A comparative genomics study of 23 Aspergillus species from section Flavi

Inge Kjærbølling; Tammi Camilla Vesth; Jens Christian Frisvad; Jane L. Nybo; Sebastian Theobald; Sara Kildgaard; Thomas Isbrandt Petersen; Alan Kuo; Atsushi Sato; Ellen Kirstine Lyhne; Martin Engelhard 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 Hasbro Mortensen; Thomas Ostenfeld 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 Camilla Vesth, Jens Christian Frisvad, Jane L. Nybo, Sebastian Theobald, Sara Kildgaard, Thomas Isbrandt Petersen, Alan Kuo, Atsushi Sato, Ellen Kirstine Lyhne, Martin Engelhard 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 Hasbro Mortensen, Thomas Ostenfeld Larsen, Ronald P. de Vries, Igor V. Grigoriev, Masayuki Machida, Scott E. Baker, Mikael R. Andersen^*

^*Corresponding author for this work

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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
Journal	Nature Communications
Volume	11
Issue number	1
Number of pages	12
ISSN	2041-1723
DOIs	https://doi.org/10.1038/s41467-019-14051-y
Publication status	Published - 2020

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Kjærbølling, I., Vesth, T. C., 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), [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 Vesth, {Tammi Camilla} and Frisvad, {Jens Christian} and Nybo, {Jane L.} and Sebastian Theobald and Sara Kildgaard and Petersen, {Thomas Isbrandt} and Alan Kuo and Atsushi Sato and Lyhne, {Ellen Kirstine} and Kogle, {Martin Engelhard} 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 Hasbro} and Larsen, {Thomas Ostenfeld} and {de Vries}, {Ronald P.} and Grigoriev, {Igor V.} and Masayuki Machida and Baker, {Scott E.} and Andersen, {Mikael R.}",

year = "2020",

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

language = "English",

volume = "11",

journal = "Nature Communications",

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Kjærbølling, I, Vesth, TC, 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

TY - JOUR

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

AU - Kjærbølling, Inge

AU - Vesth, Tammi Camilla

AU - Frisvad, Jens Christian

AU - Nybo, Jane L.

AU - Theobald, Sebastian

AU - Kildgaard, Sara

AU - Petersen, Thomas Isbrandt

AU - Kuo, Alan

AU - Sato, Atsushi

AU - Lyhne, Ellen Kirstine

AU - Kogle, Martin Engelhard

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 Hasbro

AU - Larsen, Thomas Ostenfeld

AU - de Vries, Ronald P.

AU - Grigoriev, Igor V.

AU - Machida, Masayuki

AU - Baker, Scott E.

AU - Andersen, Mikael R.

PY - 2020

Y1 - 2020

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.

U2 - 10.1038/s41467-019-14051-y

DO - 10.1038/s41467-019-14051-y

M3 - Journal article

C2 - 32107379

SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 1106

ER -

A comparative genomics study of 23 Aspergillus species from section Flavi

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