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

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

doi:10.1038/s41588-018-0246-1

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

Journal Article · 21 October 2018 · Nature Genetics

DOI: https://doi.org/10.1038/s41588-018-0246-1 · OSTI ID:1492689

Vesth, Tammi C.;

;

; Hoof, Jakob B.; Brandl, Julian; Salamov, Asaf; Riley, Robert;

; Phatale, Pallavi; Nielsen, Morten T.; Lyhne, Ellen K.; Kogle, Martin E.; Strasser, Kimchi; McDonnell, Erin; Barry, Kerrie; Clum, Alicia; Chen, Cindy more »

Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. In order to learn more about fungal speciation, as well as potential for applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as six A. niger isolates. This allowed us to quantify both inter- and intra-species genomic variation. We further predicted 17,903 CAZymes 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 A. nidulans. Experimental and computational analyses all supported a role in speciation for secondary metabolism and regulators and allowed us to propose a three-step model for fungal speciation.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: Danish National Research Foundation (DNRF); Novo Nordisk Foundation; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231; AC05-76RL01830

OSTI ID:: 1492689

Report Number(s):: PNNL-SA-133567

Journal Information:: Nature Genetics, Journal Name: Nature Genetics Journal Issue: 12 Vol. 50; ISSN 1061-4036

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 10 of Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species Huang, Lianggang; Li, Xuejie; Dong, Liangbo figshare https://doi.org/10.6084/m9.figshare.16576038	dataset	January 2021
Additional file 13 of Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species Huang, Lianggang; Li, Xuejie; Dong, Liangbo figshare https://doi.org/10.6084/m9.figshare.16576047.v1	dataset	January 2021
Additional file 14 of Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species Huang, Lianggang; Li, Xuejie; Dong, Liangbo figshare https://doi.org/10.6084/m9.figshare.16576050	dataset	January 2021
Additional file 2 of Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species Huang, Lianggang; Li, Xuejie; Dong, Liangbo figshare https://doi.org/10.6084/m9.figshare.16576056	dataset	January 2021
Additional file 3 of Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species Huang, Lianggang; Li, Xuejie; Dong, Liangbo figshare https://doi.org/10.6084/m9.figshare.16576059	dataset	January 2021
Additional file 4 of Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species Huang, Lianggang; Li, Xuejie; Dong, Liangbo figshare https://doi.org/10.6084/m9.figshare.16576062.v1	dataset	January 2021
Additional file 5 of Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species Huang, Lianggang; Li, Xuejie; Dong, Liangbo figshare https://doi.org/10.6084/m9.figshare.16576065.v1	dataset	January 2021
Additional file 6 of Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species Huang, Lianggang; Li, Xuejie; Dong, Liangbo figshare https://doi.org/10.6084/m9.figshare.16576068	dataset	January 2021
Additional file 7 of Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species Huang, Lianggang; Li, Xuejie; Dong, Liangbo figshare https://doi.org/10.6084/m9.figshare.16576071	dataset	January 2021
Additional file 8 of Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species Huang, Lianggang; Li, Xuejie; Dong, Liangbo figshare https://doi.org/10.6084/m9.figshare.16576074.v1	dataset	January 2021
Additional file 9 of Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species Huang, Lianggang; Li, Xuejie; Dong, Liangbo figshare https://doi.org/10.6084/m9.figshare.16576077.v1	dataset	January 2021
Citric acid and itaconic acid accumulation: variations of the same story? Karaffa, Levente; Kubicek, Christian P. Applied Microbiology and Biotechnology, Vol. 103, Issue 7 https://doi.org/10.1007/s00253-018-09607-9	journal	February 2019
Comparative genomics of the aconidial Aspergillus niger strain LDM3 predicts genes associated with its high protein secretion capacity Sui, Yu-Fei; Ouyang, Li-Ming; Schütze, Tabea Applied Microbiology and Biotechnology, Vol. 104, Issue 6 https://doi.org/10.1007/s00253-020-10398-1	journal	February 2020
Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus Song, Jia-Ming; Guan, Zhilin; Hu, Jianlin Nature Plants, Vol. 6, Issue 1 https://doi.org/10.1038/s41477-019-0577-7	journal	January 2020
Uncovering secondary metabolite evolution and biosynthesis using gene cluster networks and genetic dereplication Theobald, Sebastian; Vesth, Tammi C.; Rendsvig, Jakob Kræmmer Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-36561-3	journal	December 2018
Biosynthetic gene clusters and the evolution of fungal chemodiversity Rokas, Antonis; Mead, Matthew E.; Steenwyk, Jacob L. Natural Product Reports, Vol. 37, Issue 7 https://doi.org/10.1039/c9np00045c	journal	January 2020
Synthetic-biology-based discovery of a fungal macrolide from Macrophomina phaseolina Morishita, Yohei; Sonohara, Terutaka; Taniguchi, Tohru Organic & Biomolecular Chemistry, Vol. 18, Issue 15 https://doi.org/10.1039/d0ob00519c	journal	January 2020
The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi Gluck-Thaler, Emile; Haridas, Sajeet; Binder, Manfred Molecular Biology and Evolution, Vol. 37, Issue 10 https://doi.org/10.1093/molbev/msaa122	journal	May 2020
Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks Schäpe, P.; Kwon, Mj; Baumann, B. Nucleic Acids Research, Vol. 47, Issue 2 https://doi.org/10.1093/nar/gky1183	journal	November 2018
Metabolic and regulatory insights from the experimental horizontal gene transfer of the aurofusarin and bikaverin gene clusters to Aspergillus nidulans Reus, Elise; Nielsen, Mikkel Rank; Frandsen, Rasmus John Normand Molecular Microbiology, Vol. 112, Issue 6 https://doi.org/10.1111/mmi.14376	journal	September 2019
Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi Nielsen, Jens Christian; Prigent, Sylvain; Grijseels, Sietske mSystems, Vol. 4, Issue 2 https://doi.org/10.1128/msystems.00012-19	journal	April 2019
Resistance Gene-Directed Genome Mining of 50 Aspergillus Species Kjærbølling, Inge; Vesth, Tammi; Andersen, Mikael R. mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/msystems.00085-19	journal	May 2019
Genus level analysis of PKS-NRPS and NRPS-PKS hybrids reveals their origin in Aspergilli Theobald, Sebastian; Vesth, Tammi C.; Andersen, Mikael R. BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6114-2	journal	November 2019
Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery Mondo, Stephen J.; Jiménez, Diego Javier; Hector, Ronald E. Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1569-6	journal	September 2019
Cpf1 enables fast and efficient genome editing in Aspergilli Vanegas, Katherina Garcia; Jarczynska, Zofia Dorota; Strucko, Tomas Fungal Biology and Biotechnology, Vol. 6, Issue 1 https://doi.org/10.1186/s40694-019-0069-6	journal	May 2019
Practical guidance for the implementation of the CRISPR genome editing tool in filamentous fungi Kwon, Min Jin; Schütze, Tabea; Spohner, Sebastian Fungal Biology and Biotechnology, Vol. 6, Issue 1 https://doi.org/10.1186/s40694-019-0079-4	journal	October 2019
Polyphasic, Including MALDI-TOF MS, Evaluation of Freeze-Drying Long-Term Preservation on Aspergillus (Section Nigri) Strains Rodriguez, Rodrigo; Santos, Carla; Simões, Marta F. Microorganisms, Vol. 7, Issue 9 https://doi.org/10.3390/microorganisms7090291	journal	August 2019
Diversity and toxigenicity of fungi and description of Fusarium madaense sp. nov. from cereals, legumes and soils in north-central Nigeria Ezekiel, Chibundu N.; Kraak, Bart; Sandoval-Denis, Marcelo MycoKeys, Vol. 67 https://doi.org/10.3897/mycokeys.67.52716	journal	June 2020

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