ArticlePLoS genetics2009
A single molecule scaffold for the maize genome.
Article in PLoS genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed.
- Genetic diversity and population structure analyses of tropical maize inbred lines using Single Nucleotide Polymorphism markers.PloS one · 2025Article
- Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph.Algorithms for molecular biology : AMB · 2021Article
- FaNDOM: Fast nested distance-based seeding of optical maps.Patterns (New York, N.Y.) · 2021Article
- DNA Manipulation and Single-Molecule Imaging.Molecules (Basel, Switzerland) · 2021Review
- Customized optical mapping by CRISPR-Cas9 mediated DNA labeling with multiple sgRNAs.Nucleic acids research · 2021Article
- Molecular diversity and selective sweeps in maize inbred lines adapted to African highlands.Scientific reports · 2019Article
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- Error correcting optical mapping data.GigaScience · 2018Article
- Determining if DNA Stained with a Cyanine Dye Can Be Digested with Restriction Enzymes.Journal of visualized experiments : JoVE · 2018Article
- Interaction network of core ABA signaling components in maize.Plant molecular biology · 2018Article
- Intact DNA purified from flow-sorted nuclei unlocks the potential of next-generation genome mapping and assembly inMethodsX · 2018Article
- Article
- Noise reduction in single time frame optical DNA maps.PloS one · 2017Article
- BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.Plant biotechnology journal · 2016Article
- Biosynthesis of 8-O-Methylated Benzoxazinoid Defense Compounds in Maize.The Plant cell · 2016Article
- Maligner: a fast ordered restriction map aligner.Bioinformatics (Oxford, England) · 2016Article
- Analysis of single nucleic acid molecules in micro- and nano-fluidics.Lab on a chip · 2016Review
- Metabolomic profiling and genomic analysis of wheat aneuploid lines to identify genes controlling biochemical pathways in mature grain.Plant biotechnology journal · 2016Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
Abstract
About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/ approximately 23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/ approximately 2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars.
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