Genetics, Vol. 163, 1299-1313, April 2003, Copyright © 2003

Mapping by Sequencing the Pneumocystis Genome Using the Ordering DNA Sequences V3 Tool

Zheng Xub, Britton Lancea, Claudia Vargasa, Budak Arpinarb, Suchendra Bhandarkarb, Eileen Kraemerb, Krys J. Kochutb, John A. Millerb, Jeff R. Wagnerc, Michael J. Weised, John K. Wunderlichc, James Stringere, George Smulianf, Melanie T. Cushionf, and Jonathan Arnolda
a Department of Genetics, University of Georgia, Athens, Georgia 30602,
b Department of Computer Science, University of Georgia, Athens, Georgia 30602,
c Molecular Genetics Instrumentation Facility, University of Georgia, Athens, Georgia 30602,
d Accelrys, Madison, Wisconsin 53711-1060,
e Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
f Department of Internal Medicine and the Cincinnati VAMC, University of Cincinnati College of Medicine, Cincinnati, Ohio 45220

Corresponding author: Jonathan Arnold, University of Georgia, Athens, GA 30602., arnold{at}uga.edu (E-mail)

Communicating editor: Z-B. ZENG

A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is ~50% complete with ~200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock {psi} protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy.




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