arm IS of male larva of Prosimulium yezoense from Shikoku Island, Japan, 5 April 2009. Section numbers refer to the Prosimulium standard map of Ottonen (1966).
Figure 3. Chromosome arm IL in Nearctic-Palaearctic relationships of black flies (Diptera: Simuliidae): chromosomal and morphological evidence for the Prosimulium magnum species group in Japan
Figure 3. Chromosome arm IL of male larva of Prosimulium yezoense from Shikoku Island, Japan, 5 April 2009. Section numbers refer to the Prosimulium standard map of Ottonen (1966). Breakpoints of floating inversion IL-25 are shown. N.O., nucleolar organizer.
Figure 1 in Nearctic-Palaearctic relationships of black flies (Diptera: Simuliidae): chromosomal and morphological evidence for the Prosimulium magnum species group in Japan
Figure 1. Transformed centromere region (CIt) of chromosome I of male larva of Prosimulium yezoense from Shikoku Island, Japan, 5 April 2009, with sections numbered according to the Prosimulium standard map of Ottonen (1966). C, centromere; N.O., nucleolar organizer.
Figure 1 in Sex chromosome polymorphism in Bulgarian populations of Microtus guentheri (Danford & Alston, 1880)
Figure 1. Topographic location of the investigated population: 1 – Eastern Rodop Mountains (Latitude 41° 229 North; Longitude 26° 289 East), 2 – Strandzha Mountain (Latitude 42° 559 North; Longitude 27° 519 East).
Figure 6. Chromosome arm IL. A in Cytotaxonomy of the Prosimulium (Diptera: Simuliidae) of Western Asia
Figure 6. Chromosome arm IL. A, Prosimulium frontatum (female; sections 23–44). Relative to the standard sequence, IL-12 is present. B, base of chromosome IL of Prosimulium rachiliense cytoform 'A' (male) with the IL-10 sequence. Fixed rearrangements are italicized and polymorphic rearrangements are in standard type. Abbreviation: N.O, nucleolar organizer.
Figure 8. Chromosome arm IIS. A in Cytotaxonomy of the Prosimulium (Diptera: Simuliidae) of Western Asia
Figure 8. Chromosome arm IIS. A, Prosimulium tomosvaryi (female). Relative to the standard sequence, IIS-3 and IIS- 11 are present. B, Prosimulium frontatum (female) showing heterozygous inversion IIS-12; its breakpoints are indicated by arrows on the standard homologue. Limits of IIS-13 of Prosimulium rachiliense 'B' are indicated by a bracket. Fixed rearrangements are italicized and polymorphic rearrangements are in standard type. Abbreviation: RoB, ring of Balbiani.
Figure 7. Chromosome arm IL in Cytotaxonomy of the Prosimulium (Diptera: Simuliidae) of Western Asia
Figure 7. Chromosome arm IL of Prosimulium tomosvaryi (female), showing the standard sequence. Limits of IL-11 of Prosimulium rachiliense 'A' and IL-13 and IL-14 of P. rachiliense 'B' are shown by brackets. Abbreviations: hb, location of heteroband 23hb of P. tomosvaryi; N.O., nucleolar organizer.
Supporting data for: Gene-rich UV sex chromosomes harbor conserved regulators of sexual development (Carey et al., 2021)
<p>Non-recombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here we generate and use nearly gapless female and male chromosome-scale reference genomes of the moss <i>Ceratodon purpureus </i>to test for degeneration in the bryophyte UV sex chromosome system. We show the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes show signs of weaker purifying selection than autosomes, we find suppressed recombination alone is insufficient to drive gene loss on sex-specific chromosomes. Instead, the U and V sex chromosomes harbor thousands of broadly-expressed genes, including numerous key regulators of sexual development across land plants.</p>
A chromosome-level genome assembly of the orange wheat blossom midge, Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae)
<p><span>The Orange wheat blossom midge <i>Sitodiplosis mosellana </i>Géhin (Diptera: Cecidomyiidae), an important insect pest, has caused serious yield losses in most wheat-growing areas worldwide in the past half-century. In this study, we assembled the first chromosomal level genome for <i>S. mosellana</i> using PacBio long-read, Illumina short-read sequences and high-throughput chromatin conformation capture (Hi-C) genome scaffolding techniques. The final genome assembly was 180.69 Mb, with contig and scaffold N50 sizes of 998.71 kb and 44.56 Mb, respectively. Hi-C scaffolding reliably anchored four pseudochromosomes, accounting for 99.67% of the assembled genome. The assembly showed high integrity and quality, with 91.7% of short reads mapped to the genome and a coverage rate of 99.8%. The assembly quality was evaluated using Core Eukaryotic Genes Mapping Approach and Benchmarking Universal Single-Copy Orthologs. In total, 12,269 protein-coding genes were predicted, of which 91% were functionally annotated. Phylogenetic analysis indicated that <i>S. mosellana</i> and its close relative the swede midge <i>Contarinia nasturtii</i> diverged about 32.7 million years ago. <i>S. mosellana</i> genome showed high chromosomal synteny with the genome of <i>Drosophila melanogaster</i> and <i>Anopheles gambiae</i>. The key gene families involved in chemosensation and detoxification of plant secondary chemistry were analysed<i>.</i> The high-quality <i>S. mosellana</i> genome data will provide an invaluable resource for research in a broad range of areas, including the biology, ecology, genetics, and evolution of midges as well as insect-plant interactions and co-evolution, and their relatives more generally.</span></p>
SkewDB: A comprehensive database of GC and 10 other skews for over 28,000 chromosomes and plasmids
<p>GC skew denotes the relative excess of G nucleotides over C nucleotides on the leading versus the lagging replication strand of eubacteria. While the effect is small, typically around 2.5%, it is robust and pervasive. GC skew and the analogous TA skew are a localized deviation from Chargaff's second parity rule, which states that G and C, and T and A occur with (mostly) equal frequency even within a strand.</p> <p>Most bacteria also show the analogous TA skew. Different phyla show different kinds of skew and differing relations between TA and GC skew.<br> This article introduces an open access database (https://skewdb.org) of GC and 10 other skews for over 28,000 chromosomes and plasmids. Further details like codon bias, strand bias, strand lengths and taxonomic data are also included.</p> <p>The SkewDB database can be used to generate or verify hypotheses. Since the origins of both the second parity rule, as well as GC skew itself, are not yet satisfactorily explained, such a database may enhance our understanding of microbial DNA.</p>
Data from: Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits
<p>The data directory here includes all of the data and scripts necessary to recreate the results and plots for the manuscript titled "Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits". These data include a genetic map, QTL analysis, paleolog analysis, gene synteny analysis, and assembly validation for yellow starthistle (Centaurea solstitialis).</p>
A chromosome-level genome assembly of Gekko japonicus
<p>We assembled and annotated a chromosome-level genome of <em>Gekko japonicus.</em></p>
A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus
<p><span>Despite increasing sequencing efforts, numerous fish families still lack a reference genome, which complicates genetic research. One such understudied family is the sand lances (Ammodytidae, literally: 'sand burrower'), a globally distributed clade of over 30 fish species that tend to avoid tidal currents by burrowing into the sand. Here, we present the first annotated chromosome-level genome assembly of the great sand eel (<em>Hyperoplus</em> <em>lanceolatus</em>). The genome assembly was generated using Oxford Nanopore Technologies long sequencing reads and Illumina short reads for polishing. The final assembly has a total length of 808.5 Mbp, of which 97.1% were anchored into 24 chromosome-scale scaffolds using proximity-ligation scaffolding. The assembly is highly contiguous with a scaffold and contig N50 of 33.7 Mbp and 31.3 Mbp, respectively, and has a BUSCO completeness score of 96.9%. The presented genome assembly is a valuable resource for future studies of sand lances, as they are of great ecological and commercial importance and may also contribute to studies aiming to resolve the suprafamiliar taxonomy of bony fishes.</span></p>
Genome annotation associated with the publication "Chromosome-level genome assembly of the Cape cliff lizard (Hemicordylus capensis)"
<p>Genome annotation associated with the publication "Chromosome-level genome assembly of the Cape cliff lizard (<em>Hemicordylus capensis</em>)"</p> <p>rHemCap1.1.gff3 - Genome annotation in GFF3 format<br> rHemCap1.1.proteins.fa - Multi-fasta file of protein coding genes<br> rHemCap1.1.cds-transcripts.fa - Multi-fasta file of transcripts (CDS)</p> <p> </p>
Biomass data to accompany Inter-chromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance
<ul> <li>The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance.</li> <li>Here, using herbicide-resistant populations of the common morning glory (<em>Ipomoea</em> <em>purpurea</em>), we perform a multi-level analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations.</li> <li>We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost.</li> <li>Overall, our work suggests that NTSR glyphosate resistance in<em> I. purpurea</em> is conferred by multiple genes which are potentially maintained through generations <em>via</em> ILD and that the fitness cost associated with resistance in this species is likely a by-product of genetic-hitchhiking.</li> </ul>
ScienceDex guides
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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.