skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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.

Authors:
; ; ORCiD logo; ; ; ; ; ; ; ; ; ; ; ; ORCiD logo; ; ; ; ; ORCiD logo more »; ; ORCiD logo; ; ; ; ; ; ORCiD logo; ORCiD logo; ; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ; ORCiD logo; ORCiD logo « less
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Villium Foundation; Danish National Research Foundation; Villum Foundation; Jorck Foundation; USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1619580
Alternate Identifier(s):
OSTI ID: 1605144; OSTI ID: 1619163
Report Number(s):
PNNL-SA-146998
Journal ID: ISSN 2041-1723; 1106; PII: 14051
Grant/Contract Number:  
AC02-05CH11231; VKR023437; DNRF137; AC05-76RL01830
Resource Type:
Published Article
Journal Name:
Nature Communications
Additional Journal Information:
Journal Name: Nature Communications Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Aspergillus; Section Flavi; Comparative Genomics; Secondary Metabolism aflatoxin; miyakamide; CAZyme; applied microbiology; fungal genomics; industrial microbiology; small molecules

Citation Formats

Kjærbølling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J. M., Mäkelä, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K., Henrissat, Bernard, Mortensen, Uffe H., Larsen, Thomas O., de Vries, Ronald P., Grigoriev, Igor V., Machida, Masayuki, Baker, Scott E., and Andersen, Mikael R. A comparative genomics study of 23 Aspergillus species from section Flavi. United Kingdom: N. p., 2020. Web. https://doi.org/10.1038/s41467-019-14051-y.
Kjærbølling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J. M., Mäkelä, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K., Henrissat, Bernard, Mortensen, Uffe H., Larsen, Thomas O., de Vries, Ronald P., Grigoriev, Igor V., Machida, Masayuki, Baker, Scott E., & Andersen, Mikael R. A comparative genomics study of 23 Aspergillus species from section Flavi. United Kingdom. https://doi.org/10.1038/s41467-019-14051-y
Kjærbølling, Inge, Vesth, Tammi, Frisvad, Jens C., Nybo, Jane L., Theobald, Sebastian, Kildgaard, Sara, Petersen, Thomas Isbrandt, Kuo, Alan, Sato, Atsushi, Lyhne, Ellen K., Kogle, Martin E., Wiebenga, Ad, Kun, Roland S., Lubbers, Ronnie J. M., Mäkelä, Miia R., Barry, Kerrie, Chovatia, Mansi, Clum, Alicia, Daum, Chris, Haridas, Sajeet, He, Guifen, LaButti, Kurt, Lipzen, Anna, Mondo, Stephen, Pangilinan, Jasmyn, Riley, Robert, Salamov, Asaf, Simmons, Blake A., Magnuson, Jon K., Henrissat, Bernard, Mortensen, Uffe H., Larsen, Thomas O., de Vries, Ronald P., Grigoriev, Igor V., Machida, Masayuki, Baker, Scott E., and Andersen, Mikael R. Thu . "A comparative genomics study of 23 Aspergillus species from section Flavi". United Kingdom. https://doi.org/10.1038/s41467-019-14051-y.
@article{osti_1619580,
title = {A comparative genomics study of 23 Aspergillus species from section Flavi},
author = {Kjærbølling, Inge and Vesth, Tammi and Frisvad, Jens C. and Nybo, Jane L. and Theobald, Sebastian and Kildgaard, Sara and Petersen, Thomas Isbrandt and Kuo, Alan and Sato, Atsushi and Lyhne, Ellen K. and Kogle, Martin E. and Wiebenga, Ad and Kun, Roland S. and Lubbers, Ronnie J. M. and Mäkelä, Miia R. and Barry, Kerrie and Chovatia, Mansi and Clum, Alicia and Daum, Chris and Haridas, Sajeet and He, Guifen and LaButti, Kurt and Lipzen, Anna and Mondo, Stephen and Pangilinan, Jasmyn and Riley, Robert and Salamov, Asaf and Simmons, Blake A. and Magnuson, Jon K. and Henrissat, Bernard and Mortensen, Uffe H. and Larsen, Thomas O. and de Vries, Ronald P. and Grigoriev, Igor V. and Machida, Masayuki and Baker, Scott E. and Andersen, Mikael R.},
abstractNote = {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.},
doi = {10.1038/s41467-019-14051-y},
journal = {Nature Communications},
number = 1,
volume = 11,
place = {United Kingdom},
year = {2020},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1038/s41467-019-14051-y

Citation Metrics:
Cited by: 3 works
Citation information provided by
Web of Science

Figures / Tables:

Fig. 1 Fig. 1: Phylogeny and genome statistics of section Flavi plus eight other Aspergillus, Penicillium, and Neurospora species. a Phylogenetic tree constructed using RAxML, MUSCLE, and Gblocks based on 200 monocore genes (a single homolog in each of the species). The red star indicates an uncertain leaf most likely caused bymore » a different gene calling method, and the arrow shows where A. sojae should be placed in the phylogenetic tree. The zoom shows the branching in a clade around A. oryzae. b The colors illustrate the clades found within section Flavi and X indicates species sequenced in this study. Earlier sequenced genomes such as A. oryzae and A. fumigatus were assembled using optical mapping and genetic maps. c Seven bubble plots illustrating key genome numbers and sequencing quality parameter. The bubble sizes have been scaled to each panel and are not comparable across panels.« less

Save / Share:

Works referenced in this record:

Minimum Information about a Biosynthetic Gene cluster
journal, August 2015

  • Medema, Marnix H.; Kottmann, Renzo; Yilmaz, Pelin
  • Nature Chemical Biology, Vol. 11, Issue 9
  • DOI: 10.1038/nchembio.1890

Effect of easily metabolizable sugars in the production of xylanase by Aspergillus tamarii in solid-state fermentation
journal, March 2001

  • Farani de Souza, Daniela; Giatti Marques de Souza, Cristina; Peralta, Rosane Marina
  • Process Biochemistry, Vol. 36, Issue 8-9
  • DOI: 10.1016/S0032-9592(00)00295-8

Purification and characterization of two xylanases and an arabinofuranosidase from Aspergillus sojae
journal, January 1995

  • Kimura, Isao; Sasahara, Hiroyuki; Tajima, Shigeyuki
  • Journal of Fermentation and Bioengineering, Vol. 80, Issue 4
  • DOI: 10.1016/0922-338X(95)94200-B

The developmentally regulated Aspergillus nidulans wA gene encodes a polypeptide homologous to polyketide and fatty acid synthases
journal, November 1992

  • Mayorga, María E.; Timberlake, William E.
  • Molecular and General Genetics MGG, Vol. 235, Issue 2-3
  • DOI: 10.1007/BF00279362

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli
journal, September 2018


Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri
journal, October 2018


A Gene Cluster Containing Two Fungal Polyketide Synthases Encodes the Biosynthetic Pathway for a Polyketide, Asperfuranone, in Aspergillus nidulans
journal, March 2009

  • Chiang, Yi-Ming; Szewczyk, Edyta; Davidson, Ashley D.
  • Journal of the American Chemical Society, Vol. 131, Issue 8
  • DOI: 10.1021/ja8088185

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
journal, April 2000


Safety of the fungal workhorses of industrial biotechnology: update on the mycotoxin and secondary metabolite potential of Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei
journal, October 2018

  • Frisvad, Jens C.; Møller, Lars L. H.; Larsen, Thomas O.
  • Applied Microbiology and Biotechnology, Vol. 102, Issue 22
  • DOI: 10.1007/s00253-018-9354-1

Uncovering secondary metabolite evolution and biosynthesis using gene cluster networks and genetic dereplication
journal, December 2018

  • Theobald, Sebastian; Vesth, Tammi C.; Rendsvig, Jakob Kræmmer
  • Scientific Reports, Vol. 8, Issue 1
  • DOI: 10.1038/s41598-018-36561-3

Identification of a Hybrid PKS/NRPS Required for Pseurotin A Biosynthesis in the Human PathogenAspergillus fumigatus
journal, September 2007


Identification of a Major Xylanase from Aspergillus flavus as a 14-kD Protein
journal, April 2011


GH11 xylanase from Aspergillus tamarii Kita: Purification by one-step chromatography and xylooligosaccharides hydrolysis monitored in real-time by mass spectrometry
journal, March 2018


Dna Relatedness Among Wild and Domesticated Species in the Aspergillus Flavus Group
journal, November 1986


Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
journal, December 2005

  • Galagan, James E.; Calvo, Sarah E.; Cuomo, Christina
  • Nature, Vol. 438, Issue 7071
  • DOI: 10.1038/nature04341

Evaluation of holocellulase production by plant-degrading fungi grown on agro-industrial residues
journal, March 2010

  • de Siqueira, Félix Gonçalves; de Siqueira, Aline Gonçalves; de Siqueira, Eliane Gonçalves
  • Biodegradation, Vol. 21, Issue 5
  • DOI: 10.1007/s10532-010-9346-z

Genome sequencing and analysis of Aspergillus oryzae
journal, December 2005

  • Machida, Masayuki; Asai, Kiyoshi; Sano, Motoaki
  • Nature, Vol. 438, Issue 7071
  • DOI: 10.1038/nature04300

Genomics of Aspergillus oryzae: Learning from the History of Koji Mold and Exploration of Its Future
journal, May 2008


Genome-Based Cluster Deletion Reveals an Endocrocin Biosynthetic Pathway in Aspergillus fumigatus
journal, April 2012

  • Lim, Fang Yun; Hou, Yanpeng; Chen, Yiming
  • Applied and Environmental Microbiology, Vol. 78, Issue 12
  • DOI: 10.1128/AEM.07710-11

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
journal, June 2015


Aspergillus is monophyletic: Evidence from multiple gene phylogenies and extrolites profiles
journal, September 2016


Characterization of thermophilic fungi producing extracellular lignocellulolytic enzymes for lignocellulosic hydrolysis under solid-state fermentation
journal, July 2018

  • Saroj, Paramjeet; P., Manasa; Narasimhulu, Korrapati
  • Bioresources and Bioprocessing, Vol. 5, Issue 1
  • DOI: 10.1186/s40643-018-0216-6

Aspergillus flavus and Aspergillus parasiticus: Aflatoxigenic Fungi of Concern in Foods and Feeds†: A Review
journal, December 1995


Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

SMURF: Genomic mapping of fungal secondary metabolite clusters
journal, September 2010

  • Khaldi, Nora; Seifuddin, Fayaz T.; Turner, Geoff
  • Fungal Genetics and Biology, Vol. 47, Issue 9
  • DOI: 10.1016/j.fgb.2010.06.003

Biosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS–PKS hybrid enzyme
journal, October 2015

  • Yun, Choong-Soo; Motoyama, Takayuki; Osada, Hiroyuki
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms9758

Easyfig: a genome comparison visualizer
journal, January 2011


The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
journal, January 2009

  • Cantarel, B. L.; Coutinho, P. M.; Rancurel, C.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn663

CVTree: a phylogenetic tree reconstruction tool based on whole genomes
journal, July 2004

  • Qi, J.; Luo, H.; Hao, B.
  • Nucleic Acids Research, Vol. 32, Issue Web Server
  • DOI: 10.1093/nar/gkh362

A thermostable maltose-tolerantα-amylase fromAspergillus tamarii
journal, February 2004

  • Moreira, Fabiana Guillen; Lenartovicz, Veridiana; Peralta, Rosane Marina
  • Journal of Basic Microbiology, Vol. 44, Issue 1
  • DOI: 10.1002/jobm.200310302

Development of enzyme technology for Aspergillus oryzae, A. sojae, and A. luchuensis , the national microorganisms of Japan
journal, February 2016


Microprep protocol for extraction of DNA from tomato and other herbaceous plants
journal, September 1995

  • Fulton, Theresa M.; Chunwongse, Julapark; Tanksley, Steven D.
  • Plant Molecular Biology Reporter, Vol. 13, Issue 3
  • DOI: 10.1007/BF02670897

A novel pectin-degrading enzyme complex from Aspergillus sojae ATCC 20235 mutants
journal, September 2014

  • Mata-Gómez, Marco A.; Heerd, Doreen; Oyanguren-García, Iñigo
  • Journal of the Science of Food and Agriculture, Vol. 95, Issue 7
  • DOI: 10.1002/jsfa.6864

Aspergillus flavus: human pathogen, allergen and mycotoxin producer
journal, June 2007


InterPro in 2017—beyond protein family and domain annotations
journal, November 2016

  • Finn, Robert D.; Attwood, Teresa K.; Babbitt, Patricia C.
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw1107

Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse
journal, January 2011

  • de Souza, Wagner R.; de Gouvea, Paula F.; Savoldi, Marcela
  • Biotechnology for Biofuels, Vol. 4, Issue 1
  • DOI: 10.1186/1754-6834-4-40

Chrysogine Biosynthesis Is Mediated by a Two-Module Nonribosomal Peptide Synthetase
journal, June 2017

  • Wollenberg, Rasmus Dam; Saei, Wagma; Westphal, Klaus Ringsborg
  • Journal of Natural Products, Vol. 80, Issue 7
  • DOI: 10.1021/acs.jnatprod.6b00822

Two new aflatoxin producing species, and an overview of Aspergillus section Flavi
journal, June 2011


Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species
journal, January 2018

  • Kjærbølling, Inge; Vesth, Tammi C.; Frisvad, Jens C.
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 4
  • DOI: 10.1073/pnas.1715954115

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014


Aspergillus flavus: the major producer of aflatoxin
journal, November 2007


Production, Purification, Immobilization, and Characterization of a Thermostable β-Galactosidase from Aspergillus alliaceus
journal, May 2012

  • Sen, Sucharita; Ray, Lalitagauri; Chattopadhyay, Parimal
  • Applied Biochemistry and Biotechnology, Vol. 167, Issue 7
  • DOI: 10.1007/s12010-012-9732-6

Accurate prediction of secondary metabolite gene clusters in filamentous fungi
journal, December 2012

  • Andersen, M. R.; Nielsen, J. B.; Klitgaard, A.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 1
  • DOI: 10.1073/pnas.1205532110

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data
journal, May 2017


Glycosidases induced in Aspergillus tamarii. Mycelial α-d-galactosidases
journal, May 1984

  • Civas, A.; Eberhard, R.; Le Dizet, P.
  • Biochemical Journal, Vol. 219, Issue 3
  • DOI: 10.1042/bj2190849

Low-Volume Toolbox for the Discovery of Immunosuppressive Fungal Secondary Metabolites
journal, April 2013


New Antibiotics Miyakamides Produced by a Fungus.
journal, January 2002


New and revisited species in Aspergillus section Nigri
journal, June 2011


The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources
journal, November 2011

  • Arnaud, M. B.; Cerqueira, G. C.; Inglis, D. O.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr875

Genomics of Aspergillus oryzae
journal, March 2007

  • Kobayashi, Tetsuo; Abe, Keietsu; Asai, Kiyoshi
  • Bioscience, Biotechnology, and Biochemistry, Vol. 71, Issue 3
  • DOI: 10.1271/bbb.60550

On the safety of Aspergillus oryzae: a review
journal, February 1992

  • Barbesgaard, Peder; Heldt-Hansen, HansPeter; Diderichsen, B�rge
  • Applied Microbiology and Biotechnology, Vol. 36, Issue 5
  • DOI: 10.1007/BF00183230

The Fumagillin Biosynthetic Gene Cluster in Aspergillus fumigatus Encodes a Cryptic Terpene Cyclase Involved in the Formation of β- trans -Bergamotene
journal, March 2013

  • Lin, Hsiao-Ching; Chooi, Yit-Heng; Dhingra, Sourabh
  • Journal of the American Chemical Society, Vol. 135, Issue 12
  • DOI: 10.1021/ja312503y

Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum
journal, May 2014

  • Kis-Papo, Tamar; Weig, Alfons R.; Riley, Robert
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4745

The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013

  • Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1178

Identification of Two Aflatrem Biosynthesis Gene Loci in Aspergillus flavus and Metabolic Engineering of Penicillium paxilli To Elucidate Their Function
journal, October 2009

  • Nicholson, M. J.; Koulman, A.; Monahan, B. J.
  • Applied and Environmental Microbiology, Vol. 75, Issue 23
  • DOI: 10.1128/AEM.02146-08

Aspergillus flavus : an emerging non- fumigatus Aspergillus species of significance
journal, May 2009


Cyclopiazonic Acid Biosynthesis of Aspergillus flavus and Aspergillus oryzae
journal, November 2009


Taxonomy of Aspergillus section Flavi and their production of aflatoxins, ochratoxins and other mycotoxins
journal, June 2019


The genome sequence of the filamentous fungus Neurospora crassa
journal, April 2003

  • Galagan, James E.; Calvo, Sarah E.; Borkovich, Katherine A.
  • Nature, Vol. 422, Issue 6934
  • DOI: 10.1038/nature01554

Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus
journal, April 2008

  • Fedorova, Natalie D.; Khaldi, Nora; Joardar, Vinita S.
  • PLoS Genetics, Vol. 4, Issue 4, Article No. e1000046
  • DOI: 10.1371/journal.pgen.1000046

Closely related fungi employ diverse enzymatic strategies to degrade plant biomass
journal, August 2015

  • Benoit, Isabelle; Culleton, Helena; Zhou, Miaomiao
  • Biotechnology for Biofuels, Vol. 8, Issue 1
  • DOI: 10.1186/s13068-015-0285-0

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
journal, May 2011

  • Andersen, M. R.; Salazar, M. P.; Schaap, P. J.
  • Genome Research, Vol. 21, Issue 6, p. 885-897
  • DOI: 10.1101/gr.112169.110

The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae
journal, August 2012


Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus
journal, January 2012

  • Marcet-Houben, Marina; Ballester, Ana-Rosa; de la Fuente, Beatriz
  • BMC Genomics, Vol. 13, Issue 1
  • DOI: 10.1186/1471-2164-13-646

Identification and functional analysis of the aspergillic acid gene cluster in Aspergillus flavus
journal, July 2018

  • Lebar, Matthew D.; Cary, Jeffrey W.; Majumdar, Rajtilak
  • Fungal Genetics and Biology, Vol. 116
  • DOI: 10.1016/j.fgb.2018.04.009

Draft Genome Sequencing and Comparative Analysis of Aspergillus sojae NBRC4239
journal, June 2011


Genomic sequence of the aflatoxigenic filamentous fungus Aspergillus nomius
journal, July 2015


CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy
journal, October 2015


The COG database: an updated version includes eukaryotes
journal, January 2003

  • Tatusov, Roman L.; Fedorova, Natalie D.; Jackson, John D.
  • BMC Bioinformatics, Vol. 4, Article No. 41
  • DOI: 10.1186/1471-2105-4-41

Horizontal gene transfer in fungi
journal, December 2011


APE: Analyses of Phylogenetics and Evolution in R language
journal, January 2004


Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)
journal, May 2008

  • Martinez, Diego; Berka, Randy M.; Henrissat, Bernard
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1403

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

Structural Dynamics of Eukaryotic Chromosome Evolution
journal, August 2003


Isolation of fungi from dung of wild herbivores for application in bioethanol production
journal, October 2017

  • Makhuvele, Rhulani; Ncube, Ignatious; Jansen van Rensburg, Elbert Lukas
  • Brazilian Journal of Microbiology, Vol. 48, Issue 4
  • DOI: 10.1016/j.bjm.2016.11.013

Production of xylanolytic enzymes by Aspergillus tamarii in solid state fermentation
journal, April 1999


Draft Genome Sequence of an Aflatoxigenic Aspergillus Species, A. bombycis
journal, September 2016

  • Moore, Geromy G.; Mack, Brian M.; Beltz, Shannon B.
  • Genome Biology and Evolution, Vol. 8, Issue 11
  • DOI: 10.1093/gbe/evw238

Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species
journal, April 2017

  • Nielsen, Jens Christian; Grijseels, Sietske; Prigent, Sylvain
  • Nature Microbiology, Vol. 2, Issue 6
  • DOI: 10.1038/nmicrobiol.2017.44

Genome sequence of an aflatoxigenic pathogen of Argentinian peanut, Aspergillus arachidicola
journal, March 2018


MycoCosm portal: gearing up for 1000 fungal genomes
journal, December 2013

  • Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1183

A New Black Aspergillus Species, A. vadensis, Is a Promising Host for Homologous and Heterologous Protein Production
journal, July 2004


Characterization of a Silent Azaphilone Gene Cluster from Aspergillus niger ATCC 1015 Reveals a Hydroxylation-Mediated Pyran-Ring Formation
journal, August 2012


Differentiation of Aspergillus parasiticus from Aspergillus sojae by random amplification of polymorphic DNA.
journal, January 1995


Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
journal, December 2005

  • Nierman, William C.; Pain, Arnab; Anderson, Michael J.
  • Nature, Vol. 438, Issue 7071, p. 1151-1156
  • DOI: 10.1038/nature04332

    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.