The Yeast Genome Directory

Content

• The Yeast Genome Directory

  This directory was made possible by a unique international collaboration between the 633 scientists whose names appear below. It represents both the first published description of the complete sequence of most chromsomes from Saccharomyces cerevisiae, and the first published overview of the entire sequence. As such, the authors would like future papers referring to the entire sequence and/or its contents to cite this directory; future papers referring to the sequence of individual chromosomes should refer to the papers listed at the head of page 9. The authors’ affiliations appear in the papers describing the individual chromosomes.

  • A. Goffeau
  • R. Aert
  • E. Zumstein

  Introduction29 May 1997 Nature

• Overview of the yeast genome

  The collaboration of more than 600 scientists from over 100 laboratories to sequence the Saccharomyces cerevisiae genome was the largest decentralised experiment in modern molecular biology and resulted in a unique data resource representing the first complete set of genes from a eukaryotic organism. 12 million bases were sequenced in a truly international effort involving European, US, Canadian and Japanese laboratories. While the yeast genome represents only a small fraction of the information in today’s public sequence databases, the complete, ordered and non-redundant sequence provides an invaluable resource for the detailed analysis of cellular gene function and genome architecture. In terms of throughput, completeness and information content, yeast has always been the lead eukaryotic organism in genomics; it is still the largest genome to be completely sequenced.

  • H. W. Mewes
  • K. Albermann
  • A. Zollner

  Introduction29 May 1997 Nature

• Chromosome maps

  Article29 May 1997 Nature

• Chart of duplications

  Article29 May 1997 Nature

• Gazetteer

  Article29 May 1997 Nature

• Genetic and physical maps of Saccharomyces cerevisiae

  Genetic and physical maps for the 16 chromosomes of Saccharomyces cerevisiae are presented. The genetic map is the result of 40 years of genetic analysis. The physical map was produced from the results of an international systematic sequencing effort. The data for the maps are accessible electronically from the Saccharomyces Genome Database (SGD: http://genome-www.stanford.edu/Saccharomyces/).

  • J. Michael Cherry
  • Catherine Ball
  • David Botstein

  Article29 May 1997 Nature

• The nucleotide sequence of Saccharomyces cerevisiae chromosome IV

  The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome IV has been determined. Apart from chromosome XII, which contains the 1–2 Mb rDNA cluster, chromosome IV is the longest S. cerevisiae chromosome. It was split into three parts, which were sequenced by a consortium from the European Community, the Sanger Centre, and groups from St Louis and Stanford in the United States. The sequence of 1,531,974 base pairs contains 796 predicted or known genes, 318 (39.9%) of which have been previously identified. Of the 478 new genes, 225 (28.3%) are homologous to previously identified genes and 253 (32%) have unknown functions or correspond to spurious open reading frames (ORFs). On average there is one gene approximately every two kilobases. Superimposed on alternating regional variations in G+C composition, there is a large central domain with a lower G+C content that contains all the yeast transposon (Ty) elements and most of the tRNA genes. Chromosome IV shares with chromosomes II, V, XII, XIII and XV some long clustered duplications which partly explain its origin.

  • C. Jacq
  • J. Alt-Mörbe
  • P. Zaccaria

  Letter29 May 1997 Nature

• The nucleotide sequence of Saccharomyces cerevisiae chromosome V

  Here we report the sequence of 569,202 base pairs of Saccharomyces cerevisiae chromosome V. Analysis of the sequence revealed a centromere, two telomeres and 271 open reading frames (ORFs) plus 13 tRNAs and four small nuclear RNAs. There are two Ty1 transposable elements, each of which contains an ORF (included in the count of 271). Of the ORFs, 78 (29%) are new, 81 (30%) have potential homologues in the public databases, and 112 (41%) are previously characterized yeast genes.

  • F. S. Dietrich
  • J. Mulligan
  • R. W. Davis

  Letter29 May 1997 Nature

• The nucleotide sequence of Saccharomyces cerevisiae chromosome VII

  The complete nucleotide sequence of Saccharomyces cerevisiae chromosome VII has 572 predicted open reading frames (ORFs), of which 341 are new. No correlation was found between G+C content and gene density along the chromosome, and their variations are random. Of the ORFs, 17% show high similarity to human proteins. Almost half of the ORFs could be classified in functional categories, and there is a slight increase in the number of transcription (7.0 %) and translation (5.2 %) factors when compared with the complete S. cerevisiae genome. Accurate verification procedures demonstrate that there are less than two errors per 10,000 base pairs in the published sequence.

  • H. Tettelin
  • M. L. Agostoni Carbone
  • K. Kleine

  Letter29 May 1997 Nature

• The nucleotide sequence of Saccharomyces cerevisiae chromosome IX

  Large-scale systematic sequencing has generally depended on the availability of an ordered library of large-insert bacterial or viral genomic clones for the organism under study. The generation of these large insert libraries, and the location of each clone on a genome map, is a laborious and time-consuming process. In an effort to overcome these problems, several groups have successfully demonstrated the viability of the whole-genome random ‘shotgun’ method in large-scale sequencing of both viruses and prokaryotes^1–5. Here we report the sequence of Saccharomyces cerevisiae chromosome IX, determined in part by a whole-chromosome ‘shotgun’, and describe the particular difficulties encountered in the random ‘shotgun’ sequencing of an entire eukaryotic chromosome. Analysis of this sequence shows that chromosome IX contains 221 open reading frames (ORFs), of which approximately 30% have been sequenced previously. This chromosome shows features typical of a small Saccharomyces cerevisiae chromosome.

  • C. Churcher
  • S. Bowman
  • B. Barrell

  Letter29 May 1997 Nature

• The nucleotide sequence of Saccharomyces cerevisiae chromosome XII

  The yeast Saccharomyces cerevisiae is the pre-eminent organism for the study of basic functions of eukaryotic cells¹. All of the genes of this simple eukaryotic cell have recently been revealed by an international collaborative effort to determine the complete DNA sequence of its nuclear genome. Here we describe some of the features of chromosome XII.

  • M. Johnston
  • L. Hillier
  • J. D. Hoheisel

  Letter29 May 1997 Nature

• The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII

  Systematic sequencing of the genome of Saccharomyces cerevisiae has revealed thousands of new predicted genes and allowed analysis of long-range features of chromosomal organization. Generally, genes and predicted genes seem to be distributed evenly throughout the genome, having no overall preference for DNA strand. Apart from the smaller chromosomes, which can have substantially lower gene density in their telomeric regions^1–3, there is a consistent average of one open reading frame (ORF) approximately every two kilobases. However, one of the most surprising findings for a eukaryote with approximately 6,000 genes was the amount of apparent redundancy in its genome. This redundancy occurs both between individual ORFs and over more extensive chromosome regions, which have been duplicated preserving gene order and orientation^4–6. Here we report the entire nucleotide sequence of chromosome XIII, the sixth-largest S. cerevisiae chromosome, and demonstrate that its features and organization are consistent with those observed for other S. cerevisiae chromosomes. Analysis revealed 459 ORFs, 284 have not been identified previously. Both intra- and interchromosomal duplications of regions of this chromosome have occurred.

  • S. Bowman
  • C. Churcher
  • B. Barrell

  Letter29 May 1997 Nature

• The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications

  • P. Philippsen
  • K. Kleine
  • J. Hani

  Letter29 May 1997 Nature

• The nucleotide sequence of Saccharomyces cerevisiae chromosome XV

  • B. Dujon
  • K. Albermann
  • K. Kleine

  Letter29 May 1997 Nature

• The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI

  • H. Bussey
  • R. K. Storms
  • J. Hani

  Letter29 May 1997 Nature