Introduction - The Plasmodium yoelii Genome Database (PYDB)

TIGR and the Malaria Program at the Naval Medical Research Center (NMRC) are collaborating on a research program to provide low coverage sequencing of the Plasmodium yoelii genome, a rodent animal model for malaria. This project will provide the foundation for low coverage sequencing of additional Plasmodium species and should identify over 90% of all the genes of the Plasmodium yoelii genome. Funding for this project is provided by the U.S. Department of the Army and U.S. Department of the Navy.

This initiative will use a gene discovery-based approach and is highly complementary to the large-scale sequencing programs carried on by TIGR/NMRC, Sanger Center and Stanford University, which are members of the International Malaria Genome Sequencing Consortium.

The goals of the P. yoelii research program differ from the large scale, dense sequencing of individual chromosomes from the P. falciparum genome: We aim to undertake a fast, cost-effective and highly efficient whole genome shotgun method to sequence the P. yoelii genome. This approach will provide large unordered contigs for gene discovery, low density gene organization that can potentially be pinned to syntenic regions of the P. falciparum genome and/or ordered by additional sequencing of medium sized insert libraries. To accomplish this endeavor we will sequence the P. yoelii genome to the level of 5x genome representation. These sequences will be assembled, and the DNA contigs edited and annotated.

Shotgun libraries were prepared using total genomic DNA from Plasmodium yoelii, strain 17X NL, clone 1.1 raised in mice. Briefly, leukocyte-free infected erythrocytes are isolated from mice and parasite genomic DNA prepared by standard methods. Total genomic DNA was mechanically sheared, and fragments of 1-2 kb size-selected and cloned into a pUC19-derived vector using BstXI adaptors. DNA was sequenced using dye-terminator chemistry on ABI 377 and ABI 3700 DNA sequencers.

In order to provide early access to malaria researchers for "jump starting" biological experiments, we have made the P. yoelii sequences publicly available. Be advised that the DNA assemblies or raw sequence reads are considered preliminary data and the information should be used carefully. These sequences have not been verified for base call ambiguities and may contain errors.

These data are being released to the public and are governed by the data release policy established for the P. falciparum sequencing project (see below), which is subscribed by all the other genome projects carried on at TIGR. Please contact Dr. Jane Carlton should you need any further information.

As of May 29, 2001, we have 223,907 sequence reads, which corresponds to approximately 5x genome representation. The contigs and singletons can be downloaded from our ftp site.

These sequences were assembled in contigs using TIGR Assembler.

The annotation process is fully automated and therefore has not undergone extensive human review. Please be advised that these are unverified transcriptional units (or gene models) identified by GlimmerM, the gene finding software trained with P. falciparum sequences. In addition, some transcriptional units have been identified by BLAST hits of start-stop translation. A trained version of Glimmer to identify P. yoelii genes is under development. Further, contig editing will likely alter the reading frames of these transcriptional units. Therefore please use this data with caution.

The preliminary annotation of the 2x DNA assemblies with 2kb or larger can be seen. GlimmerM has identified 4,686 transcriptional units and 27 tRNAs. We are in the process of updating the annotation tables with the 5x genome data.

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