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Distribution. On basis of chromosomally determined specimens, Nairobi Grass Rat occurs in narrow band from C & W Kenya to N Tanzania; it may be present also in S Ethiopia. in Muridae
Distribution. On basis of chromosomally determined specimens, Nairobi Grass Rat occurs in narrow band from C & W Kenya to N Tanzania; it may be present also in S Ethiopia.
Data from: Chromosome scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus and Juncus inflexus
<p>The majority of sequenced genomes in the Monocots are from species belonging to the Poaceae, which includes many commercially important crops. Here, we expand the number of sequenced genomes from the Monocots to include the genomes of four related Cyperids: <em>Carex cristatella</em> and <em>Carex scoparia</em> from Cyperaceae and <em>Juncus effusus</em> and <em>Juncus inflexus</em> from Juncaceae. The high-quality, chromosome-scale genome sequences from these four Cyperids were assembled by combining whole-genome shotgun sequencing of Nanopore long reads, Illumina short reads, and Hi-C sequencing data. Some members of the Cyperaceae and Juncaceae are known to possess holocentric chromosomes. We examined the repeat landscapes in our sequenced genomes to search for potential repeats associated with centromeres. Several large satellite repeat families, comprising 3.2% to 9.5% of our sequenced genomes, showed dispersed distribution of large repeat clusters across all <em>Carex</em> chromosomes, with few instances of these repeats clustering in the same chromosomal regions. In contrast, most large <em>Juncus</em> satellite repeats were clustered in a single location on each chromosome, with sporadic instances of large satellite repeats throughout the Juncus genomes. Recognizable transposable elements account for about 20% of the assemblies, with the <em>Carex</em> genomes containing more DNA transposons than retrotransposons while the converse is true for the <em>Juncus</em> genomes. These genome sequences and annotations will facilitate better comparative analysis within monocots.</p>
Diversity of sex chromosomes in Sulawesian medaka fishes
<p><span>Recent genetic and genomic studies have revealed tremendous diversity in sex chromosomes across diverse taxa. Closely related species with different sex chromosomes provide us with excellent opportunities to investigate the driving forces and the consequences of sex chromosome turnover. In the present study, we investigated the diversity of sex chromosomes of 13 <em>Oryzias</em> species from Sulawesi, Indonesia, which diversified during the last 4.86 million years. Using pooled sequencing we found sex chromosomes in 9 species that all had XY systems, with a species being possibly modified by multiple loci. Seven species (<em>O. woworae</em>, <em>O</em>. <em>asinua</em>, <em>O</em>. <em>wolasi</em>, <em>O</em>. <em>matanensis</em>, <em>O</em>. <em>celebensis</em>, <em>O</em>. <em>hadiatyae</em>, and <em>O</em>. <em>dopingdopingensis</em>) share linkage group (LG) 24 as sex chromosomes; however, they differed in the length and magnitude of sequence divergence between the X and Y chromosomes. The sex chromosome of <em>O</em>. <em>eversi</em> was LG4, which has not been reported as a sex chromosome in any other medaka species. In <em>O</em>. <em>sarasinorum</em>, LG16 and LG22 are associated with sex. Although LG16 was found to be sex-linked in another medaka species previously examined, the sex-determining regions did not overlap. No significant signatures for sex chromosomes were identified in the other 4 species (<em>O</em>. <em>marmoratus</em>, <em>O</em>. <em>nigrimas</em>, <em>O</em>. <em>nebulosus</em>, and <em>O</em>. <em>orthognathus</em>). Frequent turnovers and the great diversity of the sex chromosomes will make Sulawesian medaka species a model system for investigating the driving forces and consequences of sex chromosome turnover.</span></p>
FIGURE. Results of FISH physical mapping on metaphase chromosomes of hyacinth 1. The distribution of 45S rDNA (red arrow) and 5S rDNA (green arrow) signals on the chromosomes; 2. The distribution of telomeric repeats signals on the chromosomes; 3. Chromosome karyotype with 45S rDNA and 5S rDNA; 4. Chromosome karyotype with telomeric repeats. A. 'Gypsy Queen' B.'Purple sensation' C.'Pink pearl' D.'Gypsy princess' E.'Blue pearl' F.'Odysseus' G.'Yellow stone' H.'Red pearl' in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE. Results of FISH physical mapping on metaphase chromosomes of hyacinth 1. The distribution of 45S rDNA (red arrow) and 5S rDNA (green arrow) signals on the chromosomes; 2. The distribution of telomeric repeats signals on the chromosomes; 3. Chromosome karyotype with 45S rDNA and 5S rDNA; 4. Chromosome karyotype with telomeric repeats. A. 'Gypsy Queen' B.'Purple sensation' C.'Pink pearl' D.'Gypsy princess' E.'Blue pearl' F.'Odysseus' G.'Yellow stone' H.'Red pearl'
Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization
<p>Data generated using <a href="https://gitlab.inria.fr/tgrohens/evotsc">EvoTSC</a> and used in the <a href="https://doi.org/10.24072/pci.mcb.100198">Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization</a> paper.</p> <p>This data is also used in Chapter 5 of my <a href="https://gitlab.inria.fr/tgrohens/phd">PhD thesis</a>.</p>
Supplemental documents for: Temperature-associated selection linked to putative chromosomal inversions in king scallop (Pecten maximus)
<p>The genomic landscape of divergence – the distribution of differences among populations or species across the genome – is increasingly characterized to understand the role that microevolutionary forces such as natural selection and recombination play in causing and maintaining genetic divergence. This line of inquiry has also revealed chromosome structure variation to be an important factor shaping the landscape of adaptive genetic variation. Due to a high prevalence of chromosome structure variation and the strong pressure for local adaptation necessitated by their sessile nature, bivalve molluscs are an ideal taxon for exploring the relationship between chromosome structure variation and local adaptation. Here, we report a population genomic survey of king scallop (<em>Pecten</em> <em>maximus</em>) across its natural range in the northeastern Atlantic Ocean, utilizing a recent chromosome-level genome assembly. We report the presence of at least three large (12-22 Mb), putative chromosomal inversions associated with sea surface temperature and whose frequencies are in contrast to neutral population structure. These results highlight a potentially large role for recombination-suppressing chromosomal inversions in local adaptation and suggest a hypothesis to explain the maintenance of differences in reproductive timing found at relatively small spatial scales across king scallop populations.</p>
Supplementary material 4 from: Dhar MK, Kour G, Kaul S (2017) B chromosome in Plantago lagopus Linnaeus, 1753 shows preferential transmission and accumulation through unusual processes. Comparative Cytogenetics 11(2): 375-392. https://doi.org/10.3897/compcytogen.v11i2.11779
Figure S3 : Explanation note: S3a, b: SSR profile of 1B mother and its selfed progeny plants. M = 100bp ladder. Lane1: 1B mother plant. Lane 2: progeny plant with 2n = 26 chromosomes. Lanes 3- 26: 1B chromosome containing progeny plants. S3c, d: SSR profile of 2B and its selfed progeny plants. M = 100bp ladder. Lane1: 2B mother plant. Lane 2: progeny plant with 2n = 28 chromosomes. Lanes 3- 14: 2B chromosome containing progeny plants. Note exactly similar band pattern of mother and higher chromosome progeny plants.
Supplementary material 3 from: Dhar MK, Kour G, Kaul S (2017) B chromosome in Plantago lagopus Linnaeus, 1753 shows preferential transmission and accumulation through unusual processes. Comparative Cytogenetics 11(2): 375-392. https://doi.org/10.3897/compcytogen.v11i2.11779
Figure S2 : Explanation note: S2a: SSAP profile of 1B mother plant and progeny plants. M = 100bp ladder. Lane1: 1B mother plant. Lane 2: progeny plant with 2n = 26 chromosomes. Lanes 3-8: 1B progeny plants. S2b: SSAP profile of 2B mother plant and progeny plants. M = 100bp ladder. Lane 1: 2B mother plant. Lane 2: progeny plant with 2n = 28 chromosomes. Lanes 3-8: 2B progeny plants.
Supplementary material 2 from: Dhar MK, Kour G, Kaul S (2017) B chromosome in Plantago lagopus Linnaeus, 1753 shows preferential transmission and accumulation through unusual processes. Comparative Cytogenetics 11(2): 375-392. https://doi.org/10.3897/compcytogen.v11i2.11779
Figure S1 : Explanation note: SSCP profile of 5S rDNA amplified from various plants. M = 100bp ladder. Lane1: 1B mother plant. Lane 2: progeny plant with 2n = 26 chromosomes. Lanes 3, 4: progeny plants (1B). Lane 5: 2B mother plant. Lane 6: progeny plant with 2n = 28 chromosomes. Lanes 7-9: progeny plants (2B). The band pattern of higher chromosome plants completely matches that of the mother plants as indicated by arrows.
Supplementary material 1 from: Di-Nizo CB, Banci KRS, Sato-Kuwabara Y, Silva MJJ (2017) Advances in cytogenetics of Brazilian rodents: cytotaxonomy, chromosome evolution and new karyotypic data. Comparative Cytogenetics 11(4): 833-892. https://doi.org/10.3897/CompCytogen.v11i4.19925
Table S1 : Explanation note: Sequences analysed for phylogenetic reconstruction (Maximum likelihood and Bayesian Inference) of Neacomys, with species, GenBank and lab/ field number, diploid and fundamental number (when available), locality and reference.
Supplementary material 1 from: Pereira T, Reis A, Cardoso D, Cristiano M (2018) Molecular phylogenetic reconstruction and localization of the (TTAGG)n telomeric repeats in the chromosomes of Acromyrmex striatus (Roger, 1863) suggests a lower ancestral karyotype for leafcutter ants. Comparative Cytogenetics 12(1): 13-21. https://doi.org/10.3897/CompCytogen.v12i1.21799
Figure S1. Phylogenomic tree used to estimate the ancestral chromosome number. : Explanation note: Numbers at nodes represent the first and second most likely haploid chromosome number followed by posterior support values under Bayesian optimization and the ancestral haploid chromosome number with best likelihood under maximum likelihood optimization, as follows: [first haploid state (P.P.%)// second haploid state (P.P.%)// ML haploid state].
FIGURE 3. Chromosomal complement from a in Pseudoendemism in Mediterranean black flies (Diptera: Simuliidae): a new record for Africa
FIGURE 3. Chromosomal complement from a female larva of Simulium ichnusae from the Djurdjura Mountains of Algeria; C, centromere. A. Centromere region and base of long (left) and short (right) arms of chromosome I, showing transposed nucleolar organizer (NO). B. End of IL, showing IL-2 sequence and limits of floating inversion IL-11 (brackets). C. IIS triple heterozygote for floating inversions IIS-2, 3, 4 (brackets and arrows) and base of IIL, showing ectopic pairing of CII with CI. D. IIIS and basal half of IIIL, showing IIIL-1, 19, 2 sequence (arrows indicate breakpoints).
Tree Sequence and Genealogical Forest Files for a Simulated Human Chromosome 20
<p>Dataset containing 640000 samples simulated using <a href="https://github.com/popsim-consortium/stdpopsim">stdpopsim</a> 0.2.0 and the <code>HapMapII_GRCh38</code> genetic map.<br>The tree sequence was converted to a genealogical forest files via <a href="https://github.com/lukashuebner/gfkit">gfkit</a> version <code>fbd2740</code>.</p>
FIGURE 20 in Markers in the polytene chromosomes of freshwater Chironomus Meigen (Diptera, Chironomidae) species
FIGURE 20 (AB). Polytene chromosomes of Chironomus parathummi. The numbers on the chromosome arms indicate the "basic"sequences. The large arrows show the localization of the centromere region. The small arrow on chromosome G indicates the marker sequences required for species identification. BR—Balbiani Ring, NOR—Nuclear Organizer Region. A, B, C, D, E, F, G—arms of the chromosomes. Scale bar, 10µm.
FIGURE 18 in Markers in the polytene chromosomes of freshwater Chironomus Meigen (Diptera, Chironomidae) species
FIGURE 18. Polytene chromosomes of Chironomus pseudothummi. The numbers on the chromosome arms indicate the "basic"sequences. The large arrows show the localization of the centromere region. The small arrow on chromosome G indicates the marker sequences required for species identification. BR—Balbiani Ring, NOR—Nuclear Organizer Region. A, B, C, D, E, F, G—arms of the chromosomes. Scale bar, 10µm.
FIGURE 15 in Markers in the polytene chromosomes of freshwater Chironomus Meigen (Diptera, Chironomidae) species
FIGURE 15. Polytene chromosomes of Chironomus aprilinus. The numbers on the chromosome arms indicate the "basic"sequences. The large arrows show the localization of the centromere region. The small arrow on chromosome G indicates the marker sequences required for species identification. BR—Balbiani Ring, NOR—Nuclear Organizer Region. A, B, C, D, E, F, G—arms of the chromosomes. Scale bar, 10µm.
FIGURE 17 in Markers in the polytene chromosomes of freshwater Chironomus Meigen (Diptera, Chironomidae) species
FIGURE 17. Polytene chromosomes of Chironomus luridus. The numbers on the chromosome arms indicate the "basic"sequences. The large arrows show the localization of the centromere region. The small arrow on chromosome G indicates the marker sequences required for species identification. BR—Balbiani Ring, NOR—Nuclear Organizer Region. A, B, C, D, E, F, G—arms of the chromosomes. Scale bar, 10µm.
FIGURE 14 in Markers in the polytene chromosomes of freshwater Chironomus Meigen (Diptera, Chironomidae) species
FIGURE 14. Polytene chromosomes of Chironomus acidophilus. The numbers on the chromosome arms indicate the "basic"sequences. The large arrows show the localization of the centromere region. The small arrow on chromosome G indicates the marker sequences required for species identification. BR—Balbiani Ring, NOR—Nuclear Organizer Region. A, B, C, D, E, F, G—arms of the chromosomes. Scale bar, 10µm.
FIGURE 13 in Markers in the polytene chromosomes of freshwater Chironomus Meigen (Diptera, Chironomidae) species
FIGURE 13. Polytene chromosomes of Chironomus acerbiphilus. The numbers on the chromosome arms indicate the "basic"sequences. The large arrows show the localization of the centromere region. The small arrow on chromosome G indicates the marker sequences required for species identification. BR—Balbiani Ring, NOR—Nuclear Organizer Region. A, B, C, D, E, F, G—arms of the chromosomes. Scale bar, 10µm.
FIGURE 16 in Markers in the polytene chromosomes of freshwater Chironomus Meigen (Diptera, Chironomidae) species
FIGURE 16. Polytene chromosomes of Chironomus dorsalis. The numbers on the chromosome arms indicate the "basic"sequences. The large arrows show the localization of the centromere region. The small arrow on chromosome G indicates the marker sequences required for species identification. BR—Balbiani Ring, NOR—Nuclear Organizer Region. A, B, C, D, E, F, G—arms of the chromosomes. Scale bar, 10µm.
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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.