Yeast Gene Duplications

(Release 3, September 1999)
Ken Wolfe, Cathal Seoighe and Denis Shields
Genetics Department, Trinity College Dublin


Introduction:

This Web site contains data on duplicated genes in the yeast (Saccharomyces cerevisiae) genome. It concentrates particularly on duplicated chromosomal regions. These are situations where one region of the genome contains a cluster of genes that has a cluster of homologues somewhere else in the genome, with conservation of both gene order and transcriptional orientation between the two copies of the duplicate chromosomal region. We have proposed that the structure and distribution of these regions indicates that the entire yeast genome underwent duplication at some stage in its distant past, i.e., that yeast is a degenerate tetraploid. We have identified 52 duplicated regions (or "blocks") that are likely to have been derived from the simultaneous duplication of the whole genome and a further 32 candidate paired regions that may also be derived from genome duplication, although the evidence is less convincing.

See:
Seoighe, C and Wolfe, K.H. (1999) Updated map of duplicated regions in the yeast genome. Gene 238:253-261

Wolfe, K.H. and Shields, D.C. (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713 (1997).

See also the "Chart of Duplications" by MIPS in the Yeast Genome Directory (H.W. Mewes et al., Nature 387 (suppl.), 33-34, 1997).

Release 3 of the data has:

Dataset:

We used a dataset of 5790 yeast proteins encoded by the 16 yeast nuclear chromosomes. These are listed under the "Browse through chromosomes" option in the Main Menu. This dataset was produced by us in Dublin from gene lists supplied by YPD, SGD and MIPS.

Our aim is to produce a gene list that includes all functional protein-coding genes but excludes all spurious ORFs and Ty elements. We have labelled these spurious ORFs as "junk" in our listings of chromosomes, and they were not included in the protein dataset used for BLAST searches. If your favourite ORF has been labelled as junk, we apologise.

Thanks to: Jim Garrels (YPD), Mike Cherry (SGD) and Kaj Albermann (MIPS) for providing gene lists.

Web pages for each gene:

There is a separate Web page for each gene, containing:

Criteria for definition of duplicated chromosomal regions:

To qualify as a duplicated block in our analysis, a pair of chromosomal regions must contain: We excluded duplicated genes located in the subtelomeric repeats, which are highly similar among multiple chromosomes.

Dot matrix plots:

To help visualise the duplicated blocks, we have produced dot matrix plots for every pair of chromosomes, and "zoom-in" views for the 55 duplicated regions we identified. These show BLASTP protein hits (with scores >= 200), plotted at the position where the genes lie on each chromosome. Duplicated chromosomal regions appear as diagonal series of points. Different symbols are used to indicate the transcriptional orientations of genes.

Previous work by other labs:

Some of the duplicated regions have already been reported by other labs. References are given below. Most of these papers describe only part of a duplicated block. Please e-mail Ken Wolfe if you know of others. See also the papers in the Nature Yeast Genome Directory:


Block 1: Bussey, H. et al. Proc. Natl. Acad. Sci. U.S.A. 92, 3809-3813 (1995); Johnston, M. et al. Science 265, 2077-2082 (1994); Steensma, H.Y. et al. Curr. Genet. 16, 131-137 (1989).

Block 2: Parle-McDermott, A.G., Hand, N.J., Goulding, S.E. & Wolfe, K.H. Yeast 12, 999-1004 (1996); Pearson, B.M., Hernando, Y., Payne, J., Wolf, S.S., Kalogeropoulos, A. & Schweizer, M. Yeast 12, 1021-1031 (1996); Purnelle, B. & Goffeau, A. Yeast 12, 1475-1481 (1996); Storms, R.K. et al. Genome 40, 151-164 (1997).

Block 3: Wolfe, K.H. & Lohan, A.J.E. Yeast 10, S41-S46 (1994).

Block 4: Logghe, M., Molemans, F., Fiers, W. & Contreras, R. Yeast 10, 1093-1100 (1994); Berroteran, R.W. & Hampsey, M. Yeast 11, 761-766 (1995).

Block 11: Lalo, D., Stettler, S., Mariotte, S., Slonimski, P.P. & Thuriaux, P. C.R. Acad. Sci. Paris 316, 367-373 (1993); Lalo, D. et al. Yeast 10, 523-533 (1994).

Block 12: Wolfl, S., Hanemann, V. & Saluz, H.P. Yeast 12, 1549-1554 (1996).

Block 25: Kail, M., Juttner, E. & Vaux, D. Yeast 12, 799-807 (1996).

Block 28: Melnick, L. & Sherman, F. J. Mol. Biol. 233, 372-388 (1993); McKnight, G.L., Cardillo, T.S. & Sherman, F. Cell 25, 409-419 (1981); Kang, H.A., Schwelberger, H.G. & Hershey, J.W.B. Mol. Gen. Genet. 233, 487-490 (1992).

Block 39: Pohlmann, R. & Philippsen, P. Yeast 12, 391-402 (1996); Nasr, F., Becam, A.-M. & Herbert, C.J. Yeast 12, 493-499 (1996).

Block 40: Galibert, F. et al. EMBO J. 15, 2031-2049 (1996).

Block 41: Galibert, F. et al. EMBO J. 15, 2031-2049 (1996); Katsoulou, C., Tzermia, M., Tavernarakis, N. & Alexandraki, D. Yeast 12: 787-797 (1996).

Block 42: Galibert, F. et al. EMBO J. 15, 2031-2049 (1996); Huang, M.-E., Manus, V., Chuat, J.-C. & Galibert, F. Yeast 12, 869-875 (1996).

Block 43: Wente, S.R., Rout, M.P. & Blobel, G. J. Cell. Biol. 119, 705-723 (1992).

Block 47: Pearson, B.M., Hernando, Y., Payne, J., Wolf, S.S., Kalogeropoulos, A. & Schweizer, M. Yeast 12, 1021-1031 (1996).

Block 49: Molenaar, C.M.T. et al. Nucleic Acids Res. 12, 7345-7358 (1984).

A tetraploid origin for the yeast genome was suggested in 1987 by M. Mitchell Smith (J. Mol. Evol. 24, 252-259), based mainly on analysis of duplicate histone loci.


The yeast gene duplications project is supported by

The Fourth Framework Biotechnology Programme of the European Union

The Wellcome Trust

Forbairt - The Irish Science and Technology Agency

The University of Dublin -- Trinity College

[go to the Main Menu]
last updated: 10 Dec 1999