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Title: Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants

Abstract

Background: Aspergillus spp. comprises a very diverse group of lower eukaryotes with a high relevance for industrial applications and clinical implications. These multinucleate species are often cultured for many generations in the laboratory, which can unknowingly propagate hidden genetic mutations. To assess the likelihood of such events, we studied the genome stability of aspergilli by using a combination of mutation accumulation (MA) lines and whole genome sequencing. Results: We sequenced the whole genomes of 30 asexual and 10 sexual MA lines of three Aspergillus species (A. flavus, A. fumigatus and A. nidulans) and estimated that each MA line accumulated mutations for over 4000 mitoses during asexual cycles. We estimated mutation rates of 4.2 × 10 -11 (A. flavus), 1.1 × 10 -11 (A. fumigatus) and 4.1 × 10 -11 (A. nidulans) per site per mitosis, suggesting that the genomes are very robust. Unexpectedly, we found a very high rate of GC → TA transversions only in A. flavus. In parallel, 30 asexual lines of the non-homologous end-joining (NHEJ) mutants of the three species were also allowed to accumulate mutations for the same number of mitoses. Sequencing of these NHEJ MA lines gave an estimated mutation rate of 5.1 × 10more » -11 (A. flavus), 2.2 × 10 -11 (A. fumigatus) and 4.5 × 10 -11 (A. nidulans) per base per mitosis, which is slightly higher than in the wild-type strains and some ~ 5–6 times lower than in the yeasts. Additionally, in A. nidulans, we found a NHEJ-dependent interference of the sexual cycle that is independent of the accumulation of mutations. Conclusions: We present for the first time direct counts of the mutation rate of filamentous fungal species and find that Aspergillus genomes are very robust. Deletion of the NHEJ machinery results in a slight increase in the mutation rate, but at a rate we suggest is still safe to use for biotechnology purposes. Unexpectedly, we found GC→TA transversions predominated only in the species A. flavus, which could be generated by the hepatocarcinogen secondary metabolite aflatoxin. Lastly, a strong effect of the NHEJ mutation in self-crossing was observed and an increase in the mutations of the asexual lines was quantified.« less

Authors:
 [1];  [2];  [3];  [4];  [4];  [4];  [4];  [4];  [4];  [5];  [5];  [6];  [7];  [8];  [2]; ORCiD logo [5]
  1. Univ. of Seville, Seville (Spain). Dept. of Genetics; Consejo Superior de Investigaciones Científicas y Univ. de Sevilla, Seville (Spain). Inst. de Bioquímica Vegetal y Fotosíntesis
  2. Georg-August-Univ., Göttingen (Germany). Genetics and Göttingen Center for Molecular Biosciences (GZMB)
  3. Univ. of Wisconsin-Madison, Madison, WI (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. Univ. of Seville, Seville (Spain). Dept. of Genetics
  6. Univ. of Seville, Seville (Spain). Dept. of Genetics; Inst. para el Estudio de la Reproducción Humana (Inebir), Seville (Spain)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
  8. Univ. of Wisconsin-Madison, Madison, WI (United States); Univ. of Wisconsin-Madison, Madison, WI (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1580973
Grant/Contract Number:  
[AC02-05CH11231]
Resource Type:
Accepted Manuscript
Journal Name:
BMC Biology
Additional Journal Information:
[ Journal Volume: 17; Journal Issue: 1]; Journal ID: ISSN 1741-7007
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Aspergillus; Aflatoxin; Mutation accumulating lines; Genome stability; Non-homologous end-joining; ku70

Citation Formats

Álvarez-Escribano, Isidro, Sasse, Christoph, Bok, Jin Woo, Na, Hyunsoo, Amirebrahimi, Mojgan, Lipzen, Anna, Schackwitz, Wendy, Martin, Joel, Barry, Kerrie, Gutiérrez, Gabriel, Cea-Sánchez, Sara, Marcos, Ana T., Grigoriev, Igor V., Keller, Nancy P., Braus, Gerhard H., and Cánovas, David. Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants. United States: N. p., 2019. Web. doi:10.1186/s12915-019-0702-0.
Álvarez-Escribano, Isidro, Sasse, Christoph, Bok, Jin Woo, Na, Hyunsoo, Amirebrahimi, Mojgan, Lipzen, Anna, Schackwitz, Wendy, Martin, Joel, Barry, Kerrie, Gutiérrez, Gabriel, Cea-Sánchez, Sara, Marcos, Ana T., Grigoriev, Igor V., Keller, Nancy P., Braus, Gerhard H., & Cánovas, David. Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants. United States. doi:10.1186/s12915-019-0702-0.
Álvarez-Escribano, Isidro, Sasse, Christoph, Bok, Jin Woo, Na, Hyunsoo, Amirebrahimi, Mojgan, Lipzen, Anna, Schackwitz, Wendy, Martin, Joel, Barry, Kerrie, Gutiérrez, Gabriel, Cea-Sánchez, Sara, Marcos, Ana T., Grigoriev, Igor V., Keller, Nancy P., Braus, Gerhard H., and Cánovas, David. Mon . "Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants". United States. doi:10.1186/s12915-019-0702-0. https://www.osti.gov/servlets/purl/1580973.
@article{osti_1580973,
title = {Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants},
author = {Álvarez-Escribano, Isidro and Sasse, Christoph and Bok, Jin Woo and Na, Hyunsoo and Amirebrahimi, Mojgan and Lipzen, Anna and Schackwitz, Wendy and Martin, Joel and Barry, Kerrie and Gutiérrez, Gabriel and Cea-Sánchez, Sara and Marcos, Ana T. and Grigoriev, Igor V. and Keller, Nancy P. and Braus, Gerhard H. and Cánovas, David},
abstractNote = {Background: Aspergillus spp. comprises a very diverse group of lower eukaryotes with a high relevance for industrial applications and clinical implications. These multinucleate species are often cultured for many generations in the laboratory, which can unknowingly propagate hidden genetic mutations. To assess the likelihood of such events, we studied the genome stability of aspergilli by using a combination of mutation accumulation (MA) lines and whole genome sequencing. Results: We sequenced the whole genomes of 30 asexual and 10 sexual MA lines of three Aspergillus species (A. flavus, A. fumigatus and A. nidulans) and estimated that each MA line accumulated mutations for over 4000 mitoses during asexual cycles. We estimated mutation rates of 4.2 × 10-11 (A. flavus), 1.1 × 10-11 (A. fumigatus) and 4.1 × 10-11 (A. nidulans) per site per mitosis, suggesting that the genomes are very robust. Unexpectedly, we found a very high rate of GC → TA transversions only in A. flavus. In parallel, 30 asexual lines of the non-homologous end-joining (NHEJ) mutants of the three species were also allowed to accumulate mutations for the same number of mitoses. Sequencing of these NHEJ MA lines gave an estimated mutation rate of 5.1 × 10-11 (A. flavus), 2.2 × 10-11 (A. fumigatus) and 4.5 × 10-11 (A. nidulans) per base per mitosis, which is slightly higher than in the wild-type strains and some ~ 5–6 times lower than in the yeasts. Additionally, in A. nidulans, we found a NHEJ-dependent interference of the sexual cycle that is independent of the accumulation of mutations. Conclusions: We present for the first time direct counts of the mutation rate of filamentous fungal species and find that Aspergillus genomes are very robust. Deletion of the NHEJ machinery results in a slight increase in the mutation rate, but at a rate we suggest is still safe to use for biotechnology purposes. Unexpectedly, we found GC→TA transversions predominated only in the species A. flavus, which could be generated by the hepatocarcinogen secondary metabolite aflatoxin. Lastly, a strong effect of the NHEJ mutation in self-crossing was observed and an increase in the mutations of the asexual lines was quantified.},
doi = {10.1186/s12915-019-0702-0},
journal = {BMC Biology},
number = [1],
volume = [17],
place = {United States},
year = {2019},
month = {11}
}

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