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Sequencing

The S. pombe genome has 3 chromosomes and is 14.1 Mb in size (12.5 Mb excluding rDNA repeats). The genome (excluding rDNA repeats) was sequenced by an international consortium in 2002, and became the second publicly available unicellular eukaryotic genome sequence^[1]. A minimal tiling path was generated by the integration of the two pre-existing physical maps and the selected constructs were sequenced on a clone by clone basis^[2][3]. Remaining gaps were covered using a long-range PCR strategy, plasmid libraries, and a BAC (bacterial artificial chromosome) library ^[1]. The sequence is available from The S. pombe Genome project and has been deposited in EMBL/GenBank.

Annotation

The S. pombe genome encodes approximately 5000 protein coding genes. A comprehensive manual annotation of genome features and manual annotation of gene products was provided on completion of the sequence in 2002 and is described in detail in the primary publication^[1]. High throughput transcriptome sequencing has recently confirmed >90% of the remaining predicted introns and provided data for the revision of ~75 gene structures and prediction of >400 additional non coding RNAs (ncRNAs)^[4]. Each gene has its own Gene Page in the GeneDB database, which contains functional annotation, links to the AmiGO Gene Ontology Browser, GBrowse genome browser and Artemis genome browser and annotation tool. Manual curation from the scientific literature and sequence analysis verifies or improves the gene structures and provides functional annotations. Functional curation consists of unique gene product assignment, Gene Ontology (GO) annotation^[5], protein family data curation, genetic and physical interactions (in collaboration with BioGRID), and post-translational modifications. Consistent gene nomenclature is implemented via an active Gene Naming Committee and community consultation.

References

1. ↑ ^{1.0 1.1 1.2} Wood V et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415: 871-80 PubMed
2. ↑ Hoheisel JD et al. (1993) High resolution cosmid and P1 maps spanning the 14 Mb genome of the fission yeast S. pombe. Cell 73: 109-20 PubMed
3. ↑ Mizukami T et al. (1993) A 13 kb resolution cosmid map of the 14 Mb fission yeast genome by nonrandom sequence-tagged site mapping. Cell 73: 121-32 PubMed
4. ↑ Wilhelm BT et al. (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453: 1239-43 PubMed
5. ↑ Aslett M & Wood V (2006) Gene Ontology annotation status of the fission yeast genome: preliminary coverage approaches 100%. Yeast 23: 913-9 PubMed