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High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome
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...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3599269/ https://www.ncbi.nlm.nih.gov/pubmed/23368932 http://dx.doi.org/10.1186/1471-2164-14-69 |
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author | Liti, Gianni Ba, Alex N Nguyen Blythe, Martin Müller, Carolin A Bergström, Anders Cubillos, Francisco A Dafhnis-Calas, Felix Khoshraftar, Shima Malla, Sunir Mehta, Neel Siow, Cheuk C Warringer, Jonas Moses, Alan M Louis, Edward J Nieduszynski, Conrad A |
author_facet | Liti, Gianni Ba, Alex N Nguyen Blythe, Martin Müller, Carolin A Bergström, Anders Cubillos, Francisco A Dafhnis-Calas, Felix Khoshraftar, Shima Malla, Sunir Mehta, Neel Siow, Cheuk C Warringer, Jonas Moses, Alan M Louis, Edward J Nieduszynski, Conrad A |
author_sort | Liti, Gianni |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3599269 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35992692013-03-17 High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome Liti, Gianni Ba, Alex N Nguyen Blythe, Martin Müller, Carolin A Bergström, Anders Cubillos, Francisco A Dafhnis-Calas, Felix Khoshraftar, Shima Malla, Sunir Mehta, Neel Siow, Cheuk C Warringer, Jonas Moses, Alan M Louis, Edward J Nieduszynski, Conrad A BMC Genomics Research Article 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. BioMed Central 2013-01-31 /pmc/articles/PMC3599269/ /pubmed/23368932 http://dx.doi.org/10.1186/1471-2164-14-69 Text en Copyright ©2013 Liti et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Liti, Gianni Ba, Alex N Nguyen Blythe, Martin Müller, Carolin A Bergström, Anders Cubillos, Francisco A Dafhnis-Calas, Felix Khoshraftar, Shima Malla, Sunir Mehta, Neel Siow, Cheuk C Warringer, Jonas Moses, Alan M Louis, Edward J Nieduszynski, Conrad A High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome |
title | High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome |
title_full | High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome |
title_fullStr | High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome |
title_full_unstemmed | High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome |
title_short | High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome |
title_sort | high quality de novo sequencing and assembly of the saccharomyces arboricolus genome |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3599269/ https://www.ncbi.nlm.nih.gov/pubmed/23368932 http://dx.doi.org/10.1186/1471-2164-14-69 |
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