The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi

M. V. Aguilar-Pontes, J. Brandl, E. McDonnell, K. Strasser, T.T.M. Nguyen, R. Riley, S. Mondo, A. Salamov, J.L. Nybo, T.C. Vesth, I.V. Grigoriev, M.R. Andersen, A. Tsang*, R.P. de Vries

*Corresponding author for this work

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Abstract

The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism. Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source.
Original languageEnglish
JournalStudies in Mycology
Volume91
Pages (from-to)61-78
ISSN0166-0616
DOIs
Publication statusPublished - 2018

Keywords

  • Aspergillus
  • Genomic diversity
  • Gold standard genome
  • Sugar catabolism

Cite this

Aguilar-Pontes, M. V., Brandl, J., McDonnell, E., Strasser, K., Nguyen, T. T. M., Riley, R., ... de Vries, R. P. (2018). The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi. Studies in Mycology, 91, 61-78. https://doi.org/10.1016/j.simyco.2018.10.001
Aguilar-Pontes, M. V. ; Brandl, J. ; McDonnell, E. ; Strasser, K. ; Nguyen, T.T.M. ; Riley, R. ; Mondo, S. ; Salamov, A. ; Nybo, J.L. ; Vesth, T.C. ; Grigoriev, I.V. ; Andersen, M.R. ; Tsang, A. ; de Vries, R.P. / The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi. In: Studies in Mycology. 2018 ; Vol. 91. pp. 61-78.
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abstract = "The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism. Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source.",
keywords = "Aspergillus, Genomic diversity, Gold standard genome, Sugar catabolism",
author = "Aguilar-Pontes, {M. V.} and J. Brandl and E. McDonnell and K. Strasser and T.T.M. Nguyen and R. Riley and S. Mondo and A. Salamov and J.L. Nybo and T.C. Vesth and I.V. Grigoriev and M.R. Andersen and A. Tsang and {de Vries}, R.P.",
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Aguilar-Pontes, MV, Brandl, J, McDonnell, E, Strasser, K, Nguyen, TTM, Riley, R, Mondo, S, Salamov, A, Nybo, JL, Vesth, TC, Grigoriev, IV, Andersen, MR, Tsang, A & de Vries, RP 2018, 'The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi', Studies in Mycology, vol. 91, pp. 61-78. https://doi.org/10.1016/j.simyco.2018.10.001

The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi. / Aguilar-Pontes, M. V.; Brandl, J.; McDonnell, E.; Strasser, K.; Nguyen, T.T.M.; Riley, R.; Mondo, S.; Salamov, A.; Nybo, J.L.; Vesth, T.C.; Grigoriev, I.V.; Andersen, M.R.; Tsang, A.; de Vries, R.P.

In: Studies in Mycology, Vol. 91, 2018, p. 61-78.

Research output: Contribution to journalJournal articleResearchpeer-review

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T1 - The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi

AU - Aguilar-Pontes, M. V.

AU - Brandl, J.

AU - McDonnell, E.

AU - Strasser, K.

AU - Nguyen, T.T.M.

AU - Riley, R.

AU - Mondo, S.

AU - Salamov, A.

AU - Nybo, J.L.

AU - Vesth, T.C.

AU - Grigoriev, I.V.

AU - Andersen, M.R.

AU - Tsang, A.

AU - de Vries, R.P.

PY - 2018

Y1 - 2018

N2 - The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism. Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source.

AB - The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism. Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source.

KW - Aspergillus

KW - Genomic diversity

KW - Gold standard genome

KW - Sugar catabolism

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DO - 10.1016/j.simyco.2018.10.001

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JF - Studies in Mycology

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