A comparative genomics study of 23 Aspergillus species from section Flavi

Inge Kjærbølling; Tammi Vesth; Jens C. Frisvad; Jane L. Nybo; Sebastian Theobald; Sara Kildgaard; Thomas Isbrandt Petersen; Alan Kuo; Atsushi Sato; Ellen K. Lyhne; Martin E. Kogle; Ad Wiebenga; Roland S. Kun; Ronnie J.M. Lubbers; Miia R. Mäkelä; Kerrie Barry; Mansi Chovatia; Alicia Clum; Chris Daum; Sajeet Haridas; Guifen He; Kurt LaButti; Anna Lipzen; Stephen Mondo; Jasmyn Pangilinan; Robert Riley; Asaf Salamov; Blake A. Simmons; Jon K. Magnuson; Bernard Henrissat; Uffe H. Mortensen; Thomas O. Larsen; Ronald P. de Vries; Igor V. Grigoriev; Masayuki Machida; Scott E. Baker; Mikael R. Andersen

doi:10.1038/s41467-019-14051-y

A comparative genomics study of 23 Aspergillus species from section Flavi

Inge Kjærbølling, Tammi Vesth, Jens C. Frisvad, Jane L. Nybo, Sebastian Theobald, Sara Kildgaard, Thomas Isbrandt Petersen, Alan Kuo, Atsushi Sato, Ellen K. Lyhne, Martin E. Kogle, Ad Wiebenga, Roland S. Kun, Ronnie J.M. Lubbers, Miia R. Mäkelä, Kerrie Barry, Mansi Chovatia, Alicia Clum, Chris Daum, Sajeet HaridasGuifen He, Kurt LaButti, Anna Lipzen, Stephen Mondo, Jasmyn Pangilinan, Robert Riley, Asaf Salamov, Blake A. Simmons, Jon K. Magnuson, Bernard Henrissat, Uffe H. Mortensen, Thomas O. Larsen, Ronald P. de Vries, Igor V. Grigoriev, Masayuki Machida, Scott E. Baker, Mikael R. Andersen^*

^*Corresponding author for this work

Molecular Plant Physiology

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

Abstract

Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi.

Original language	English
Article number	1106
Number of pages	12
Journal	Nature Communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-019-14051-y
Publication status	Published - 27 Feb 2020

Funding

Genome sequencing was kindly supported by Joint BioEnergy Institute and Joint Genome Institute. M.R.A., J.L.N., S.T. and T.C.V. gratefully acknowledge funding from the Villum Foundation, Grant VKR023437. M.R.A. and T.C.V. further acknowledge funding from the Danish National Research Foundation, grant number DNRF137. M.R.A. further acknowledges support from the Jorck Foundation. The work conducted by the US Department of Energy Joint Genome Institute, a US Department of Energy Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. The US Department of Energy Joint BioEnergy Institute (www.jbei.org) is supported by the US Department of Energy, Office of Science, and Office of Biological and Environmental Research, through Contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the US Department of Energy.

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Kjærbølling, I., Vesth, T., Frisvad, J. C., Nybo, J. L., Theobald, S., Kildgaard, S., Petersen, T. I., Kuo, A., Sato, A., Lyhne, E. K., Kogle, M. E., Wiebenga, A., Kun, R. S., Lubbers, R. J. M., Mäkelä, M. R., Barry, K., Chovatia, M., Clum, A., Daum, C., ... Andersen, M. R. (2020). A comparative genomics study of 23 Aspergillus species from section Flavi. Nature Communications, 11(1), Article 1106. https://doi.org/10.1038/s41467-019-14051-y

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title = "A comparative genomics study of 23 Aspergillus species from section Flavi",

abstract = "Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi.",

author = "Inge Kj{\ae}rb{\o}lling and Tammi Vesth and Frisvad, {Jens C.} and Nybo, {Jane L.} and Sebastian Theobald and Sara Kildgaard and Petersen, {Thomas Isbrandt} and Alan Kuo and Atsushi Sato and Lyhne, {Ellen K.} and Kogle, {Martin E.} and Ad Wiebenga and Kun, {Roland S.} and Lubbers, {Ronnie J.M.} and M{\"a}kel{\"a}, {Miia R.} and Kerrie Barry and Mansi Chovatia and Alicia Clum and Chris Daum and Sajeet Haridas and Guifen He and Kurt LaButti and Anna Lipzen and Stephen Mondo and Jasmyn Pangilinan and Robert Riley and Asaf Salamov and Simmons, {Blake A.} and Magnuson, {Jon K.} and Bernard Henrissat and Mortensen, {Uffe H.} and Larsen, {Thomas O.} and {de Vries}, {Ronald P.} and Grigoriev, {Igor V.} and Masayuki Machida and Baker, {Scott E.} and Andersen, {Mikael R.}",

year = "2020",

month = feb,

day = "27",

doi = "10.1038/s41467-019-14051-y",

language = "English",

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journal = "Nature Communications",

issn = "2041-1723",

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Kjærbølling, I, Vesth, T, Frisvad, JC, Nybo, JL, Theobald, S, Kildgaard, S, Petersen, TI, Kuo, A, Sato, A, Lyhne, EK, Kogle, ME, Wiebenga, A, Kun, RS, Lubbers, RJM, Mäkelä, MR, Barry, K, Chovatia, M, Clum, A, Daum, C, Haridas, S, He, G, LaButti, K, Lipzen, A, Mondo, S, Pangilinan, J, Riley, R, Salamov, A, Simmons, BA, Magnuson, JK, Henrissat, B, Mortensen, UH, Larsen, TO, de Vries, RP, Grigoriev, IV, Machida, M, Baker, SE & Andersen, MR 2020, 'A comparative genomics study of 23 Aspergillus species from section Flavi', Nature Communications, vol. 11, no. 1, 1106. https://doi.org/10.1038/s41467-019-14051-y

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T1 - A comparative genomics study of 23 Aspergillus species from section Flavi

AU - Kjærbølling, Inge

AU - Vesth, Tammi

AU - Frisvad, Jens C.

AU - Nybo, Jane L.

AU - Theobald, Sebastian

AU - Kildgaard, Sara

AU - Petersen, Thomas Isbrandt

AU - Kuo, Alan

AU - Sato, Atsushi

AU - Lyhne, Ellen K.

AU - Kogle, Martin E.

AU - Wiebenga, Ad

AU - Kun, Roland S.

AU - Lubbers, Ronnie J.M.

AU - Mäkelä, Miia R.

AU - Barry, Kerrie

AU - Chovatia, Mansi

AU - Clum, Alicia

AU - Daum, Chris

AU - Haridas, Sajeet

AU - He, Guifen

AU - LaButti, Kurt

AU - Lipzen, Anna

AU - Mondo, Stephen

AU - Pangilinan, Jasmyn

AU - Riley, Robert

AU - Salamov, Asaf

AU - Simmons, Blake A.

AU - Magnuson, Jon K.

AU - Henrissat, Bernard

AU - Mortensen, Uffe H.

AU - Larsen, Thomas O.

AU - de Vries, Ronald P.

AU - Grigoriev, Igor V.

AU - Machida, Masayuki

AU - Baker, Scott E.

AU - Andersen, Mikael R.

PY - 2020/2/27

Y1 - 2020/2/27

N2 - Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi.

AB - Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi.

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DO - 10.1038/s41467-019-14051-y

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SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

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M1 - 1106

ER -

A comparative genomics study of 23 Aspergillus species from section Flavi

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