Hill, R. orcid.org/0000-0002-1046-5528, Levicky, Q., Pitsillides, F. et al. (9 more authors) (2023) Tapping culture collections for fungal endophytes: first genome assemblies for three genera and five species in the Ascomycota. Genome Biology and Evolution, 15 (3). evad038. ISSN 1759-6653
Abstract
The Ascomycota form the largest phylum in the fungal kingdom and show a wide diversity of lifestyles, some involving associations with plants. Genomic data are available for many ascomycetes that are pathogenic to plants, but endophytes, which are asymptomatic inhabitants of plants, are relatively understudied. Here, using short- and long-read technologies, we have sequenced and assembled genomes for 15 endophytic ascomycete strains from CABI’s culture collections. We used phylogenetic analysis to refine the classification of taxa, which revealed that 7 of our 15 genome assemblies are the first for the genus and/or species. We also demonstrated that cytometric genome size estimates can act as a valuable metric for assessing assembly “completeness”, which can easily be overestimated when using BUSCOs alone and has broader implications for genome assembly initiatives. In producing these new genome resources, we emphasise the value of mining existing culture collections to produce data that can help to address major research questions relating to plant–fungal interactions.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Editors: |
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Copyright, Publisher and Additional Information: | © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
Keywords: | Ascomycota; culture collections; cytometric completeness; fungal endophytes |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 24 Apr 2023 13:22 |
Last Modified: | 24 Apr 2023 13:22 |
Published Version: | http://dx.doi.org/10.1093/gbe/evad038 |
Status: | Published |
Publisher: | Oxford University Press (OUP) |
Refereed: | Yes |
Identification Number: | 10.1093/gbe/evad038 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:198379 |