Comparative genomics of biotechnologically important yeasts

Robert Riley; Sajeet Haridas; Kenneth H Wolfe; Mariana R Lopes; Chris Todd Hittinger; Markus Göker; Asaf A Salamov; Jennifer H Wisecaver; Tanya M Long; Christopher H Calvey; Andrea L Aerts; Kerrie W Barry; Cindy Choi; Alicia Clum; Aisling Y Coughlan; Shweta Deshpande; Alexander P Douglass; Sara J Hanson; Hans-Peter Klenk; Kurt M LaButti; Alla Lapidus; Erika A Lindquist; Anna M Lipzen; Jan P Meier-Kolthoff; Robin A Ohm; Robert P Otillar; Jasmyn L Pangilinan; Yi Peng; Antonis Rokas; Carlos A Rosa; Carmen Scheuner; Andriy A Sibirny; Jason C Slot; J Benjamin Stielow; Hui Sun; Cletus P Kurtzman; Meredith Blackwell; Igor V Grigoriev; Thomas W Jeffries

doi:10.1073/pnas.1603941113

Comparative genomics of biotechnologically important yeasts

Robert Riley, Sajeet Haridas, Kenneth H Wolfe, Mariana R Lopes, Chris Todd Hittinger, Markus Göker, Asaf A Salamov, Jennifer H Wisecaver, Tanya M Long, Christopher H Calvey, Andrea L Aerts, Kerrie W Barry, Cindy Choi, Alicia Clum, Aisling Y Coughlan, Shweta Deshpande, Alexander P Douglass, Sara J Hanson, Hans-Peter Klenk, Kurt M LaButtiAlla Lapidus, Erika A Lindquist, Anna M Lipzen, Jan P Meier-Kolthoff, Robin A Ohm, Robert P Otillar, Jasmyn L Pangilinan, Yi Peng, Antonis Rokas, Carlos A Rosa, Carmen Scheuner, Andriy A Sibirny, Jason C Slot, J Benjamin Stielow, Hui Sun, Cletus P Kurtzman, Meredith Blackwell, Igor V Grigoriev, Thomas W Jeffries

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253 Citaten (Scopus)

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Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.

Originele taal-2	Engels
Pagina's (van-tot)	9882-7
Aantal pagina's	6
Tijdschrift	Proceedings of the National Academy of Sciences of the United States of America
Volume	113
Nummer van het tijdschrift	35
DOI's	https://doi.org/10.1073/pnas.1603941113
Status	Gepubliceerd - 30 aug. 2016

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10.1073/pnas.1603941113

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Riley, R., Haridas, S., Wolfe, K. H., Lopes, M. R., Hittinger, C. T., Göker, M., Salamov, A. A., Wisecaver, J. H., Long, T. M., Calvey, C. H., Aerts, A. L., Barry, K. W., Choi, C., Clum, A., Coughlan, A. Y., Deshpande, S., Douglass, A. P., Hanson, S. J., Klenk, H.-P., ... Jeffries, T. W. (2016). Comparative genomics of biotechnologically important yeasts. Proceedings of the National Academy of Sciences of the United States of America, 113(35), 9882-7. https://doi.org/10.1073/pnas.1603941113

@article{01986720b75343b68f0be89c6c42cd28,

title = "Comparative genomics of biotechnologically important yeasts",

abstract = "Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.",

author = "Robert Riley and Sajeet Haridas and Wolfe, {Kenneth H} and Lopes, {Mariana R} and Hittinger, {Chris Todd} and Markus G{\"o}ker and Salamov, {Asaf A} and Wisecaver, {Jennifer H} and Long, {Tanya M} and Calvey, {Christopher H} and Aerts, {Andrea L} and Barry, {Kerrie W} and Cindy Choi and Alicia Clum and Coughlan, {Aisling Y} and Shweta Deshpande and Douglass, {Alexander P} and Hanson, {Sara J} and Hans-Peter Klenk and LaButti, {Kurt M} and Alla Lapidus and Lindquist, {Erika A} and Lipzen, {Anna M} and Meier-Kolthoff, {Jan P} and Ohm, {Robin A} and Otillar, {Robert P} and Pangilinan, {Jasmyn L} and Yi Peng and Antonis Rokas and Rosa, {Carlos A} and Carmen Scheuner and Sibirny, {Andriy A} and Slot, {Jason C} and Stielow, {J Benjamin} and Hui Sun and Kurtzman, {Cletus P} and Meredith Blackwell and Grigoriev, {Igor V} and Jeffries, {Thomas W}",

year = "2016",

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day = "30",

doi = "10.1073/pnas.1603941113",

language = "English",

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journal = "Proceedings of the National Academy of Sciences of the United States of America",

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Riley, R, Haridas, S, Wolfe, KH, Lopes, MR, Hittinger, CT, Göker, M, Salamov, AA, Wisecaver, JH, Long, TM, Calvey, CH, Aerts, AL, Barry, KW, Choi, C, Clum, A, Coughlan, AY, Deshpande, S, Douglass, AP, Hanson, SJ, Klenk, H-P, LaButti, KM, Lapidus, A, Lindquist, EA, Lipzen, AM, Meier-Kolthoff, JP, Ohm, RA, Otillar, RP, Pangilinan, JL, Peng, Y, Rokas, A, Rosa, CA, Scheuner, C, Sibirny, AA, Slot, JC, Stielow, JB, Sun, H, Kurtzman, CP, Blackwell, M, Grigoriev, IV & Jeffries, TW 2016, 'Comparative genomics of biotechnologically important yeasts', Proceedings of the National Academy of Sciences of the United States of America, vol. 113, nr. 35, blz. 9882-7. https://doi.org/10.1073/pnas.1603941113

Comparative genomics of biotechnologically important yeasts. / Riley, Robert; Haridas, Sajeet; Wolfe, Kenneth H et al.
In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, Nr. 35, 30.08.2016, blz. 9882-7.

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

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T1 - Comparative genomics of biotechnologically important yeasts

AU - Riley, Robert

AU - Haridas, Sajeet

AU - Wolfe, Kenneth H

AU - Lopes, Mariana R

AU - Hittinger, Chris Todd

AU - Göker, Markus

AU - Salamov, Asaf A

AU - Wisecaver, Jennifer H

AU - Long, Tanya M

AU - Calvey, Christopher H

AU - Aerts, Andrea L

AU - Barry, Kerrie W

AU - Choi, Cindy

AU - Clum, Alicia

AU - Coughlan, Aisling Y

AU - Deshpande, Shweta

AU - Douglass, Alexander P

AU - Hanson, Sara J

AU - Klenk, Hans-Peter

AU - LaButti, Kurt M

AU - Lapidus, Alla

AU - Lindquist, Erika A

AU - Lipzen, Anna M

AU - Meier-Kolthoff, Jan P

AU - Ohm, Robin A

AU - Otillar, Robert P

AU - Pangilinan, Jasmyn L

AU - Peng, Yi

AU - Rokas, Antonis

AU - Rosa, Carlos A

AU - Scheuner, Carmen

AU - Sibirny, Andriy A

AU - Slot, Jason C

AU - Stielow, J Benjamin

AU - Sun, Hui

AU - Kurtzman, Cletus P

AU - Blackwell, Meredith

AU - Grigoriev, Igor V

AU - Jeffries, Thomas W

PY - 2016/8/30

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N2 - Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.

AB - Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.

U2 - 10.1073/pnas.1603941113

DO - 10.1073/pnas.1603941113

M3 - Article

C2 - 27535936

SN - 0027-8424

VL - 113

SP - 9882

EP - 9887

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 - 35

ER -

Comparative genomics of biotechnologically important yeasts

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