Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. (nature.com)
Release of the first human genome assembly was a landmark achievement, and after nearly two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. (labroots.com)
To address this challenge, I will present a whole-genome de novo assembly that surpasses the continuity of GRCh38, along with the first complete, telomere-to-telomere assembly of a human X chromosome. (labroots.com)
Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. (weigelworld.org)
Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between the Eyach15-2 accession and the reference accession Col-0. (weigelworld.org)
We were able to generate enough data to put together a human genome assembly that was in many respects superior to that initial draft," continued Paten, who currently oversees the Center for Big Data in Translational Genomics and is an assistant professor in the Department of Biomolecular Engineering at the University of California, Santa Cruz. (medscape.com)
We talk about 'whole-genome sequencing,' but it's a misnomer because there are parts of the genome that have been unseen, and there have been parts that have, what I'd call, weak assembly," Topol told Medscape Medical News . (medscape.com)
Centromeres are central to chromosome segregation and genome stability, and thus their molecular foundations are important for understanding their function and the ways in which they go awry. (duke.edu)
Consequently, it has been difficult to achieve genome assemblies at centromeres using traditional next generation sequencing approaches, so that centromeres represent gaps in the current human genome assembly. (duke.edu)
In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. (doe.gov)
CONCLUSIONS: On the basis of outgroup comparison, 2n = 18 is the ancestral number, and repeated chromosomal fusions with simultaneous genome size increase as a result of repetitive elements accumulating near centromeres characterize the papaya clade. (uni-muenchen.de)
These results have implications for ongoing genome assemblies in Caricaceae. (uni-muenchen.de)
Sufficient for centromere1
Conversely, the simple presence of alpha satellite DNA is not sufficient for centromere function since chromosomes with multiple alpha satellite arrays only exhibit a single location of centromere assembly. (duke.edu)
Chromosome segregation3
Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. (antikoerper-online.de)
Chromosome segregation relies on coordinated activity of a large assembly of proteins, the kinetochore interaction network (KIN). (oregonstate.edu)
We show that Mhf1 and Mhf2 in fission yeast, as in vertebrates, serve a dual function, aiding DNA repair/recombination and localizing to centromeres to promote chromosome segregation. (elsevierpure.com)
ParABS partition systems, comprising the centromere-like DNA sequence parS, the parS -binding ParB-CTPase and the nucleoid-binding ParA-ATPase, ensure faithful segregation of bacterial chromosomes and low-copy-number plasmids. (biorxiv.org)
Moreover, SL5.0 contains 19.3 Mb more sequences than SL4.0 (801.8 Mb versus 782.5 Mb), with 43 contigs (99.8% of the assembly) ordered and oriented on the 12 chromosomes (Fig. 1a and Extended Data Fig. 2b ). (nature.com)
Centromere protein B is a highly conserved protein that facilitates centromere formation. (wikipedia.org)
Centromere protein B is a potential biomarker of small-cell lung cancer. (wikipedia.org)
Entrez Gene: centromere protein B". Sugimoto K, Yata H, Himeno M (July 1993). (wikipedia.org)
Epigenetic6
Understanding nucleosome assembly mechanisms by its chaperones is a crucial not only to understand how newly synthesized histones are recruited during DNA replication and repair, but also important to reveal transferring mechanism of epigenetic information to newly incorporated nucleosomes. (umich.edu)
Here, we discuss the organization of human centromeres as well as genomic and functional variation in human centromere location, and current understanding of the genomic and epigenetic mechanisms that underlie centromere flexibility in humans. (duke.edu)
The specification of metazoan centromeres does not depend strictly on centromeric DNA sequences, but also requires epigenetic factors. (rupress.org)
An alternative view is that centromere identity is specified by an epigenetic mark on the chromosome that is independent of its underlying DNA ( Karpen and Allshire 1997 ). (rupress.org)
How conserved the underlying mechanisms driving the epigenetic phenomenon of centromere and kinetochore assembly and maintenance are remains unclear, even though various eukaryotic models have been studied. (oregonstate.edu)
Constitutive1
First, they are components of the constitutive centromere-associated network, aiding kinetochore assembly and function. (elsevierpure.com)
Genomes5
Single molecule assembly for genomes large and small. (speakerdeck.com)
Automated ensemble assembly and validation of microbial genomes. (speakerdeck.com)
Reducing assembly complexity of microbial genomes with single-molecule sequencing. (speakerdeck.com)
Glunčić M, Rosandić M, Jelovina D, Dekanić K, Vlahović I, Paar V. Global Repeat Map Method for Higher Order Repeat Alpha Satellites in Human and Chimpanzee Genomes (Build 37.2 Assembly). (srce.hr)
Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. (weigelworld.org)
To study the extent of this variation, I have performed a comprehensive study of centromere sequence structural variation using a panel of high-coverage, long read datasets from individuals from diverse populations. (labroots.com)
Microtubules1
The kinetochore is a large macromolecular assembly that physically connects the centromere to spindle microtubules to ensure accurate distribution of sister chromatids to daughter cells during mitosis. (umich.edu)
Induces1
The CPC complex has essential functions at the centromere in ensuring correct chromosome alignment and segregation and is required for chromatin-induced microtubule stabilization and spindle assembly, fosters AURKB activity, its overexpression induces swelling of mitochondria and reduces mitochondrial membrane potential. (novusbio.com)
Human5
Chaisson, Wilson, Eichler (2015) emphasize the importance of complete de novo assembly as opposed to read mapping as the primary means to understanding the full range of human genetic variation. (speakerdeck.com)
Alpha satellites are tandemly repeated sequences found in all human centromeres. (srce.hr)
Genomic and functional variation of human centromeres. (duke.edu)
Human centromeres typically form at large megabase-sized arrays of alpha satellite DNA for which there is little genomic understanding due to its repetitive nature. (duke.edu)
Recombination1
Erratum: MHF1-2/CENP-S-X performs distinct roles in centromere metabolism and genetic recombination (Open Biology (2013) 3 (130102) DOI: 10.1098/rsob.130102), Sonali Bhattacharjee, Fekret Osman, Laura Feeney, Alexander Lorenz, Claire Bryer, Matthew C. Whitby, 2018, vol. 8, issue 2. (elsevierpure.com)
Functional1
In addition to the functional and structural role within centromere they are also a suitable model for evolutionary stud-ies, because of being subject to concerted evolution. (srce.hr)
Gaps1
85% of the unfilled gaps in our best HiFi assemblies. (weigelworld.org)
Replication2
Cytological analysis of DNA replication further demonstrated that centromeres replicate asynchronously in parallel with numerous other genomic regions. (rupress.org)
Quantitative fluorescence microscopy and transient transfection in the presence of aphidicolin, an inhibitor of DNA replication, show that CENP-A can assemble into centromeres in the absence of DNA replication. (rupress.org)
Genomic1
Finally, we emphasize the utility of PacBio technology in dealing with difficult genomic regions: as was the case with the Mst77Y region, [MHAP] produced a seemingly error-free assembly of the FDY region, something that has eluded us for years of hard work. (speakerdeck.com)
Role1
The role of alpha satellite DNA has been debated since centromeres can form, albeit rarely, on non-alpha satellite DNA. (duke.edu)
Alpha-satellite1
Using GRM, we identify in Build 37.2 assembly fifteen different alpha satellite HORs, three of them novel, not reported previously. (srce.hr)
Reads1
Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Eyach15-2 to HiFi assemblies of the same sample. (weigelworld.org)
Found1
We also found that the normal recruitment of SYCP3 and HORMAD1 to the inner centromere in prometaphase I spermatocytes did not occur. (figshare.com)
Complex3
We studied CTP- and parS F -modulated ParA F -ParB F complex assembly, in which DNA-bound ParA F -ATP dimers are activated for ATP hydrolysis by interacting with two ParB F N-terminal domains. (biorxiv.org)
CTP or parS F enhances the ATPase rate without significantly accelerating ParA F -ParB F complex assembly. (biorxiv.org)
Magnetic-tweezers experiments showed that CTP promotes multiple ParB F loading onto parS F -containing DNA, generating condensed partition complex-like assemblies. (biorxiv.org)
The centromere is a specialized chromosomal site involved in chromosome architecture and movement, and when defective, is linked to cancer, birth defects, and infertility. (duke.edu)