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151 results for “Chromosomal Evolution”
Figure 4 in Chromosomal evolution of the genus Nannospalax (Palmer 1903) (Rodentia, Muridae) from western Turkey
Figure 4. Chromosome banding comparisons between the following chromosomal races: a) 2n = 38 and 2n = 36, b) 2n = 38 and 2n = 60, c) 2n = 40 and 2n = 60, d) 2n = 50W and 2n = 38, e) 2n = 52N and 2n = 60, f) 2n = 54N and 2n = 60K, g) 2n = 56W and 2n = 60, h) 2n = 58N and 2n = 60K, i) 2n = 60 and 60K. Rearrangements in figures were coded as 1 in the analyses.
Figure 6 in Chromosomal evolution of the genus Nannospalax (Palmer 1903) (Rodentia, Muridae) from western Turkey
Figure 6. Geographic distributions of chromosomal races of Nannospalax in western Turkey. In the figure the numbers indicate chromosome number, and the letters indicate the position of the chromosomal races (S: south; N: north; E: east, W: west; Tr: Thrace; C: central).
Figure 3. C in Chromosomal evolution of the genus Nannospalax (Palmer 1903) (Rodentia, Muridae) from western Turkey
Figure 3. C-banding results of the following chromosomal races: a) 2n = 60, b) 2n = 36, c) 2n = 38, d) 2n = 40, e) 2n = 50W, f) 2n = 52N, g) 2n = 54N, h) 2n = 56W, i) 2n = 56Tr, and j) 2n = 58N).
FIGURE 4 in Chromosome analysis in Saccodon wagneri (Characiformes) and insights into the karyotype evolution of Parodontidae
FIGURE 4 | Saccodon wagneri metaphase plates after A. Double FISH with 5S rDNA (green-thin arrows) and 18S rDNA (red-thick arrows) probes; B. FISH using telomeric probes showing positive signals in the terminal positions of all chromosomes.
FIGURE 3 in Chromosome analysis in Saccodon wagneri (Characiformes) and insights into the karyotype evolution of Parodontidae
FIGURE 3 | Saccodon wagneri C-banded metaphases. A. Female; B. Male. The arrows indicate the sex chromosomes.
FIGURE 2 in Chromosome analysis in Saccodon wagneri (Characiformes) and insights into the karyotype evolution of Parodontidae
FIGURE 2 | Saccodon wagneri Giemsa karyotypes. A. Female; B. Male. Sex chromosomes are indicated. The NOR-carrying chromosomes, after silver staining, are boxed.
Data from: Female-limited X-chromosome evolution effects on male pre- and post-copulatory success
<p>In our article, entitled "Female-limited X-chromosome evolution effects on male pre- and post-copulatory success", we carried out a female-limited X chromosome evolution experiment to study the effect of X-linked sexually antagonistic genetic variance on male reproductive traits.</p> <p>By limiting expression of the X chromosome to females for multiple generations, we removed male selective constraints, which should allow X-linked female-beneficial alleles to increase in frequency. </p> <p>As a result, expressing the experimentally evolved X chromosome in males, we found a small reduction in male fitness caused by the trade-off between male attractiveness and sperm competitiveness. These results indicate that the X chromosome in <i>D. melanogaster</i> harbors sexually antagonistic genetic variance for pre- and post- copulatory success in males.</p>
Data from: High-resolution chromosome-level genome of Scylla paramamosain provides molecular insights into adaptive evolution in crab
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Data from: Female-limited X-chromosome evolution effects on male pre- and post-copulatory success
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The microevolutionary response to male-limited X-chromosome evolution in Drosophila melanogaster reflects macroevolutionary patterns
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Data from: Chromosome-level genome of the melon thrips yields insights into evolution of a sap-sucking lifestyle and pesticide resistance
<p>Thrips are tiny insects from the order Thysanoptera (Hexapoda: Condylognatha), including many sap-sucking pests that are causing increasing damage to crops worldwide. In contrast to their closest relatives of Hemiptera (Hexapoda: Condylognatha) including numerous sap-sucking species, there are few genomic resources available for thrips. In this study, we assembled the first thrips genome at the chromosome level from the melon thrips, <i>Thrips palmi</i>, a notorious pest in agriculture, using PacBio long-read and Illumina short-read sequences. The assembled genome was 270.43 Mb in size with 4,120 contigs and a contig N50 of 426 kb. All contigs were assembled into 16 linkage groups assisted by the Hi-C technique. In total, 16,333 protein-coding genes were predicted, of which 88.13% were functionally annotated. Among sap-sucking insects, polyphagous species usually possess more detoxification genes than oligophagous species. The polyphagous thrips genomes characterized so far have relatively more detoxification genes in the GST and CCE families than polyphagous aphids, but they have fewer UGTs. HSP genes, especially from the Hsp70s group, have expanded in thrips compared to other hemipteran insects. These differences point to different genetic mechanisms associated with detoxification and stress responses in these two groups of sap-sucking insects. The expansion of these gene families may contribute to the rapid development of pesticide resistance in thrips, as supported by a transcriptome comparison of resistant and sensitive populations of <i>T. palmi</i>. The high-quality genome developed here provides an invaluable resource for understanding the ecology, genetics and evolution of thrips as well as their relatives more generally.</p>
Lineage-specific patterns of chromosome evolution are the rule not the exception in Polyneoptera insects
The structure of a genome can be described at its simplest by the number of chromosomes and the sex chromosome system it contains. Despite over a century of study, the evolution of genome structure on this scale remains recalcitrant to broad generalisations that can be applied across clades. To address this issue, we have assembled a dataset of 823 karyotypes from the insect group Polyneoptera. This group contains orders with a range of variations in chromosome number, and offer the opportunity to explore the possible causes of these differences. We have analysed this data using both phylogenetic and taxonomic approaches. Our analysis allows us to assess the importance of rates of evolution, phylogenetic history, sex chromosome systems, parthenogenesis, and genome size on variation in chromosome number within clades. We find that fusions play a key role in the origin of new sex chromosomes and that orders exhibit striking differences in rates of fusions, fissions, and polyploidy. Our results suggest that the difficulty in finding consistent rules that govern evolution at this scale may be due to the presence of many interacting forces that can lead to variation among groups.
Widespread recombination suppression facilitates plant sex chromosome evolution
<p>Classical models suggest that recombination rates on sex chromosomes evolve in a stepwise manner to localize sexually antagonistic variants in the sex in which they are beneficial, thereby lowering rates of recombination between X and Y chromosomes. However, it is also possible that sex chromosome formation occurs in regions with pre-existing recombination suppression. To evaluate these possibilities, we constructed linkage maps and a chromosome-scale genome assembly for the dioecious plant <i>Rumex hastatulus</i>. This species has a polymorphic karyotype with a young neo-sex chromosome, resulting from a Robertsonian fusion between the X chromosome and an autosome, in part of its geographical range. We identified the shared and neo-sex chromosome using comparative genetic maps of the two cytotypes. We found that sex-linked regions of both the ancestral and the neo-sex chromosome are embedded in large regions of low recombination. Furthermore, our comparison of the recombination landscape of the neo-sex chromosome to its autosomal homologue indicates that low recombination rates preceded sex linkage. These patterns are not unique to the sex chromosomes; all chromosomes were characterized by massive regions of suppressed recombination spanning most of each chromosome. This represents an extreme case of the periphery-biased recombination seen in other systems with large chromosomes. Across all chromosomes, gene and repetitive sequence density correlated with recombination rate, with patterns of variation differing between repetitive element type. Our findings suggest that ancestrally low rates of recombination may facilitate the formation and subsequent evolution of heteromorphic sex chromosomes.</p>
Ancestral reconstruction of sunflower karyotypes reveals non-random chromosomal evolution
<p>Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous methods while being systematic and repeatable and can be used to map chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower<i>,</i> <i>Helianthus</i> <i>petiolaris</i> ssp. <i>petiolaris</i> and <i>H. petiolaris</i> ssp. <i>fallax.</i> Using <i>syntR</i>, and we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years – a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between 1 and 3 translocations involving only 8 of the 17 chromosomes. This non-random exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that <i>Helianthus</i> has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.</p>
Heterogeneous evolution of sex chromosomes in the torrent frog genus Amolops
<p>In sharp contrast with birds and mammals, sex chromosomes have been described as homomorphic in cold-blooded vertebrates. This sex-chromosome homomorphy has been suggested to result from high turnovers when they are often observed across deeply diverged clades. However, little is known about the tempo and mode of sex chromosome evolution among most closely related species. Here, we examine patterns of sex chromosome evolution among nine species of the torrent frog genus <em>Amolops</em>. Through the analysis of male and female GBS and RAD-seq from 182 individuals and of PCR verification for 176 individuals, we identify signatures of sex chromosomes involving two pairs of chromosomes. We find that the sex-chromosome homomorphy results from both turnover and X–Y recombination in the <em>Amolops</em> species, simultaneously exhibiting heterogeneous evolution on homologous and non-homologous sex chromosomes. The lower turnover rate of non-homologous sex chromosomes exists in these torrent frogs, whereas the ongoing X–Y recombination in homologous sex chromosomes would act as an indispensable force to prevent the sex chromosomes from differentiations. </p>
Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens
<p><span>Variations in chromosome number are occasionally observed among oomycetes, a group that includes many plant pathogens, but the emergence of such variations and their effects on genome and virulence evolution remain ambiguous. We generated complete telomere-to-telomere genome assemblies for <em>Phytophthora sojae</em>, <em>Globisporangium ultimum</em>, <em>Pythium oligandrum</em>, and <em>G. spinosum</em>. Reconstructing the karyotype of the most recent common ancestor in Peronosporales revealed that frequent chromosome fusion and fission drove changes in chromosome number. Centromeres enriched with <em>Copia</em>-like transposons may contribute to chromosome fusion and fission events. Chromosome fusion facilitated the emergence of pathogenicity genes and their adaptive evolution. Effectors tended to duplicate in the sub-telomere regions of fused chromosomes, which exhibited evolutionary features distinct to the non-fused chromosomes. By integrating ancestral genomic dynamics and structural predictions, we have identified secreted Ankyrin repeat-containing proteins (ANKs) as a novel class of effectors in <em>P. sojae</em>. Phylogenetic analysis and experiments further revealed that ANK is a specifically expanded effector family in oomycetes. These results revealed chromosome dynamics in oomycete plant pathogens, and provided novel insights into karyotype and effector evolution.</span></p>
Bryozoan genomes reveal extensive chromosome rearrangement and the evolution of bilaterian genome structure
<p>Orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, can be seen between bilaterian phyla as divergent as Chordata, Echinodermata, Mollusca, and Nemertea and likely reflects the importance of genome organization to gene regulatory landscapes. Here, we report a unique pattern of genome evolution in Bryozoa, an understudied phylum of colonial invertebrates. Using comparative genomics, including phylogenetic reconstruction and orthologous gene mapping, we reconstruct the chromosomal evolutionary history of five bryozoans. We infer the ancestral bryozoan genome organization and identify multiple ancient chromosome fusions followed by gene mixing, leading to the near-complete loss of bilaterian linkage groups. A second wave of rearrangements, including chromosome fission, occurred independently in two bryozoan classes, further shuffling bryozoan genomes. We also discover at least five derived chromosomal fusion events shared between bryozoans and brachiopods, supporting the traditional yet highly debated Lophophorata hypothesis. Finally, we show that chromosome fusion and fission processes led to the separation of bryozoan Hox clusters. Our findings demonstrate that the canonical bilaterian genome structure has been lost across an entire phylum, reveal that linkage group fission can occur very frequently in specific lineages, and provide a powerful source of phylogenetic information.</p>
FIGURE 1 in Chromosome analysis in Saccodon wagneri (Characiformes) and insights into the karyotype evolution of Parodontidae
FIGURE 1 | Map of Ecuador, highlighting the sampling site of Saccodon wagneri.
Chromosome-level assemblies of the Pieris mannii butterfly genome suggest Z-origin and rapid evolution of the W chromosome
<p><span>The insect order Lepidoptera (butterflies and moths) represents the largest group of organisms with ZW/ZZ sex determination. While the origin of the Z chromosome predates the evolution of the Lepidoptera, the W chromosomes are considered younger, but their origin is debated. To shed light on the origin of the lepidopteran W, we here produce chromosome-level genome assemblies for the butterfly <em>Pieris</em> <em>mannii</em>, and compare the sex chromosomes within and between <em>P. mannii </em>and its sister species <em>P. rapae</em>. Our analyses clearly indicate a common origin of the W chromosomes of the two <em>Pieris</em> species, and reveal similarity between the Z and W in chromosome sequence and structure. This supports the view that the W in these species originates from Z-autosome fusion rather than from a redundant B chromosome. We further demonstrate the extremely rapid evolution of the W relative to the other chromosomes and argue that this may preclude reliable conclusions about the origins of W chromosomes based on comparisons among distantly related Lepidoptera. Finally, we find that sequence similarity between the Z and W chromosomes is greatest toward the chromosome ends, perhaps reflecting selection for the maintenance of recognition sites essential to chromosome segregation. Our study highlights the utility of long-read sequencing technology for illuminating chromosome evolution.</span></p>
Chromosome evolution in Lepidoptera
<p>Supplementary data sets associated with the manuscript 'Chromosome evolution in Lepidoptera'.</p> <p><strong>repeat_libraries_all_species.zip</strong> - Repeat libraries for each of the 209 Lepidopteran and 4 Trichopteran species analysed with Earl Grey. Supplied in fasta format.</p> <p><strong>repeat_annotation_gffs_all_species.zip </strong>- Repeat annotations for each of the 209 Lepidopteran and 4 Trichopteran species annotated with Earl Grey. Supplied in gff format.</p> <p><strong>phylogeny_210Leps_5Trichop.treefile </strong>- Lepidopteran<em> </em>species tree in newick format from IQ-TREE. </p> <p><strong>orthologs2Merian_elements_all_species.zip -</strong> tsv files containing assignments of orthologues to Merian elements for each of the 210 Lepidopteran and 4 Trichopteran species analysed.</p> <p><strong>merian_paints_all_species.zip </strong>- PDF files displaying Merian elements painted across the chromosomes of each analysed species.</p> <p><strong>merian_paints_all_species_differences_only.zip </strong>- PDF files displaying Merian elements painted across the chromosomes of each analysed species. Orthologues that belong the 'dominant' Merian element for a given chromosome are painted grey while all other orthologues are painted by Merian element identity. </p>
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Allen Brain Atlas
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International Brain Laboratory public data
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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.