Details
| Original language | English |
|---|---|
| Article number | 21 |
| Journal | IMA FUNGUS |
| Volume | 12 |
| Issue number | 1 |
| Publication status | Published - 9 Aug 2021 |
Abstract
Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales), respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 (Hypocreales, Ascomycota) was isolated from the sponge Stelletta normani. A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica. Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica. The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.
Keywords
- Bioprospecting, Genome mining, Illumina, Lignocellulolytic enzymes, Physiology, Taxonomy, 1 new taxon
ASJC Scopus subject areas
- Agricultural and Biological Sciences(all)
- Ecology, Evolution, Behavior and Systematics
- Agricultural and Biological Sciences(all)
- Agricultural and Biological Sciences (miscellaneous)
Sustainable Development Goals
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In: IMA FUNGUS, Vol. 12, No. 1, 21, 09.08.2021.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation
AU - Hagestad, Ole Christian
AU - Hou, Lingwei
AU - Andersen, Jeanette H.
AU - Hansen, Espen H.
AU - Altermark, Bjorn
AU - Li, Chun
AU - Kuhnert, Eric
AU - Cox, Russell J.
AU - Crous, Pedro W.
AU - Spatafora, Joseph W.
AU - Lail, Kathleen
AU - Amirebrahimi, Mojgan
AU - Lipzen, Anna
AU - Pangilinan, Jasmyn
AU - Andreopoulos, William
AU - Hayes, Richard D.
AU - Ng, Vivian
AU - Grigoriev, Igor, V
AU - Jackson, Stephen A.
AU - Sutton, Thomas D. S.
AU - Dobson, Alan D. W.
AU - Rama, Teppo
N1 - Funding Information: Digibiotics (Digital Life Norway) and Centre for New Antibacterial Strategies at UiT The Arctic University of Norway, through the Research Council of Norway (Project 269425) provided funding for Teppo Rämä. This research was performed within the Community Sequence Program “1KFG” conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, which was supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-05CH11231. This work benefitted from the sharing of expertise within the DFG priority program “Taxon-Omics: New Approaches for Discovering and Naming Biodiversity” (SPP 1991) to RJC and EK.
PY - 2021/8/9
Y1 - 2021/8/9
N2 - Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales), respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 (Hypocreales, Ascomycota) was isolated from the sponge Stelletta normani. A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica. Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica. The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.
AB - Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales), respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 (Hypocreales, Ascomycota) was isolated from the sponge Stelletta normani. A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica. Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica. The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.
KW - Bioprospecting
KW - Genome mining
KW - Illumina
KW - Lignocellulolytic enzymes
KW - Physiology
KW - Taxonomy
KW - 1 new taxon
UR - http://www.scopus.com/inward/record.url?scp=85112365826&partnerID=8YFLogxK
U2 - 10.1186/s43008-021-00072-0
DO - 10.1186/s43008-021-00072-0
M3 - Article
VL - 12
JO - IMA FUNGUS
JF - IMA FUNGUS
SN - 2210-6340
IS - 1
M1 - 21
ER -