Submitted to: Meeting Abstract
Publication Type: Abstract only
Publication Acceptance Date: 9/7/2006
Publication Date: 9/7/2006
Citation: Zhou, S., Bechner, M., Pape, L., Konstantinos, P., Churas, C., Lamers, C., Runnhelm, R., Goldstein, S., Forrest, D.K., Leong, S.A., Wing, R., Valouev, A., Nguyen, J., Waterman, M., Schwartz, D.C. 2006. A Physical Map of the Whole Maize Genome via Single Molecule Analysis. Poster presented at the National Science Foundation, Arlington, VA, Sept. 7-8, 2006. Interpretive Summary:
Technical Abstract: Maize is one of the most important crops in the U. S., and a classical genetic and cytogenetic model system for plants. Although genetic and cytogenetic analyses provides a global view of the genome organization, a comprehensive insights will emerge from full sequence data and its annotation. As part of this effort, we are constructing a genome-wide restriction map for maize using the well-established whole genome shotgun single molecule optical mapping approach. Although our map assembly approach uses ordered restriction maps created from individual DNA molecules, the map "assembler", which shares many functionalities with software commonly used for shotgun sequence assembly, will build optical map contigs that span the entire genome. The maize genome is notorious for harboring a very complex and extensive panoply of repeats which is likely to confound traditional sequence assembly approaches. The completion of this optical map of maize genome will greatly facilitate sequence finishing by providing scaffolds for the ordering of nascent sequence contigs, that will characterize gaps and validate assemblies. The finshed B73 map/sequence will become a reference for other studies aimed at finding structural differences in other lines, cultivars or varieties of maize. Project Status: 1. We are using Swa I restriction enzyme ( 5' -ATTTAAAT- 3'), which is methylation insensitive to map the maize inbred line B73 genome. To date, approximately 927.60 Gb raw genomic DNA single molecule maps were acquired, or about 371.04 x coverage of the genome. The average fragment size of this raw data is 26.12 kb and the average single DNA molecule size is 438.36 kb. 2. De novo map assembly was performed for this large dataset. In total, there are 319,290 single DNA moleculemaps with a total mass of 143.01 Gb which have formed optical map contigs , thus the contig formation rate is about 15.42%. So far, we have constructed 231 optical map contigs larger than 2 Mb with a total mass of 2373.00 Mb, spanning ~95% of the maize genome, and the largest optical map consensus has reached ~73 Mb. We are also exploring a new graph based map assembly algorithm, and this will help greatly speed up our optical map assembly process. 3. Comparison of the in silico maps of 448 BAC sequences from TIGR show that 133 BAC in silico maps can be aligned with our current optical map consenses. Fig. 4 shows several aligned BACs, with good correspondence to the FPC map. We are integrating optical and FPC maps for cross-validating phyiscal map resources used as part of the sequencing effort. We have also enlarged optical map contigs using two combined BAC sequences located near chromosome 3 centromere provided by Dr. Roger Wise.