Maize HICF FPC Map

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The Sequencing the Maize Genome project is a collaboration with Joachim Messing at PGIR (Plant Genome Initiative at Rutgers), funded by NSF #0211851 as part of an effort to develope a stratey to sequence the maize genome. As part of this award, we are building an HICF (High Information Content Fingerprint) map. This will allow us to verify and finish the NSF funded agarose-based FPC map and aid in selecting clones for sequencing.

WebFPC *Java display of the Maize FPC contigs
WebChrom view maize chromosomes
FTP a tar file of FPC files
Maize Genome Sequencing information about this project.
Information about data and assembly
Other Relevant Sites sites directly associated with this project.

*New release WebFPC V2.1: If the contig page will not load, install Java 1.4.0_03. We have tested this on Internet Explorer 5.0, Netscape 6.2 and Netscape 7. It does not work on Netscape 4.7.

Contig Sizes
Date Clone Cov Marker Anchor Contig Single >200 200:101 100:51 50:26 25:10 9:3 =2
11/5/04 350253 18x 15479 806(587) 1500 28510 569 251 155 86 66 122 251
2/18/04 350253 18x 15479 1547(849) 2906 28136 526 638 521 325 249 312 335

(11/5/04): Further end-merges, terminating at 1e-21.

Note(2/18/04): Clones screened for same-plate overlaps at 1e-45, followed by removal of all remaining clones over 175 bands. Build performed at 1e-70, followed by end-merging at 1e-61, 1e-52, 1e-43, 1e-40. Merges required at least two distinct overlapping end-clone pairs. DQing was performed with threshold 15% (the effect was not large). Singletons were placed at 1e-43 to their best location, before the final end-merge.

Disclaimer: We do not consider this map complete or verified. We are still studying the parameters and might rebuilt each data set. Therefore, each release might still be retroactively modified. Until these parameters are optimized, the agarose based map is the main FPC maize map. It is our objective to integrate both data sets from the agarose-based map and the HICF map to build a high-resolution physical map of the maize genome.

Maize Genome Sequencing Strategy

  • The Sequencing the Maize Genome project is creating the HICF map, sequencing 450,000 BAC ends and 140 BACs. An overview of the entire project, participants, results, and downloadable databases are available at this link.
  • The Consortium for Maize Genomics project is sequencing and assembling 500,000 reads from Methyl filtered, High Cot, and unfiltered libraries.
  • The Maize Genome Sequencing site represents the collaboration between these two projects.

Information

  • Description of clones, markers and anchors (these are the same as used for the agarose based map).
  • The build was performed with 1e-50. The DQer was run with a step size of 5; therefore, cutoffs of 1e-55, 1e-60, 1e-65 were used to remove Q contigs.
  • The metric of a FPC contig is the CB (consensus band) unit. If the length of a contig is N CB units, then its approximate length in base pairs is N * 1400. The 1400 was calculated as the average size restriction fragment as follows: the average number of scored bands per fingerprint is 107, and since the average clone size is 150 kb, there is approximately one band for every 1400 b of sequence. Note that this is not the same as the average size of a detected fragment, which is approximately 200 bp.

Other relevant sites

References

Nelson, W. and C. Soderlund. Software for restriction fragment physical maps. In K. Meksem, G. Kahl (ed) The Handbook of Genome Mapping: Genetic and Physical Mapping, Wiley-VCH. pp. 285-306.

Nelson, W, A Bharti, E Butler, F Wei, G Fuks, H Kim, R Wing, J Messing, and C Soderlund (2005). Whole-Genome Validation of High-Information-Content Fingerprinting. /Plant Physiology/ *139*:27-38.

Email comments to webmaster@genome.arizona.edu