ArticlePloS one2013
Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- Aegilops tauschii genome assembly v6.0 with improved sequence contiguity differentiates assembly errors from genuine differences with the D subgenome of Chinese Spring wheat assembly IWGSC RefSeq v2.1.G3 (Bethesda, Md.) · 2025Article
- Comparison of Optical Genome Mapping With Conventional Diagnostic Methods for Structural Variant Detection in Hematologic Malignancies.Annals of laboratory medicine · 2024Article
- Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection.GigaScience · 2023Article
- 'Nebbiolo' genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.).BMC genomics · 2022Article
- Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation.G3 (Bethesda, Md.) · 2021Article
- Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly.The Plant journal : for cell and molecular biology · 2021Article
- Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale.Essays in biochemistry · 2021Article
- Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet).BMC genomics · 2021Article
- Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping.Journal of personalized medicine · 2021Article
- The Impact of Whole Genome Data on Therapeutic Decision-Making in Metastatic Prostate Cancer: A Retrospective Analysis.Cancers · 2020Article
- From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish.Science advances · 2020Article
- Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal.GigaScience · 2020Article
- Article
- Understanding divergent domestication traits from the whole-genome sequencing of swamp- and river-buffalo populations.National science review · 2020Article
- Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping.PLoS genetics · 2020Article
- Long walk to genomics: History and current approaches to genome sequencing and assembly.Computational and structural biotechnology journal · 2020Review
- Article
- Rapid evolution of α-gliadin gene family revealed by analyzing Gli-2 locus regions of wild emmer wheat.Functional & integrative genomics · 2019Article
- A micropatterned substrate for on-surface enzymatic labelling of linearized long DNA molecules.Scientific reports · 2019Article
- Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes.Genome biology and evolution · 2019Review
19 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
Abstract
Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far. Using two-color genome mapping of tiling bacterial artificial chromosomes (BAC) clones on nanochannel arrays, we completed high-confidence assembly of a 2.1-Mb, highly repetitive region in the large and complex genome of Aegilops tauschii, the D-genome donor of hexaploid wheat (Triticum aestivum). Genome mapping is based on direct visualization of sequence motifs on single DNA molecules hundreds of kilobases in length. With the genome map as a scaffold, we anchored unplaced sequence contigs, validated the initial draft assembly, and resolved instances of misassembly, some involving contigs <2 kb long, to dramatically improve the assembly from 75% to 95% complete.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.