Genomic DNA Sequencing P.carinii Libraries Contig Mapping Sequence Acquisition Sequence Assembly Sequence Annotation

The concept for a Pneumocystis carinii (Pc) Genome Project was presented to the community at the 5th International Workshop on Pneumocystis held in Lille, France, September, 1997 (Cushion MT and Arnold JA. 1998. Proposal for a Pneumocystis Genome project. J. Euk. Microbiol. 44: 7s.). There, consensus for such a project, the approach to be used, the genome (s) of focus, and the reagents to be generated were decided upon.

The consensus of the community was to embark on a Pc Genome project using a physical mapping strategy followed by directed sequencing. The cosmid libraries created would become the property of the Pc Community and freely distributed to any requesting investigator with a legitimate purpose. It was also agreed to begin the project using the rat Form 1 P. carinii f. sp. carinii followed by the human P. carinii f. sp. hominis (see below). A steering committee was formed to determine such issues as information dissemination, authorship, reagent dispersal and sequencing allocation.

Project Goals

The goals of this project will be to provide physical maps and gene sequences for the entire genomes of 2 populations of Pneumocystis; Pneumocystis carinii f. sp. carinii (from rat) and P. carinii f. sp. hominis (from human) to understand better their molecular structure and develop publicly available, centralized information and reagents that will be used to expedite research. This project will accomplish the following specific goals over a 5 year period starting February 15, 1999 through February 14, 2004:

  1. Construct cosmid libraries of the rat P. carinii genome in 2 vector systems.

  2. Sequence cDNAs of rat Pc for creation of expression sequence tags (ESTs).

  3. Assign unique clones to chromosomes and create chromosome-specific libraries.

  4. Order the clones containing the rat P. carinii DNA along the chromosome of origin to create an in vitro reconstruction of each chromosome.

  5. Produce a gene inventory of the rat P. carinii genome by subcloning of the ordered cosmids or construction of a library for shotgun sequencing.
  6. Construct and characterize cosmid libraries of the human P. carinii genome and create a physical map and gene inventory.
  7. Perform concurrent functional genomic studies to address basic biological questions in Pneumocystis research.