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29 results for “chromosome pairing”
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.
Supplemental Movie Files for "Agent-Based Modeling of a Nuclear Chromosome Ensemble Identifies Determinants of Homolog Pairing During Meiosis" by Chriss et al.
<p>This set of Supplemental Information contains two movies made from the simulations from the model developed in the manuscript "<strong>Agent-Based Modeling of a Nuclear Chromosome Ensemble Identifies Determinants of Homolog Pairing During Meiosis</strong>" by A. Chriss, G. V. Börner, and S. D. Ryan. </p> <p> </p> <p>Supplemental Movie S1: <strong>WT Chromosome Trajectories during Prophase I. </strong>The first file "movie_WT..." contains the file for the results of simulations for the wild-type chromosomes and the exact parameter values can be found in Table 1 of the manuscript. The movie shows one realization of the agent-based model. The simulation movie covers the homology search process from <em>t = 3h </em>to <em>t = 9h</em>. Matching colors correspond to homologous pairs. True chromosome lengths are incorporated and scale the relevant interaction radii. The radius represents the attractive and non-homologous repulsive region.</p> <p> </p> <p>Supplemental Movie S2: <strong>WT Chromosome Trajectories during Prophase I with active dumbbell model. </strong> The second file "movie<em>WT</em>_activedumbbell..." contains the file for the results of the simulations for the modeling of chromosomes as active dumbbells (from polymers) to allow for the study of the effects of elongation, orientation, and flexibility. The movie shows one realization of the agent-based active dumbbell model which is closer to modeling a chromosome as a polymer. The simulation movie covers the homology search process from <em>t = 3h </em>to <em>t = 9h</em>. Matching colors correspond to homologous pairs. True chromosome lengths are incorporated and scale the relevant interaction radii, but are allowed to change in time as the two beads expand and contract. The radius represents the attractive and non-homologous repulsive region.</p> <p> </p> <p>Supplemental Movie S3: <strong><em>spo11</em> hypomorph (30% WT DSB levels) Chromosome Trajectories during Prophase I (parameters from Fig 7B)</strong>. The third file "movie_spo11..." contains the file for the results of the simulations for the spo-11 hypomorph and the associated parameter values can be found in Table 1 of the manuscript. The movie depicts one realization of the agent-based model for the {\it spo11} hypomorphic mutant. The simulation movie covers the homology search process from <em>t = 3h</em> to <em>t = 9h</em> where mutant <em>spo11</em> is associated with a weaker attractive and repulsive force (e.g., reduction to 77% of WT values). True chromosome lengths are incorporated and scale the relevant interaction radii. Matching colors correspond to homologous pairs. The radii represent the homologous attractive and the non-homologous repulsive region. Note that the reduction in interaction strength delays homologous pairing consistent with experimental observations in [13]. </p> <p> </p> <p> </p> <p>The codes that generated these movies were written in Matlab and freely available via GitHub: <a href="https://github.com/sdryan/ChromosomeDynamicsProphase1">https://github.com/sdryan/ChromosomeDynamicsProphase1</a></p> <p> </p> <p>For questions please contact the corresponding authors: G. Valentin Börner <a href="mailto:g.boerner@csuohio.edu">g.boerner@csuohio.edu</a> (Biology) or Shawn D. Ryan <a href="mailto:s.d.ryan@csuohio.edu">s.d.ryan@csuohio.edu</a> (Math).</p>
Coverage data in males and females, and genetic markers used for genetic mapping of the guppy LG12 (sex chromosome pair)
<p>The study used genetic mapping and coverage data in genome sequences of multiple male and female individuals of <i>M. picta</i> from multiple natural populations to investigate genetic degeneration of the Y chromosome, and quantify gene loss from the Y. The files include coverage results from the sex chromosome that were (i) used for sexing the sequenced individuals, and (ii) combined with autosomal results to analyze M/F, M/A and F/A depth of coverage ratios. Genetic mapping was also used to validate sex linkage, and the data set includes files with genotypes of genetic markers.</p>
Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome
<p>This repository contains the trajectory data from "Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome".</p> <p><strong>Data sets</strong></p> <p>We provide data sets for the following constructs and imaging conditions, where we give the name of the construct and the MS2-parS genomic separation in kb:</p> <ul> <li>data_line0.csv: parS-homie-evePr-PP7, 58 kb</li> <li>data_line1.csv: parS-homie-evePr-PP7, 82 kb</li> <li>data_line2.csv: parS-homie-evePr-PP7, 88 kb</li> <li>data_line3.csv: parS-homie-evePr-PP7, 149 kb</li> <li>data_line4.csv: parS-homie-evePr-PP7, 190 kb</li> <li>data_line5.csv: parS-homie-evePr-PP7, 595 kb</li> <li>data_line6.csv: parS-homie-evePr-PP7, 3.3 Mb</li> <li>data_line3_5s.csv: parS-homie-evePr-PP7, 149 kb, 5 second time interval</li> <li>data_line0_nohomie.csv: parS-lambda-evePr-PP7, 58 kb</li> <li>data_line3_nohomie.csv: parS-lambda-evePr-PP7, 149 kb</li> </ul> <p><strong>Structure of Data</strong></p> <p>The trajectory data are provided as csv files consisting of 13 columns. The column headers are:</p> <ul> <li>cell_id: a unique cell index</li> <li>time_point: the time frame</li> <li>x_blue: x-coordinate of the locus in the blue channel (units in nm)</li> <li>y_blue: y-coordinate of the locus in the blue channel (units in nm)</li> <li>z_blue: z-coordinate of the locus in the blue channel (units in nm)</li> <li>x_green: x-coordinate of the locus in the green channel (units in nm) </li> <li>y_green: y-coordinate of the locus in the green channel (units in nm)</li> <li>z_green: z-coordinate of the locus in the green channel (units in nm) </li> <li>x_Rij: x-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)</li> <li>y_Rij: y-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)</li> <li>z_Rij: z-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)</li> <li>red: intensity in the red channel (a.u.)</li> <li>state: inferred state using a 3-state HMM, with entries 0 (O_off), 1 (P_off), 2 (P_on)</li> </ul>
Coverage data in males and females, and genetic markers used for genetic mapping of the guppy LG12 (sex chromosome pair)
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SCC3 is an axial element essential for homologous chromosome pairing and synapsis
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Data from: The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate 'genomic island of speciation'
Speciation with gene flow may be aided by reduced recombination helping to build linkage between genes involved in the early stages of reproductive isolation. Reduced recombination on chromosome X has been implicated in speciation within the Anopheles gambiae complex, species of which represent the major Afrotropical malaria vectors. The most recently diverged, morphologically indistinguishable, species pair, A. gambiae and Anopheles coluzzii, ubiquitously displays a 'genomic island of divergence' spanning over 4 Mb from chromosome X centromere, which represents a particularly promising candidate region for reproductive isolation genes, in addition to containing the diagnostic markers used to distinguish the species. Very low recombination makes the island intractable for experimental recombination studies, but an extreme hybrid zone in Guinea Bissau offers the opportunity for natural investigation of X-island recombination. SNP analysis of chromosome X hemizygous males revealed: (i) strong divergence in the X-island despite a lack of autosomal divergence; (ii) individuals with multiple-recombinant genotypes, including likely double crossovers and localized gene conversion; (iii) recombination-driven discontinuity both within and between the molecular species markers, suggesting that the utility of the diagnostics is undermined under high hybridization. The largely, but incompletely protected nature of the X centromeric genomic island is consistent with a primary candidate area for accumulation of adaptive variants driving speciation with gene flow, while permitting some selective shuffling and removal of genetic variation.
Distribution. WC core and SE peninsula of Sulawesi, including Mt Kanino, Mt Nokilalaki, Mt Lehio, Rano Rano, and Mamasa regions, Quarles Range, Mt Rantemario, and Mt Latimojong. Descriptive notes. er 155-242 mm, tail 138-190 mm, ear 23-29 mm, hind-foot 28-45 mm; weight 95-170 g. The Montane Hill Rat is the largest member of the B. fratrorum species group, with broad head, long rostrum, and robust body. Pelage is moderately long, soft, and lustrous, with shortish blackish guard hairs mixed throughout. Dorsum is brownish gray, speckled with buff that is a mix of dark gray underfur and overhairs with brown tips and buffy bands, being dark gray for the most part. Sides are paler grayish brown and fade into ventral pelage. Sides of muzzle are white. Venter is grayish white or dark grayish white, although some are grayish buff, with gray hairs and unpigmented tips or unpigmented altogether, respectively. Juveniles are duller and darker, with more grayish white underparts. Feet are long and slender, with white digits. Ears are large, covered in short unpigmented hair, rubbery, and gray and brown hues. Tail is 88-102% of head-body length and mainly bicolored, brownish gray to blackish gray dorsally and glossy white ventrally, with white tip most of the time. Scrotum is gray. Skull is large, with long and wide rostrum and narrow zygomatic plate. Fleas (e.g. Sigmactenus, Stivalius, Musserella, and Dasypsyllus), ticks (Rhipicephalus) pseudoscorpions (Magachernes and Chiridiochernes), and nematodes (Bunomystrongylus and Sibulura) have been recorded from the Montane Hill Rat. There are two pairs of inguinal mammae. Chromosomal complement is 2n = 42, FN = 60 (females) or FN = 61 (males). in Muridae
Distribution. WC core and SE peninsula of Sulawesi, including Mt Kanino, Mt Nokilalaki, Mt Lehio, Rano Rano, and Mamasa regions, Quarles Range, Mt Rantemario, and Mt Latimojong. Descriptive notes. er 155-242 mm, tail 138-190 mm, ear 23-29 mm, hind-foot 28-45 mm; weight 95-170 g. The Montane Hill Rat is the largest member of the B. fratrorum species group, with broad head, long rostrum, and robust body. Pelage is moderately long, soft, and lustrous, with shortish blackish guard hairs mixed throughout. Dorsum is brownish gray, speckled with buff that is a mix of dark gray underfur and overhairs with brown tips and buffy bands, being dark gray for the most part. Sides are paler grayish brown and fade into ventral pelage. Sides of muzzle are white. Venter is grayish white or dark grayish white, although some are grayish buff, with gray hairs and unpigmented tips or unpigmented altogether, respectively. Juveniles are duller and darker, with more grayish white underparts. Feet are long and slender, with white digits. Ears are large, covered in short unpigmented hair, rubbery, and gray and brown hues. Tail is 88-102% of head-body length and mainly bicolored, brownish gray to blackish gray dorsally and glossy white ventrally, with white tip most of the time. Scrotum is gray. Skull is large, with long and wide rostrum and narrow zygomatic plate. Fleas (e.g. Sigmactenus, Stivalius, Musserella, and Dasypsyllus), ticks (Rhipicephalus) pseudoscorpions (Magachernes and Chiridiochernes), and nematodes (Bunomystrongylus and Sibulura) have been recorded from the Montane Hill Rat. There are two pairs of inguinal mammae. Chromosomal complement is 2n = 42, FN = 60 (females) or FN = 61 (males).
Fig. 4 Chromosome pair 6 bearing 5S in Integrated analysis reveals a new species of Corydoras Lacépède, 1803 (Siluriformes: Callichthyidae) in the lower Iguassu River, Brazil
Fig. 4 Chromosome pair 6 bearing 5S (red) and 18S (green) rDNA showing the synteny of these sites. In the first line is C. carlae and in the second line is Corydoras sp
Data from: The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate ‘genomic island of speciation’
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Data from: Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation
The role of chromosome changes in speciation remains a debated topic, although demographic conditions associated with divergence should promote their appearance. We tested a potential relationship between chromosome changes and speciation by studying two Lake Whitefish (Coregonus clupeaformis) lineages that recently colonized postglacial lakes following allopatry. A dwarf limnetic species evolved repeatedly from the normal benthic species, becoming reproductively isolated. Lake Whitefish hybrids experience mitotic and meiotic instability, which may result from structurally divergent chromosomes. Motivated by this observation, we test the hypothesis that chromosome organization differs between Lake Whitefish species pairs using cytogenetics. While chromosome and fundamental numbers are conserved between the species (2n = 80, NF = 98), we observe extensive polymorphism of subtle karyotype traits. We describe intrachromosomal differences associated with heterochromatin and repetitive DNA, and test for parallelism among three sympatric species pairs. Multivariate analyses support the hypothesis that differentiation at the level of subchromosomal markers mostly appeared during allopatry. Yet we find no evidence for parallelism between species pairs among lakes, consistent with colonization effect or postcolonization differentiation. The reported intrachromosomal polymorphisms do not appear to play a central role in driving adaptive divergence between normal and dwarf Lake Whitefish. We discuss how chromosomal differentiation in the Lake Whitefish system may contribute to the destabilization of mitotic and meiotic chromosome segregation in hybrids, as documented previously. The chromosome structures detected here are still difficult to sequence and assemble, demonstrating the value of cytogenetics as a complementary approach to understand the genomic bases of speciation.
Data from: Anolis sex chromosomes are derived from a single ancestral pair
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Data from: Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation
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Regulation of Sex-biased Gene Expression by the X-Y Chromosomal Gene Pair Kdm5c-Kdm5d in Pluripotent Cells
GEO Series GSE277494. Mus musculus. 27 samples. Type: Expression profiling by high throughput sequencing.
Base pair resolution chromosome conformation capture reveals mechanistic insights into the nature of chromatin structure [TT-Seq]
GEO Series GSE281416. Mus musculus. 14 samples. Type: Expression profiling by high throughput sequencing.
The genome-wide, multi-layered architecture of chromosome pairing in early Drosophila embryos
GEO Series GSE121255. Drosophila melanogaster. 2 samples. Type: Other.
Maintenance DNA methylation in pre-meiotic germ cells regulates meiotic prophase by facilitating homologous chromosome pairing
GEO Series GSE169575. Mus musculus. 4 samples. Type: Methylation profiling by high throughput sequencing.
Maintenance DNA methylation in pre-meiotic germ cells regulates meiotic prophase by facilitating homologous chromosome pairing
GEO Series GSE169482. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
A pair of effectors in a conditionally dispensable chromosome of Fusarium oxysporum suppresses host-specific immunity
GEO Series GSE157823. Brassica oleracea; Fusarium oxysporum; Arabidopsis thaliana. 25 samples. Type: Expression profiling by high throughput sequencing.
Centromere Pairing Enables Correct Segregation of Meiotic Chromosomes
GEO Series GSE254215. Saccharomyces cerevisiae. 6 samples. Type: Other.
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