Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti
Journal Article
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· Studies in Mycology
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- Technical Univ. of Denmark, Lyngby (Denmark); Novonesis A/S, Bagsværd (Denmark)
- Technical Univ. of Denmark, Lyngby (Denmark); LifeMine Therapeutics, Cambridge, MA (United States)
- Technical Univ. of Denmark, Lyngby (Denmark)
- USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
- Univ. of California, Riverside, CA (United States)
- Centre National de la Recherche Scientifique (CNRS), Marseille (France). Architecture et Fonction des Macromolécules Biologiques (AFMB); Aix-Marseille Univ., Marseille (France); French National Research Institute for Agriculture, Food and Environment (INRAE), Marseille (France). Biodiversité et Biotechnologie Fongiques (BBF)
- Westerdijk Fungal Biodiversity Institute, Utrecht (Netherlands)
- Aalto Univ. (Finland)
- USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
- USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
The genus Aspergillus is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. Aspergillus includes species from sections Usti and Cavernicolus, which until recently were joined in section Usti, but have now been proposed to be non-monophyletic and were split by section Nidulantes, Aenei and Raperi. To learn more about these sections, we have sequenced the genomes of 13 Aspergillus species from section Cavernicolus (A. cavernicola, A. californicus, and A. egyptiacus), section Usti (A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus and A. pseudoustus), and section Nidulantes (A. quadrilineatus, previously A. tetrazonus). We compared these genomes with 16 additional species from Aspergillus to explore their genetic diversity, based on their genome content, repeat-induced point mutations (RIPs), transposable elements, carbohydrate-active enzyme (CAZyme) profile, growth on plant polysaccharides, and secondary metabolite gene clusters (SMGCs). All analyses support the split of section Usti and provide additional insights: Analyses of genes found only in single species show that these constitute genes which appear to be involved in adaptation to new carbon sources, regulation to fit new niches, and bioactive compounds for competitive advantages, suggesting that these support species differentiation in Aspergillus species. Sections Usti and Cavernicolus have mainly unique SMGCs. Section Usti contains very large and information-rich genomes, an expansion partially driven by CAZymes, as section Usti contains the most CAZyme-rich species seen in genus Aspergillus. Section Usti is clearly an underutilized source of plant biomass degraders and shows great potential as industrial enzyme producers.
- Research Organization:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Organization:
- US Department of Energy; USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
- Grant/Contract Number:
- AC02-05CH11231; AC05-76RL01830
- OSTI ID:
- 3003980
- Alternate ID(s):
- OSTI ID: 2568627
- Report Number(s):
- PNNL-SA--208281
- Journal Information:
- Studies in Mycology, Journal Name: Studies in Mycology Journal Issue: 1 Vol. 111; ISSN 0166-0616
- Publisher:
- ElsevierCopyright Statement
- Country of Publication:
- United States
- Language:
- English
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