Submitted to: PLoS Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 10/5/2009
Publication Date: 11/20/2009
Publication URL: www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000711
Citation: Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M.R., Churas, C., Pasternak, S., Forrest, D.K., Wise, R.P., Ware, D., Wing, R., Waterman, M., Livny, M., Schwartz, D.C. 2009. A Single Molecule Scaffold for the Maize Genome. PLoS Genetics. 5(11):1-14. Interpretive Summary: The maize genome is challenging to sequence because it harbors an abundance of highly repetitive sequences that are interspersed by low copy, gene-coding sequences. Such genomic complexity is gauged by current Bacterial Artificial Chromosome (BAC) sequence assemblies, which typically yield 11 contigs per clone. The maize iMap deals with such complexity by judicious integration of genetic (intermated B73 x Mo17 population; "IBM") and physical Fingerprinted Contigs (FPC) maps. However, the genome structure of the sequenced B73 genome could differ from the IBM population because of genetic recombination and subsequent rearrangements. Accordingly, we report a genome-wide high-resolution optical map of the maize inbred line B73 genome that was constructed from the direct analysis of genomic DNA molecules and assembled without the use of genetic markers. The integration of optical and iMap resources and comparisons to FPC maps enabled a uniquely comprehensive and scalable assessment of a BAC’s sequence assembly, its placement within a FPC contig, and the location of this FPC contig within the chromosome-wide pseudomolecule. As such, the overall utility of the maize optical map, for sequence assembly validation, has been significant and demonstrates the inherent advantages of single molecule platforms. This approach is of broad significance to plant scientists who utilize molecular and genomic methods for crop improvement.
Technical Abstract: About 80% 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 may not be sufficient for improving the quality of the current sequence build. Here we report a genome-wide high resolution optical map of maize inbred line B73 genome containing more than 91,000 restriction sites (averaging 1 site/approximately 23 kb) accrued from mapping genomic DNA molecules. Our maize optical map comprises 66 contigs, averaging 31.88 Mb in size and spans 91.5% (2,103.93 Mb/approximately 2,300 Mb) of maize genome. A new algorithm was created that considered both optical map and unfinished Bacterial Artificial Chromosome (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 proved comprehensive, revealing, and productive. Gaps were uncovered and characterized in 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 superior reference for comparative studies among cereals, or other maize inbred lines and cultivars.