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Journal article
Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome
PloS one, v 8(2), pp e55864-e55864
06 Feb 2013
PMID: 23405223
Featured in Collection : UN Sustainable Development Goals @ Drexel
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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Details
- Title
- Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome
- Creators
- Alex R. Hastie - BioNano GenomicsLingli Dong - University of California, DavisAlexis Smith - BioNano Genomics (United States)Jeff Finklestein - BioNano Genom, San Diego, CA USAErnest T. Lam - BioNano GenomicsNaxin Huo - University of California, DavisHan Cao - BioNano GenomicsPui-Yan Kwok - University of California, San FranciscoKarin R. Deal - University of California, DavisJan Dvorak - University of California, DavisMing-Cheng Luo - University of California, DavisYong Gu - University of California, DavisMing Xiao - BioNano Genomics
- Publication Details
- PloS one, v 8(2), pp e55864-e55864
- Publisher
- Public Library Science
- Number of pages
- 10
- Grant note
- R01HG005946 / NATIONAL HUMAN GENOME RESEARCH INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI) R01 HG005946 / US National Institutes of Health (NIH); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000315153400168
- Scopus ID
- 2-s2.0-84873545544
- Other Identifier
- 991019173896604721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Genetics & Heredity