Stanford Genome Technology Center
Saccharomyces cerevisiae
YJM789 Genome Project

October 2007

We have determined, and published, the YJM789 genome sequence. The sequence itself is publicly available.

June 2007

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the project accession AAFW00000000.

The version described in our Proc. Natl. Acad. Sci. U.S.A. in press paper is the second version, AAFW02000000. The mitochondrial genome's accession number is EU004203.

October 16, 2007:

We have determined, and published, the YJM789 genome sequence. The sequence itself is publicly available. The whole genome shotgun has been deposited in GenBank (project accession number AAFW00000000). The version described in our Proc. Natl. Acad. Sci. U.S.A. paper is the second version (AAFW02000000). The accession number for the mitochondrial genome is EU004203.

There are no restrictions on the use of the public data. However, any work using the YJM789 genome sequence, in whole or in part, should include a citation to our Proc. Natl. Acad. Sci. U.S.A. paper (http://www.pnas.org/cgi/content/full/104/31/12825).


Saccharomyces cerevisiae YJM789 is derived from a yeast that was isolated from the lung of an AIDS patient with pneumonia [1, 2]. S. cerevisiae YJM789 differs in important phenotypes from standard laboratory strains of baker's yeast. For example, S. cerevisiae YJM789 grows well at high temperature (41°C). The S. cerevisiae YJM789 Genome Project has been undertaken at the Stanford Genome Technology Center (SGTC) to provide the DNA sequence underlying important and interesting phenotypes, such as robust growth at high temperature.

The S. cerevisiae YJM789 Genome Project is composed of several parts. For shotgun sequencing, several independent whole genome shotgun libraries were employed to achieve a combined total of approximately ten-fold genome coverage. Individual reads were assigned to chromosomes based upon their DNA homology to the S. cerevisiae S288c genome sequence. The reads for each chromosome were assembled into contigs. The contigs were positioned relative to each other on a chromosome based upon their DNA homology to the S. cerevisiae S288c genome sequence. Finishing and annotation follow.

In the real world, there are real constraints on time and money. Therefore, we are not aiming for a fully finished S. cerevisiae YJM789 genome sequence. Rather, our goal is to produce a significantly finished S. cerevisiae YJM789 genome sequence. Version 1 of our data is comprised of the assembled contigs. Version 2 is comprised of the assembled contigs assigned to positions on individual chromosomes, with some finishing. As of this date (19 Nov 2004), we are posting version 2.

Finishing the S. cerevisiae YJM789 genome sequence is ongoing. During finishing, physical gaps in the sequence are closed, ambiguities in the sequence are resolved, contaminating sequences are removed, and errors in the sequence are identified and corrected. Finishing is a slow process. We expect to complete our work in approximately one year from this posting (19 Nov 2004). Therefore, we request that users of our unpublished sequence data have patience. In addition, you can help us finish the S. cerevisiae YJM789 genome sequence. If you find an apparent problem in our S. cerevisiae YJM789 genome sequence, please communicate that information directly to Lars Steinmetz (larsms@stanford.edu). Thank you.

The Saccharomyces cerevisiae YJM789 Genome Project is supported by grant numbers HG02052 and HG00205 from the NIH.

References

1. Tawfik OW, Papasian CJ, Dixon AY, and Potter LM. Saccharomyces cerevisiae pneumonia in a patient with acquired immune deficiency syndrome. J Clin Microbiol. 27: 1689–1691, 1989.

2. McCusker JH, Clemons KV, Stevens DA, Davis RW. Genetic characterization of pathogenic Saccharomyces cerevisiae isolates. Genetics 136: 1261–1269, 1994.


Before we proceed into the S. cerevisiae YJM789 genome sequence data, we would like you to read our data release policy.

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