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Nucleic Acids Research 2005 33(5):e50; doi:10.1093/nar/gni037
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Published online 14 March 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum

Zhanyou Xu, Marco A. van den Berg2, Chantel Scheuring, Lina Covaleda, Hong Lu1, Felipe A. Santos, Taesik Uhm, Mi-Kyung Lee, Chengcang Wu, Steve Liu1 and Hong-Bin Zhang*

Department of Soil and Crop Sciences, Texas A&M University College Station, TX 77843, USA 1Department of Computer Science, Texas A&M University College Station, TX 77843, USA 2DAI/INNO (624-0270), DSM PO Box 425, 2600 AK Delft, The Netherlands

*To whom correspondence should be addressed. Tel: +1 979 862 2244; Fax: +1 979 862 4790; Email: hbz7049{at}tamu.edu

Received November 22, 2004. Revised February 4, 2005. Accepted February 4, 2005.

Physical mapping with large-insert clones is becoming an active area of genomics research, and capillary electrophoresis (CE) promises to revolutionize the physical mapping technology. Here, we demonstrate the utility of the CE technology for genome physical mapping with large-insert clones by constructing a robust, binary bacterial artificial chromosome (BIBAC)-based physical map of Penicillium chrysogenum. We fingerprinted 23.1x coverage BIBAC clones with five restriction enzymes and the SNaPshot kit containing four fluorescent-ddNTPs using the CE technology, and explored various strategies to construct quality physical maps. It was shown that the fingerprints labeled with one or two colors, resulting in 40–70 bands per clone, were assembled into much better quality maps than those labeled with three or four colors. The selection of fingerprinting enzymes was crucial to quality map construction. From the dataset labeled with ddTTP–dROX, we assembled a physical map for P.chrysogenum, with 2–3 contigs per chromosome and anchored the map to its chromosomes. This map represents the first physical map constructed using the CE technology, thus providing not only a platform for genomic studies of the penicillin-producing species, but also strategies for efficient use of the CE technology for genome physical mapping of plants, animals and microbes.

Correspondence may also be addressed to Marco A. van den Berg. Tel: +31 (0) 15 279 3087; Fax: +31 (0) 15 279 3779; Email: Marco.Berg-van-den{at}dsm.com


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[Abstract] [Full Text] [PDF]


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