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138 results for “Chromosome structure”
Figure 5. A chromosome structure in case we have 2 visible states and 3 invisible states-Neuroevolution Mechanism for Hidden Markov Model
<p>Generating a population of size n of HMMs at random can be performed with some<br> restrictions:<br> - The weights representing the input layer in the chromosome should be always negligible as<br> initial values.<br> - The weights which are involved in summation of 1.0 in the hidden layer part of the<br> chromosome should be exactly 1.0.<br> Let us assume the following case<br> Visible states are 2 and invisible states (observations) are 3, , then we shall have a<br> chromosome as shown in Figure 5.</p>
Figure 4. A chromosome structure for HMM shown in Figure 2.-Neuroevolution Mechanism for Hidden Markov Model
<p>The chromosome which represents the HMM can be extracted from its corresponding neural<br> network. The general structure of the chromosome is divided into two sections, input layer and<br> hidden layer. Each section contains many slots, and each slot represents a weight from one node in<br> that layer to a node in the next layer (from input to hidden and from hidden to output). The number<br> of slots in the input layer is the same number of input nodes in the neural network. In the hidden<br> layer, number of slots is equal to nodes in the output layer multiplied by the nodes in the hidden<br> layer.</p>
Using the Genetic Algorithm for the Optimization of Dynamic School Bus Routing Problem-Figure 4. Example of a chromosome structure with permutation coding
<p>Each chromosome found in the population formed in the GA is structurally an equal-length coded series. The chromosomes are made of genes. For coding purposes, binary, permutation, and value coding methods are widely used. In the travelling salesman or other similar VRPs, permutation coding technique is preferred over the other techniques. Using the permutation coding technique, each chromosome found in the population is expressed in terms of the numbers of each stop to be followed in the route, as shown in Figure 4.</p>
FIGURE 4 in Population structuration and chromosomal features homogeneity in Parodon nasus (Characiformes: Parodontidae): A comparison between Lower and Upper Paraná River representatives
FIGURE 4 | Molecular data of Parodon nasus from La Plata basin. A. Haplotype network showing the relationship among the sequences. B. Structural population inference by BAPs (K = 2) for the four populations showing the division between Upper and Lower Paraná River systems; C. Bayesian inference tree showing the phylogenetic relationship of the sequences (numbers on the branches correspond to posterior probability; numbers in parentheses correspond to specimen voucher ID).
FIGURE 3 in Population structuration and chromosomal features homogeneity in Parodon nasus (Characiformes: Parodontidae): A comparison between Lower and Upper Paraná River representatives
FIGURE 3 | Karyotypes of the four populations of Parodon nasus submitted to fluorescence in situ hybridization using 18S rDNA (green signal) and 5S rDNA (red signal) probes. Chromosomes with signals for the pPh2004 probe were highlighted in boxes. A. Cuiabá River; B. Mogi-Guaçu River; C. Passa Cinco River; D. Paiol Grande stream. Scale bar = 10µm.
FIGURE 1 in Population structuration and chromosomal features homogeneity in Parodon nasus (Characiformes: Parodontidae): A comparison between Lower and Upper Paraná River representatives
FIGURE 1 | A. Adult specimen of Parodon nasus. B. Partial map of the South America showing the La Plata basin, the principal rivers of the basin, and the collection sites of the P. nasus species analyzed.
FIGURE 2 in Population structuration and chromosomal features homogeneity in Parodon nasus (Characiformes: Parodontidae): A comparison between Lower and Upper Paraná River representatives
FIGURE 2 | Karyotypes of the four populations of Parodon nasus submitted to the C-banding procedure. A. Cuiabá River; B. Mogi-Guaçu River; C. Passa Cinco River; D. Paiol Grande stream. Scale bar = 10µm.
Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones (<em>Haliotis</em>)
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Topoisomerase IIA is essential for maintenance of mitotic chromosome structure
<p>Data files for the manuscript #2020-01760 "Topoisomerase IIA is essential for maintenance of mitotic chromosome structure" in press in the journal "Preceedings of the National Academy of Sciences" (PNAS).</p> <p> </p> <p>Abstract</p> <p>Topoisomerase IIa (TOP2A) is a core component of mitotic chromosomes and important for establishing mitotic chromosome condensation. The primary roles of TOP2A in mitosis have been difficult to decipher due to its multiple functions across the cell cycle. To more precisely understand the role of TOP2A in mitosis, we used the auxin inducible degron (AID) system to rapidly degrade the protein at different stages of the human cell cycle. Removal of TOP2A prior to mitosis does not affect prophase timing or the initiation of chromosome condensation. Instead, it prevents chromatin condensation in prometaphase, extends the length of prometaphase and ultimately causes cells to exit mitosis without chromosome segregation occurring. Surprisingly, we find that removal of TOP2A from cells arrested in prometaphase or metaphase cause dramatic loss of compacted mitotic chromosome structure and conclude that TOP2A is crucial for maintenance of mitotic chromosomes. Treatments with drugs used to poison/inhibit TOP2A function, such as etoposide and ICRF-193, does not phenocopy the effects on chromosome structure of TOP2A degradation by AID. Our data, points to a role for TOP2A as a structural chromosome maintenance enzyme component locking in condensation states once sufficient compaction is achieved.</p>
Somatic copy number and structural variation in RPE-1 cells with induced chromosomal instability
<p><span><span><span><span><span><span><span><span><span><span><span>The chromosome breakage-fusion-bridge (BFB) cycle is a mutational process that produces gene amplification and genome instability. Signatures of BFB cycles can be observed in cancer genomes alongside chromothripsis, another catastrophic mutational phenomenon. Here, we explain this association by elucidating a mutational cascade, downstream of <a>th</a></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>e single cell division error of chromosome bridge formation, that rapidly generates extreme genomic complexity. We show that actomyosin forces are required for initial bridge breakage and mutagenesis, following which chromothripsis accumulates with aberrant interphase replication of bridge DNA. This is then followed by an unexpected burst of DNA replication in the next mitosis, generating extensive DNA damage. During this second cell division, broken bridge chromosomes frequently mis-segregate and form micronuclei, promoting additional chromothripsis. We <a>fu</a></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>rther show that this mutational cascade generates the continuing evolution and sub-clonal heterogeneity characteristic of many human cancers.</span></span></span></span></span></span></span></span></span></span></span></p>
A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes
<p>Quinoa (<em>Chenopodium</em> <em>quinoa</em> Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for three accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we used in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean quinoa accession PI 614886 (QQ74). The final assembly spanned 1.326 Gb, of which 90.5% was assembled into 18 chromosome-scale scaffolds. The genome was annotated with 54,499 protein-coding genes, 97% of which were located on the 18 largest scaffolds. We also produced an updated genome assembly for the B-genome diploid <em>C. suecicum</em> and used it, together with the A-genome diploid<em> C. pallidicaule</em>, to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.20%, 48.61%, and 57.91% of the quinoa, <em>C. pallidicaule</em>, and <em>C. suecicum</em> genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.</p>
Striking variation in chromosome structure within Musa acuminata and its diploid cultivars
<p>The majority of cultivated bananas originated from inter- and intra(sub)specific crosses between two wild diploid species, <em>Musa acuminata</em> and <em>Musa balbisiana</em>. Hybridization and polyploidization events during the evolution of bananas led to the formation of clonally propagated cultivars characterized by a high level of genome heterozygosity and reduced fertility. The combination of low fertility of edible clones and differences in the chromosome structure among <em>M. acuminata</em> subspecies greatly hampers the breeding of improved banana cultivars. Using comparative oligo painting we investigated large chromosomal rearrangements in a set of wild <em>M. acuminata</em> subspecies and cultivars that originated by natural crosses. Additionally, we analyzed chromosome structure of F1 progeny that resulted from crosses between Mchare bananas and wild <em>M. acuminata </em>'Calcutta 4' genotype. Analysis of chromosome structure within <em>M. acuminata</em> revealed the presence of a large number of chromosomal rearrangements showing a correlation with banana speciation. Chromosome painting of F1 hybrids was complemented by Illumina resequencing, which enabled to identify the contribution of parental subgenomes to the diploid hybrid clones. Balanced presence of both parental genomes was revealed in all F1 hybrids with the exception of one clone, which contained only Mchare specific SNPs, and thus most probably originated from an unreduced diploid gamete of Mchare.</p>
Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes
Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism contributes to the convergent evolution of Y chromosome organization across organisms.
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>
Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes
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Striking variation in chromosome structure within Musa acuminata and its diploid cultivars
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Bryozoan genomes reveal extensive chromosome rearrangement and the evolution of bilaterian genome structure
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Chromosome-level genome assembly of Dynastes reidi reveals structural evolution of autosomes and the sex chromosomes in Hercules Beetles
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A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes
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Somatic copy number and structural variation in RPE-1 cells with induced chromosomal instability
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