Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789

Wu Wei; John H. McCusker; Richard W. Hyman; Ted Jones; Ye Ning; Zhiwei Cao; Zhenglong Gu; Dan Bruno; Molly Miranda; Michelle Nguyen; Julie Wilhelmy; Caridad Komp; Raquel Tamse; Xiaojing Wang; Peilin Jia; Philippe Luedi; Peter J. Oefner; Lior David; Fred S. Dietrich; Yixue Li; Ronald W. Davis; Lars M. Steinmetz

doi:10.1073/pnas.0701291104

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789

Wu Wei, John H. McCusker, Richard W. Hyman, Ted Jones, Ye Ning, Zhiwei Cao, Zhenglong Gu, Dan Bruno, Molly Miranda, Michelle Nguyen, Julie Wilhelmy, Caridad Komp, Raquel Tamse, Xiaojing Wang, Peilin Jia, Philippe Luedi, Peter J. Oefner, Lior David, Fred S. Dietrich, Yixue LiRonald W. Davis, Lars M. Steinmetz^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

217 Scopus citations

Abstract

We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal infections and quantitative genetics because of its extensive phenotypic differences to the laboratory reference strain, including growth at high temperature and deadly virulence in mouse models. Here we show that the ≈12-Mb genome of YJM789 contains ≈60,000 SNPs and ≈6,000 indels with respect to the reference S288c genome, leading to protein polymorphisms with a few known cases of phenotypic changes. Several ORFs are found to be unique to YJM789, some of which might have been acquired through horizontal transfer. Localized regions of high polymorphism density are scattered over the genome, in some cases spanning multiple ORFs and in others concentrated within single genes. The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits.

Original language	English
Pages (from-to)	12825-12830
Number of pages	6
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	104
Issue number	31
DOIs	https://doi.org/10.1073/pnas.0701291104
State	Published - 31 Jul 2007
Externally published	Yes

Keywords

Comparative genomics
Genome architecture
Introgression
Lateral gene transfer

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1073/pnas.0701291104

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Wei, W., McCusker, J. H., Hyman, R. W., Jones, T., Ning, Y., Cao, Z., Gu, Z., Bruno, D., Miranda, M., Nguyen, M., Wilhelmy, J., Komp, C., Tamse, R., Wang, X., Jia, P., Luedi, P., Oefner, P. J., David, L., Dietrich, F. S., ... Steinmetz, L. M. (2007). Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proceedings of the National Academy of Sciences of the United States of America, 104(31), 12825-12830. https://doi.org/10.1073/pnas.0701291104

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title = "Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789",

abstract = "We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal infections and quantitative genetics because of its extensive phenotypic differences to the laboratory reference strain, including growth at high temperature and deadly virulence in mouse models. Here we show that the ≈12-Mb genome of YJM789 contains ≈60,000 SNPs and ≈6,000 indels with respect to the reference S288c genome, leading to protein polymorphisms with a few known cases of phenotypic changes. Several ORFs are found to be unique to YJM789, some of which might have been acquired through horizontal transfer. Localized regions of high polymorphism density are scattered over the genome, in some cases spanning multiple ORFs and in others concentrated within single genes. The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits.",

keywords = "Comparative genomics, Genome architecture, Introgression, Lateral gene transfer",

author = "Wu Wei and McCusker, {John H.} and Hyman, {Richard W.} and Ted Jones and Ye Ning and Zhiwei Cao and Zhenglong Gu and Dan Bruno and Molly Miranda and Michelle Nguyen and Julie Wilhelmy and Caridad Komp and Raquel Tamse and Xiaojing Wang and Peilin Jia and Philippe Luedi and Oefner, {Peter J.} and Lior David and Dietrich, {Fred S.} and Yixue Li and Davis, {Ronald W.} and Steinmetz, {Lars M.}",

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doi = "10.1073/pnas.0701291104",

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Wei, W, McCusker, JH, Hyman, RW, Jones, T, Ning, Y, Cao, Z, Gu, Z, Bruno, D, Miranda, M, Nguyen, M, Wilhelmy, J, Komp, C, Tamse, R, Wang, X, Jia, P, Luedi, P, Oefner, PJ, David, L, Dietrich, FS, Li, Y, Davis, RW & Steinmetz, LM 2007, 'Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789', Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 31, pp. 12825-12830. https://doi.org/10.1073/pnas.0701291104

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T1 - Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789

AU - Wei, Wu

AU - McCusker, John H.

AU - Hyman, Richard W.

AU - Jones, Ted

AU - Ning, Ye

AU - Cao, Zhiwei

AU - Gu, Zhenglong

AU - Bruno, Dan

AU - Miranda, Molly

AU - Nguyen, Michelle

AU - Wilhelmy, Julie

AU - Komp, Caridad

AU - Tamse, Raquel

AU - Wang, Xiaojing

AU - Jia, Peilin

AU - Luedi, Philippe

AU - Oefner, Peter J.

AU - David, Lior

AU - Dietrich, Fred S.

AU - Li, Yixue

AU - Davis, Ronald W.

AU - Steinmetz, Lars M.

PY - 2007/7/31

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N2 - We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal infections and quantitative genetics because of its extensive phenotypic differences to the laboratory reference strain, including growth at high temperature and deadly virulence in mouse models. Here we show that the ≈12-Mb genome of YJM789 contains ≈60,000 SNPs and ≈6,000 indels with respect to the reference S288c genome, leading to protein polymorphisms with a few known cases of phenotypic changes. Several ORFs are found to be unique to YJM789, some of which might have been acquired through horizontal transfer. Localized regions of high polymorphism density are scattered over the genome, in some cases spanning multiple ORFs and in others concentrated within single genes. The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits.

AB - We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal infections and quantitative genetics because of its extensive phenotypic differences to the laboratory reference strain, including growth at high temperature and deadly virulence in mouse models. Here we show that the ≈12-Mb genome of YJM789 contains ≈60,000 SNPs and ≈6,000 indels with respect to the reference S288c genome, leading to protein polymorphisms with a few known cases of phenotypic changes. Several ORFs are found to be unique to YJM789, some of which might have been acquired through horizontal transfer. Localized regions of high polymorphism density are scattered over the genome, in some cases spanning multiple ORFs and in others concentrated within single genes. The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits.

KW - Comparative genomics

KW - Genome architecture

KW - Introgression

KW - Lateral gene transfer

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SN - 0027-8424

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JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 31

ER -

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789

Abstract

Keywords

UN SDGs

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