Plant Physiology 139:27-38 (2005)
© 2005 American Society of Plant Biologists
BIOINFORMATICS
Whole-Genome Validation of High-Information-Content Fingerprinting1
William M. Nelson2,
Arvind K. Bharti2,
Ed Butler,
Fusheng Wei,
Galina Fuks,
HyeRan Kim,
Rod A. Wing,
Joachim Messing and
Carol Soderlund*
Arizona Genomics Computational Laboratory, BIO5 Institute (W.M.N., C.S.) and Arizona Genomics Institute, Department of Plant Sciences (E.B., F.W., H.K., R.A.W.), University of Arizona, Tucson, Arizona 85721 (W.M.N., C.S.); and The Plant Genome Initiative at Rutgers, Waksman Institute, Rutgers, State University of New Jersey, Piscataway, New Jersey 08854 (A.K.B., G.F., J.M.)
Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing instruments to enable both high-resolution and high-throughput fingerprinting. In this article, we report the construction of a whole-genome HICF FPC map for maize (Zea mays subsp. mays cv B73), using a variant of HICF in which a type IIS restriction enzyme is used to generate the fluorescently labeled fragments. The HICF maize map was constructed from the same three maize bacterial artificial chromosome libraries as previously used for the whole-genome agarose FPC map, providing a unique opportunity for direct comparison of the agarose and HICF methods; as a result, it was found that HICF has substantially greater sensitivity in forming contigs. An improved assembly procedure is also described that uses automatic end-merging of contigs to reduce the effects of contamination and repetitive bands. Several new features in FPC v7.2 are presented, including shared-memory multiprocessing, which allows dramatically faster assemblies, and automatic end-merging, which permits more accurate assemblies. It is further shown that sequenced clones may be digested in silico and located accurately on the HICF assembly, despite size deviations that prevent the precise prediction of experimental fingerprints. Finally, repetitive bands are isolated, and their effect on the assembly is studied.
1 This work was supported by the National Science Foundation Plant Genome (grant no. 0211851). Additional support for multithreading of FPC was provided by the National Science Foundation (grant no. 0213764).
2 These authors contributed equally to the paper.
www.plantphysiol.org/cgi/doi/10.1104/pp.105.061978.
* Corresponding author; e-mail cari{at}agcol.arizona.edu; fax 520–626–4824.
Received February 25, 2005;
returned for revision May 20, 2005;
accepted May 20, 2005.
This article has been cited by other articles:
|
|
|
|
 
J.-H. Choi, S. Kim, H. Tang, J. Andrews, D. G. Gilbert, and J. K. Colbourne
A machine-learning approach to combined evidence validation of genome assemblies
Bioinformatics,
March 15, 2008;
24(6):
744 - 750.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
F. I. E. Amarillo and H. W. Bass
A Transgenomic Cytogenetic Sorghum (Sorghum propinquum) Bacterial Artificial Chromosome Fluorescence in Situ Hybridization Map of Maize (Zea mays L.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion
Genetics,
November 1, 2007;
177(3):
1509 - 1526.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y. Han, K. Gasic, and S. S. Korban
Multiple-Copy Cluster-Type Organization and Evolution of Genes Encoding O-Methyltransferases in the Apple
Genetics,
August 1, 2007;
176(4):
2625 - 2635.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Troggio, G. Malacarne, G. Coppola, C. Segala, D. A. Cartwright, M. Pindo, M. Stefanini, R. Mank, M. Moroldo, M. Morgante, et al.
A Dense Single-Nucleotide Polymorphism-Based Genetic Linkage Map of Grapevine (Vitis vinifera L.) Anchoring Pinot Noir Bacterial Artificial Chromosome Contigs
Genetics,
August 1, 2007;
176(4):
2637 - 2650.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Kim, P. S. Miguel, W. Nelson, K. Collura, M. Wissotski, J. G. Walling, J. P. Kim, S. A. Jackson, C. Soderlund, and R. A. Wing
Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type)
Genetics,
May 1, 2007;
176(1):
379 - 390.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Xiao, A. Phong, C. Ha, T.-F. Chan, D. Cai, L. Leung, E. Wan, A. L. Kistler, J. L. DeRisi, P. R. Selvin, et al.
Rapid DNA mapping by fluorescent single molecule detection
Nucleic Acids Res.,
February 16, 2007;
35(3):
e16 - e16.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. A. Jackson, D. Rokhsar, G. Stacey, R. C. Shoemaker, J. Schmutz, and J. Grimwood
Toward a Reference Sequence of the Soybean Genome: A Multiagency Effort
Crop Sci.,
November 1, 2006;
46(Supplement_1):
S-55 - S-61.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
R. Bruggmann, A. K. Bharti, H. Gundlach, J. Lai, S. Young, A. C. Pontaroli, F. Wei, G. Haberer, G. Fuks, C. Du, et al.
Uneven chromosome contraction and expansion in the maize genome
Genome Res.,
October 1, 2006;
16(10):
1241 - 1251.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
C. Soderlund, W. Nelson, A. Shoemaker, and A. Paterson
SyMAP: A system for discovering and viewing syntenic regions of FPC maps.
Genome Res.,
September 1, 2006;
16(9):
1159 - 1168.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
G. Haberer, S. Young, A. K. Bharti, H. Gundlach, C. Raymond, G. Fuks, E. Butler, R. A. Wing, S. Rounsley, B. Birren, et al.
Structure and Architecture of the Maize Genome
Plant Physiology,
December 1, 2005;
139(4):
1612 - 1624.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
