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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION OF FUNCTIONAL SEQUENCE IN PLANT GENOMES THROUGH BIOINFORMATIC, GENOMIC, AND GENETIC APPROACHES Title: A single molecule scaffold for the maize genome

Authors
item Zhou, Shiguo -
item Fusheng, Wei -
item Pasternak, Shiran -
item Ware, Doreen
item Wing, Rod -
item Livny, Miron -
item Schwartz, David -

Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 5, 2009
Publication Date: November 20, 2009
Citation: Zhou, S., Fusheng, W., Pasternak, S., Ware, D., Wing, R., Livny, M., Schwartz, D.C. 2009. A single molecule scaffold for the maize genome. PLoS Genetics. 5(11):1-14.

Interpretive Summary: In this paper we are reporting on the construction of an optical map for maize. The optical map is generated from single molecule sequences that are digested with a restriction enzyme. The advantage of an optical map over other types of physical maps is the lack of bias generated at the cloning step. The current optical map of maize B73 consists of 66 fragments, with an average size of 31 MB and spans approximately 91% of the maize genome. As part of this report a new method was developed to make use of the available Maize Bacterial Artificial Chromosome (BAC) sequences that allowed the anchoring of 60 of the 66 optical map fragments. Combining information from both the optical and finger-print-BAC contig maps provides a more robust resource for the maize community than one resource alone.

Technical 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/~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/~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.

Last Modified: 12/20/2014
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