Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Tammi Camilla Vesth; Jane L Nybo; Sebastian Theobald; Jens Christian Frisvad; Thomas Ostenfeld Larsen; Kristian Fog Nielsen; Jakob Blæsbjerg Hoof; Julian Brandl; Asaf Salamov; Robert Riley; John M Gladden; Pallavi Phatale; Morten T. Nielsen; Ellen K. Lyhne; Martin Engelhard Kogle; Kimchi Strasser; Erin McDonnell; Kerrie Barry; Alicia Clum; Cindy Chen; Kurt LaButti; Sajeet Haridas; Matt Nolan; Laura Sandor; Alan Kuo; Anna Lipzen; Matthieu Hainaut; Elodie Drula; Adrian Tsang; Jon K Magnuson; Bernard Henrissat; Ad Wiebenga; Blake A Simmons; Miia R Mäkelä; Ronald P de Vries; Igor V Grigoriev; Uffe Hasbro Mortensen; Scott E Baker; Mikael Rørdam Andersen

doi:10.1038/s41588-018-0246-1

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Tammi Camilla Vesth, Jane L Nybo, Sebastian Theobald, Jens Christian Frisvad, Thomas Ostenfeld Larsen, Kristian Fog Nielsen, Jakob Blæsbjerg Hoof, Julian Brandl, Asaf Salamov, Robert Riley, John M Gladden, Pallavi Phatale, Morten T. Nielsen, Ellen K. Lyhne, Martin Engelhard Kogle, Kimchi Strasser, Erin McDonnell, Kerrie Barry, Alicia Clum, Cindy ChenKurt LaButti, Sajeet Haridas, Matt Nolan, Laura Sandor, Alan Kuo, Anna Lipzen, Matthieu Hainaut, Elodie Drula, Adrian Tsang, Jon K Magnuson, Bernard Henrissat, Ad Wiebenga, Blake A Simmons, Miia R Mäkelä, Ronald P de Vries, Igor V Grigoriev, Uffe Hasbro Mortensen, Scott E Baker, Mikael Rørdam Andersen^*

^*Corresponding author for this work

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Abstract

Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter- and intraspecies genomic variation. We further predicted 17,903 carbohydrate-active enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.

Original language	English
Journal	Nature Genetics
Volume	50
Pages (from-to)	1688–1695
ISSN	1061-4036
DOIs	https://doi.org/10.1038/s41588-018-0246-1
Publication status	Published - 2018

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Vesth, T. C., Nybo, J. L., Theobald, S., Frisvad, J. C., Larsen, T. O., Nielsen, K. F., Hoof, J. B., Brandl, J., Salamov, A., Riley, R., Gladden, J. M., Phatale, P., Nielsen, M. T., Lyhne, E. K., Kogle, M. E., Strasser, K., McDonnell, E., Barry, K., Clum, A., ... Andersen, M. R. (2018). Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. Nature Genetics, 50, 1688–1695. https://doi.org/10.1038/s41588-018-0246-1

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title = "Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri",

abstract = "Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter- and intraspecies genomic variation. We further predicted 17,903 carbohydrate-active enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.",

author = "Vesth, {Tammi Camilla} and Nybo, {Jane L} and Sebastian Theobald and Frisvad, {Jens Christian} and Larsen, {Thomas Ostenfeld} and Nielsen, {Kristian Fog} and Hoof, {Jakob Bl{\ae}sbjerg} and Julian Brandl and Asaf Salamov and Robert Riley and Gladden, {John M} and Pallavi Phatale and Nielsen, {Morten T.} and Lyhne, {Ellen K.} and Kogle, {Martin Engelhard} and Kimchi Strasser and Erin McDonnell and Kerrie Barry and Alicia Clum and Cindy Chen and Kurt LaButti and Sajeet Haridas and Matt Nolan and Laura Sandor and Alan Kuo and Anna Lipzen and Matthieu Hainaut and Elodie Drula and Adrian Tsang and Magnuson, {Jon K} and Bernard Henrissat and Ad Wiebenga and Simmons, {Blake A} and M{\"a}kel{\"a}, {Miia R} and {de Vries}, {Ronald P} and Grigoriev, {Igor V} and Mortensen, {Uffe Hasbro} and Baker, {Scott E} and Andersen, {Mikael R{\o}rdam}",

year = "2018",

doi = "10.1038/s41588-018-0246-1",

language = "English",

volume = "50",

pages = "1688–1695",

journal = "Nature Genetics",

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Vesth, TC, Nybo, JL, Theobald, S, Frisvad, JC , Larsen, TO, Nielsen, KF, Hoof, JB, Brandl, J, Salamov, A, Riley, R, Gladden, JM, Phatale, P, Nielsen, MT, Lyhne, EK, Kogle, ME, Strasser, K, McDonnell, E, Barry, K, Clum, A, Chen, C, LaButti, K, Haridas, S, Nolan, M, Sandor, L, Kuo, A, Lipzen, A, Hainaut, M, Drula, E, Tsang, A, Magnuson, JK, Henrissat, B, Wiebenga, A, Simmons, BA, Mäkelä, MR, de Vries, RP, Grigoriev, IV, Mortensen, UH, Baker, SE & Andersen, MR 2018, 'Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri', Nature Genetics, vol. 50, pp. 1688–1695. https://doi.org/10.1038/s41588-018-0246-1

TY - JOUR

T1 - Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

AU - Vesth, Tammi Camilla

AU - Nybo, Jane L

AU - Theobald, Sebastian

AU - Frisvad, Jens Christian

AU - Larsen, Thomas Ostenfeld

AU - Nielsen, Kristian Fog

AU - Hoof, Jakob Blæsbjerg

AU - Brandl, Julian

AU - Salamov, Asaf

AU - Riley, Robert

AU - Gladden, John M

AU - Phatale, Pallavi

AU - Nielsen, Morten T.

AU - Lyhne, Ellen K.

AU - Kogle, Martin Engelhard

AU - Strasser, Kimchi

AU - McDonnell, Erin

AU - Barry, Kerrie

AU - Clum, Alicia

AU - Chen, Cindy

AU - LaButti, Kurt

AU - Haridas, Sajeet

AU - Nolan, Matt

AU - Sandor, Laura

AU - Kuo, Alan

AU - Lipzen, Anna

AU - Hainaut, Matthieu

AU - Drula, Elodie

AU - Tsang, Adrian

AU - Magnuson, Jon K

AU - Henrissat, Bernard

AU - Wiebenga, Ad

AU - Simmons, Blake A

AU - Mäkelä, Miia R

AU - de Vries, Ronald P

AU - Grigoriev, Igor V

AU - Mortensen, Uffe Hasbro

AU - Baker, Scott E

AU - Andersen, Mikael Rørdam

PY - 2018

Y1 - 2018

N2 - Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter- and intraspecies genomic variation. We further predicted 17,903 carbohydrate-active enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.

AB - Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter- and intraspecies genomic variation. We further predicted 17,903 carbohydrate-active enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.

U2 - 10.1038/s41588-018-0246-1

DO - 10.1038/s41588-018-0246-1

M3 - Journal article

C2 - 30349117

SN - 1061-4036

VL - 50

SP - 1688

EP - 1695

JO - Nature Genetics

JF - Nature Genetics

ER -

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

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