Abstract:
:Sorting of individual chromosomes by Flow Cytometry (flow-sorting) is an enrichment method to potentially simplify genome assembly by isolating chromosomes from the context of the genome. We have recently developed a workflow to sequence native, unamplified DNA and applied it to the smallest human chromosome, the Y chromosome. Here, we modify improve upon that workflow to increase DNA recovery from chromosome sorting as well as sequencing yield. We apply it to sequence and assemble the largest human chromosome - chromosome 1 - of a Chinese individual using a single Oxford Nanopore MinION flow cell. We generate a selective and highly continuous assembly whose continuity reaches into the order of magnitude of the human reference GRCh38. We then use this assembly to call candidate structural variants against the reference and find 685 putative novel SV candidates. We propose this workflow as a potential solution to assemble structurally complex chromosomes, or the study of very large plant or animal genomes that might challenge traditional assembly strategies.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Kuderna LFK,Solís-Moruno M,Batlle-Masó L,Julià E,Lizano E,Anglada R,Ramírez E,Bote A,Tormo M,Marquès-Bonet T,Fornas Ò,Casals Fdoi
10.3389/fgene.2019.01315subject
Has Abstractpub_date
2020-01-09 00:00:00pages
1315issn
1664-8021journal_volume
10pub_type
杂志文章abstract::In situ adaptation to climate change will be critical for the persistence of many ectotherm species due to their relative lack of dispersal capacity. Climate change is causing increases in both the mean and the variance of environmental temperature, each of which may act as agents of selection on different traits. Imp...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.538226
更新日期:2020-09-18 00:00:00
abstract::We evaluated differences in gene expression in pigs from the Porcine Reproductive and Respiratory Syndrome (PRRS) Host Genetics Consortium initiative showing a range of responses to PRRS virus infection. Pigs were allocated into four phenotypic groups according to their serum viral level and weight gain. RNA obtained ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00321
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abstract::Cyprinids are the most important group of farmed fish globally in terms of production volume, with common carp (Cyprinus carpio) being one of the most valuable species of the group. The use of modern selective breeding methods in carp is at a formative stage, implying a large scope for genetic improvement of key produ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00082
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
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abstract::Bovine leukemia virus (BLV) affects cattle health and productivity worldwide, causing abnormal immune function and immunosuppression. Transfer RNA fragments (tRFs) are known to be involved in inhibition of gene expression and have been associated with stress and immune response, tumor growth, and viral infection. The ...
journal_title:Frontiers in genetics
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journal_title:Frontiers in genetics
pub_type: 杂志文章
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00195
更新日期:2012-09-28 00:00:00
abstract::[This corrects the article on p. 23 in vol. 9, PMID: 29456554.]. ...
journal_title:Frontiers in genetics
pub_type: 杂志文章,已发布勘误
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更新日期:2018-04-04 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
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pub_type: 杂志文章,评审
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journal_title:Frontiers in genetics
pub_type: 杂志文章
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更新日期:2019-08-15 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00417
更新日期:2019-05-10 00:00:00
abstract::The study of microorganisms that pervade each and every part of this planet has encountered many challenges through time such as the discovery of unknown organisms and the understanding of how they interact with their environment. The aim of this review is to take the reader along the timeline and major milestones tha...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2015.00348
更新日期:2015-12-17 00:00:00
abstract::Background: Papillary renal cell carcinoma (PRCC), although the second-most common type of renal cell carcinoma, still lacks specific biomarkers for diagnosis, treatment, and prognosis. TopBP1-interacting checkpoint and replication regulator (TICRR) is a DNA replication initiation regulator upregulated in various canc...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.605378
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abstract::The interesting history of Southern Africa has put the region in the spotlight for population medical genetics. Major events including the Bantu expansion and European colonialism have imprinted unique genetic signatures within autochthonous populations of Southern Africa, this resulting in differential allele frequen...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.00905
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pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.607532
更新日期:2021-01-12 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00930
更新日期:2020-08-14 00:00:00
abstract::Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP) data analysis, such as genome-wide association study data, because it allows the interpretation of variants with respect to the biological p...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2017.00174
更新日期:2017-11-07 00:00:00
abstract::Advanced castrate-resistant prostate cancer (CRPC) is a poorly prognostic disease currently lacking effective cure. Understanding the molecular mechanism that underlies the initiation and progression of CRPC will provide new strategies for treating this deadly disease. One candidate target is the fibroblast growth fac...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.00012
更新日期:2019-01-30 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00200
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00684
更新日期:2019-01-07 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01273
更新日期:2019-12-17 00:00:00
abstract::Trauma is a leading cause of morbidity and mortality. It is unclear why some trauma victims follow a complicated clinical course and die, while others, with apparently similar injury characteristics, do not. Interpatient genomic differences, in the form of single nucleotide polymorphisms (SNPs), have been associated p...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01115
更新日期:2019-11-08 00:00:00
abstract::Pacu (Piaractus mesopotamicus) is a Neotropical fish of major importance for South American aquaculture. Septicemia caused by Aeromonas hydrophila bacteria is currently considered a substantial threat for pacu aquaculture that have provoked infectious disease outbreaks with high economic losses. The understanding of m...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00604
更新日期:2020-06-09 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2017.00104
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abstract::Background: Alcohol use has been linked to a number of physical conditions, but the relationship between alcohol drinking and depression, one of the most common mental disorders that is a significant contributor to the global burden of disease, is still under debate. We aim to help fill the literature gap on the causa...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.585351
更新日期:2020-10-19 00:00:00
abstract::In light of the complex nature of multiple sclerosis (MS) and the recently estimated contribution of low-frequency variants into disease, decoding its genetic risk components requires novel variant prioritization strategies. We selected, by reviewing MS Genome Wide Association Studies (GWAS), 107 candidate loci marked...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00573
更新日期:2019-06-26 00:00:00
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journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00110
更新日期:2013-06-20 00:00:00