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151 results for “Chromosomal Evolution”
Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system
<p><em>Schistosoma mansoni </em>has a diploid genome of approximately 380 MB, organized in 7 pairs of autosomes and 2 sex chromosomes. The original <em>Schistosoma mansoni </em>Genome Project was completed by the Wellcome Sanger Institute in collaboration with The Institute for Genome Research using a Whole Genome Shotgun sequencing strategy. The draft assembly was subsequently improved first by incorporating Illumina reads from a clonal (single-miracidial) infection and more recently by incorporating long PacBio reads, HiC, and optical mapping data.</p> <p>Associated manuscript can be found at https://www.biorxiv.org/content/10.1101/2021.08.13.456314v1</p>
A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrix
<p>Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen <em>Hemileia vastatrix,</em> have constrained the sustainable production of Arabica coffee for over 150 years. The ability of <em>H. vastatrix </em>to overcome resistance in coffee cultivars and evolve new races is inexplicable for a pathogen that supposedly only utilizes clonal reproduction. Understanding the evolutionary complexity between <em>H. vastatrix</em> and its only known host, including determining how the pathogen evolves virulence so rapidly is crucial for disease management. Achieving such goals relies on the availability of a comprehensive and high-quality genome reference assembly. To date, two reference genomes have been assembled and published for <em>H. vastatrix</em> that, while useful, remain fragmented and do not represent chromosomal scaffolds. Here, we present a complete scaffolded pseudochromosome-level genome resource for <em>H. vastatrix </em>strain 178a (Hv178a). Our initial assembly revealed an unusually high degree of gene duplication (over 50% BUSCO basidiomycota_odb10 genes). Upon inspection, this was predominantly due to a single scaffold that itself showed 91.9% BUSCO Completeness. Taxonomic analysis of predicted BUSCO genes placed this scaffold in Exobasidiomycetes and suggests it is a distinct genome, which we have named Hv178a associated fungal genome (Hv178a AFG). The high depth of coverage and close association with Hv178a raises the prospect of symbiosis, although we cannot completely rule out contamination at this time. The main Ca. 546 Mbp Hv178a genome was primarily (97.7%) localised to 11 pseudochromosomes (51.5 Mb N50), building the foundation for future advanced studies of genome structure and organization. Citation: https://doi.org/10.1101/2022.07.29.502101</p>
FIGURE 1 in Chromosome Numbers of Some Cultivated Acanthaceae with Notes on Chromosomal Evolution in the Family
FIGURE 1 (upper right). Chromosomes of Acanthaceae in pollen mother cells. A. Dyschoriste thunbergiiflora, metaphase II (only half of cell shown), n = 15. B. Brillantaisia owariensis, telophase I, n = 16 (with one lagging chromosome toward "upper" pole). C. Brillantaisia owariensis, metaphase I, n = 16. D. Ruellia elegans, diakenesis (showing nucleolus, n), n = 17. E. Crossandra infundibuliformis, metaphase I, n = 19. F. Ruellia dipteracanthus, metaphase I, n = 17. G. Justicia scheidweileri, metaphase I, n = 14. Chromosomes shown in outline only are touching or overlapping other chromosomes. Scale applies to all figures. See Table 1 for voucher information.
FIGURE 3 in Chromosome Numbers of Some Cultivated Acanthaceae with Notes on Chromosomal Evolution in the Family
FIGURE 3. Flowers of some species for which chromosome numbers are reported here. A. Ruellia costaricensis. B. Graptophyllum pictum. C. Ruellia elegans. D. Brillantaisia owariensis. E. Justicia fulvicoma. F. Ruellia dipteracanthus. G. Ruellia makoyana. H. Thunbergia grandiflora (white-flowered form). I. Megaskepasma erythrochlamys. J. Odontonema tubaeforme. K. Thunbergia mysorensis. L. Strobilanthes hamiltoniana. M. Justicia scheidweileri. N. Peristrophe speciosa. Photos by the author.
FIGURE 2 in Chromosome Numbers of Some Cultivated Acanthaceae with Notes on Chromosomal Evolution in the Family
FIGURE 2 (lower right). Chromosomes of Acanthaceae in pollen mother cells. A. Ruellia costaricensis, telophase II, n = 17. B. Strobilanthes hamiltoniana, telophase I (distance between poles of cell reduced for presentation), n = 11. C. Pseuderanthemum graciliflorum, metaphase I, n = 21. D. Peristrophe speciosa, metaphase I, n = 30. E. Strobilanthes hamiltoniana, diakinesis (showing nucleolus, n), n = 11. Chromosomes shown in outline only are touching or overlapping other chromosomes. Scale applies to all figures. See Table 1 for voucher information.
FIGURE 3 in Reassessing the causal connection between satDNA dynamics and chromosomal evolution in Ctenomys (Rodentia, Ctenomyidae): Unveiling the overlooked importance of the Y chromosome
FIGURE 3 Ancestral RPCS copy number reconstruction. RPCS copy number was mapped along the mtDNA phylogeny using the phytools function anc.ML, for males and females of the Ctenomys Corrientes group separately. The projection of the reconstruction onto the edges of the tree was made with the function contMap. RPCS copy number is expressed as thousands of copies. The scale of the tree is expressed in substitutions per site. Letters A–D correspond to the four main clades of the group.
FIGURE 2 in Reassessing the causal connection between satDNA dynamics and chromosomal evolution in Ctenomys (Rodentia, Ctenomyidae): Unveiling the overlooked importance of the Y chromosome
FIGURE 2 Geographic distribution of mean RPCS copy number. The Corrientes group lineages are surrounded by dashed lines. Locality numbers are: 1 – San Alonso, 2 – Loreto, 3 – Contreras_Cué, 4 – Estancia La Tacuarita, 5 – Saladas Sur, 6 – Saladas, 7 – Santa Rosa, 8 – San Roque, 9 – Estancia San Luis, 10 – Pago Alegre, 11 – Mbarigüí, 12 – Paraje Angostura, 13 – Goya, 14 – Chavarría, 15 – Colonia 3 de abril, 16 – Rincón de Ambrosio.
FIGURE 1 in Reassessing the causal connection between satDNA dynamics and chromosomal evolution in Ctenomys (Rodentia, Ctenomyidae): Unveiling the overlooked importance of the Y chromosome
FIGURE 1 Differences in RPCS copy number in males and females. Scatter plot showing differences in RPCS copy numbers between males and females of the Ctenomys Corrientes group, expressed as thousands of copies. Clades A-D correspond to the four different clades of the phylogeny (figs 3 and 4). A smoothing function was applied with the package ggplot2.
FIGURE 4 in Reassessing the causal connection between satDNA dynamics and chromosomal evolution in Ctenomys (Rodentia, Ctenomyidae): Unveiling the overlooked importance of the Y chromosome
FIGURE 4 Ancestral reconstruction of diploid numbers (2n) and main RPCS reductions and amplifications in the Ctenomys Corrientes group. Ancestral diploid numbers were inferred with the ChromEvol model implemented in RevBayes, over the mtDNA Bayesian phylogeny of the Corrientes group. Numbers in internal nodes/ terminals represent inferred/observed 2n. Colored circles depict 2n (size) and posterior probability of the inferred value (color). Red and green branches depict significant reductions and amplifications in diploid numbers, respectively. Smaller equal-sized black circles show well-supported nodes (posterior probability> 0.75). Black arrowheads denote a marked increase/decrease in RPCS copy numbers (inferred from females). The scale bar is expressed in substitutions per site.
Fig. 2 in Diversity and chromosomal evolution in the genus Ancistrus Kner, 1854 (Loricariidae: Ancistrini) from three hydrographic basins of Mato Grosso State, Brazil
Fig. 2. Karyotypes of Ancistrus with AgRONs in boxes (a-g); C band of Ancistrus sp. 13 (g'). Bars 10µm.
Fig. 3 in Diversity and chromosomal evolution in the genus Ancistrus Kner, 1854 (Loricariidae: Ancistrini) from three hydrographic basins of Mato Grosso State, Brazil
Fig. 3. Metaphases of Ancistrus with C band showing chromosomes NOR positive with large heterochromatin block (arrows). Bars 10 μm.
Fig. 1 in Diversity and chromosomal evolution in the genus Ancistrus Kner, 1854 (Loricariidae: Ancistrini) from three hydrographic basins of Mato Grosso State, Brazil
Fig. 1. Map of Mato Grosso State and sites crop (highlight-) showing Amazon, Araguaia-Tocantins and Paraguay hydrographic basins. Scale of original map 1:100.000.
Fig. 3. Metacentric chromosomal pair 1 in The role of chromosomal fusion in the karyotypic evolution of the genus Ageneiosus (Siluriformes: Auchenipteridae)
Fig. 3. Metacentric chromosomal pair 1 (a) stained with Giemsa, (b) C-banded and (c) hybridized with [TTAGGG]n. The schematic illustration in (d) represents the possible fusion rearrangement which originated this pair.
Fig. 2 in The role of chromosomal fusion in the karyotypic evolution of the genus Ageneiosus (Siluriformes: Auchenipteridae)
Fig. 2. Karyotype of Ageneiosus inermis hybridized with (a) 5S rDNA (digoxigenin, red) and 18S rDNA (FITC, green). Metaphases of Ageneiosus inermis hybridized with (b) [TTAGGG]n telomeric sequence and with (d) [GATA]n repeats. The arrows indicate the metacentric chromosomal pair 1, which was originated by fusion.
Fig. 1 in The role of chromosomal fusion in the karyotypic evolution of the genus Ageneiosus (Siluriformes: Auchenipteridae)
Fig. 1. Karyotypes of Ageneiosus inermis stained with Giemsa (a) and sequentially C-banded (b). The AgNORs bearing chromosomes pair is presented in the box.
Fig. 2 in Chromosome evolution in fishes: a new challenging proposal from Neotropical species
Fig. 2. Scatter-plot of (a, c) diploid number (2n), and (b, d) pg of DNA per haploid nucleus (C-Value), against the phylogenetic position of Actinopterygii families presented by Nelson (2006). Data include all available species (a, b) or exclude possible polyploidy species (c, d). Ellipses with 95% confidence are used as a correlation indicator.
Fig. 1 in Chromosome evolution in fishes: a new challenging proposal from Neotropical species
Fig. 1. Scatter-plot of (a) diploid number (2n) and (b) fundamental number (FN), against the phylogenetic position of Actinopterygii families presented by Nelson (2006) for 103 fish species. Ellipses with 95% confidence are used as a correlation indicator.
Fig. 2 in Evolution of chromosome number in grasshoppers (Orthoptera: Caelifera: Acrididae)
Fig. 2 Male chromosome numbers mapped on the phylogeny of Acrididae constructed by Song et al. (2018). Mapping and ancestral state reconstruction of chromosome number with Mesquite
Fig. 1 Histogram displaying A in Evolution of chromosome number in grasshoppers (Orthoptera: Caelifera: Acrididae)
Fig. 1 Histogram displaying A: the distribution of chromosome numbers across Caelifera and B: chromosome numbers across the different subfamilies of Acrididae. Chromosome numbers are shown as relative frequencies in percent; here, just subfamilies with more than ten records are shown as separated units. Subfamilies with lower sam-
RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" in Journal of Evolutionary Biology
<p>This a data set from the paper RAD-SEQ LINKAGE MAPPING AND PATTERNS OF SEGREGATION DISTORTION IN SEDGES: MEIOSIS AS A DRIVER OF KARYOTYPIC EVOLUTION IN ORGANISMS WITH HOLOCENTRIC CHROMOSOMES" to be published in Journal of Evolutionary Biology</p>
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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.
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DANDI Archive for NWB datasets
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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.