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Open Access Highly Accessed Research article

High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome

Gianni Liti1*, Alex N Nguyen Ba23, Martin Blythe4, Carolin A Müller5, Anders Bergström1, Francisco A Cubillos56, Felix Dafhnis-Calas5, Shima Khoshraftar2, Sunir Malla4, Neel Mehta5, Cheuk C Siow5, Jonas Warringer7, Alan M Moses23, Edward J Louis5 and Conrad A Nieduszynski5

Author Affiliations

1 Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U1081, Université de Nice Sophia Antipolis, 06107, NICE Cedex 2, France

2 Department of Cell & Systems Biology, University of Toronto, M5S 2 J4, Toronto, Canada

3 Centre for the Analysis of Genome Evolution and Function, University of Toronto, M5S 3B2, Toronto, Ontario, Canada

4 DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, NG7 2UH, Nottingham, UK

5 Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, NG7 2UH, Nottingham, UK

6 Current address: INRA, UMR1318, Institut Jean-Pierre Bourgin, F-78000, Versailles, France

7 Department of Chemistry and Molecular Biology, University of Gothenburg, 41390, Gothenburg, Sweden

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BMC Genomics 2013, 14:69  doi:10.1186/1471-2164-14-69

Published: 31 January 2013

Abstract

Background

Comparative genomics is a formidable tool to identify functional elements throughout a genome. In the past ten years, studies in the budding yeast Saccharomyces cerevisiae and a set of closely related species have been instrumental in showing the benefit of analyzing patterns of sequence conservation. Increasing the number of closely related genome sequences makes the comparative genomics approach more powerful and accurate.

Results

Here, we report the genome sequence and analysis of Saccharomyces arboricolus, a yeast species recently isolated in China, that is closely related to S. cerevisiae. We obtained high quality de novo sequence and assemblies using a combination of next generation sequencing technologies, established the phylogenetic position of this species and considered its phenotypic profile under multiple environmental conditions in the light of its gene content and phylogeny.

Conclusions

We suggest that the genome of S. arboricolus will be useful in future comparative genomics analysis of the Saccharomyces sensu stricto yeasts.