Genomic overview of closely related fungi with different Protea host ranges

dc.contributor.authorAylward, Janneke
dc.contributor.authorWingfield, Brenda D.
dc.contributor.authorDreyer, Leanne Laurette
dc.contributor.authorRoets, Francois
dc.contributor.authorWingfield, Michael J.
dc.contributor.authorSteenkamp, Emma Theodora
dc.date.accessioned2018-11-28T05:15:27Z
dc.date.issued2018-12
dc.descriptionSupplementary File 1: Summary of repeat-induced-point mutation (RIP) per scaffold.en_ZA
dc.descriptionSupplementary File 2: Examples of the sequence depth and number of mismatches across repetitive regions in Knoxdaviesia capensis and K. proteae.en_ZA
dc.descriptionSupplementary File 3: Overview of the classification of Knoxdaviesia genome-wide speciesspecific proteins in Functional Catalogue categories.en_ZA
dc.descriptionSupplementary File 4: Classification and annotation of the genome-wide species-specific proteins of Knoxdaviesia capensis and K. proteae.en_ZA
dc.descriptionSupplementary File 5: Knoxdaviesia species-specific proteins putatively involved in secondary metabolism.en_ZA
dc.descriptionSupplementary File 6: Summary of proteins excluded from and included in the final secretome dataset.en_ZA
dc.descriptionSupplementary File 7: Overview of the classification of Knoxdaviesia secreted proteins in Functional Catalogue categories.en_ZA
dc.descriptionSupplementary File 8: Classification and annotation of the putative secreted proteins of Knoxdaviesia capensis and K. proteae.en_ZA
dc.descriptionSupplementary File 9: Classification and annotation of the small secreted cysteine-rich proteins (SSCPs) identified in the two Knoxdaviesia genomes.en_ZA
dc.descriptionSupplementary Table S1: Occurrence of the TTAGGGTTAC / GTAACCCTAA Knoxdaviesia telomere repeat in K. capensis and K. proteae. Supplementary Table S2: Populous orthogroups in the Knoxdaviesia genomes. Supplementary Table S3: Outcome of the protein BLAST for the Knoxdaviesia capensis and K. proteae species-specific proteins. Supplementary Table S4: Cysteine-rich secreted proteins and proteins with hits to the Pathogen Host Interaction (PHI) database in Knoxdaviesia capensis and K. proteae. Supplementary Table S5: Amplification of the T1PKS-4 cluster deletion in Knoxdaviesia capensis and K. proteae.en_ZA
dc.descriptionSupplementary Data: The predicted proteins of Knoxdaviesia capensis and K. proteae in FASTA format and the gff3 annotation files of the transposable elements identified by the REPET package have been made available on Mendeley Data (https://data.mendeley.com/), DOI:10.17632/rbx32w7crp.1en_ZA
dc.description.abstractGenome comparisons of species with distinctive ecological traits can elucidate genetic divergence that influenced their differentiation. The interaction of a microorganism with its biotic environment is largely regulated by secreted compounds, and these can be predicted from genome sequences. In this study, we considered Knoxdaviesia capensis and Knoxdaviesia proteae, two closely related saprotrophic fungi found exclusively in Protea plants. We investigated their genome structure to compare their potential inter-specific interactions based on gene content. Their genomes displayed macrosynteny and were approximately 10 % repetitive. Both species had fewer secreted proteins than pathogens and other saprotrophs, reflecting their specialized habitat. The bulk of the predicted species-specific and secreted proteins coded for carbohydrate metabolism, with a slightly higher number of unique carbohydrate-degrading proteins in the broad host-range K. capensis. These fungi have few secondary metabolite gene clusters, suggesting minimal competition with other microbes and symbiosis with antibiotic-producing bacteria common in this niche. Secreted proteins associated with detoxification and iron sequestration likely enable these Knoxdaviesia species to tolerate antifungal compounds and compete for resources, facilitating their unusual dominance. This study confirms the genetic cohesion between Protea-associated Knoxdaviesia species and reveals aspects of their ecology that have likely evolved in response to their specialist niche.en_ZA
dc.description.departmentBiochemistryen_ZA
dc.description.departmentForestry and Agricultural Biotechnology Institute (FABI)en_ZA
dc.description.departmentGeneticsen_ZA
dc.description.departmentMicrobiology and Plant Pathologyen_ZA
dc.description.embargo2019-12-01
dc.description.librarianhj2018en_ZA
dc.description.sponsorshipThe National Research Foundation (NRF) and the Department of Science and Technology (DST) - NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and the SARChI chair in Fungal Genomics.en_ZA
dc.description.urihttp://www.elsevier.com/locate/funbioen_ZA
dc.identifier.citationAylward, J., Wingfield, B.D., Dreyer, L.L. et al. 2018, 'Genomic overview of closely related fungi with different Protea host ranges', Fungal Biology, vol. 122, no. 12, pp. 1201-1214.en_ZA
dc.identifier.issn1878-6146 (print)
dc.identifier.issn1878-6162 (online)
dc.identifier.other10.1016/j.funbio.2018.10.001
dc.identifier.urihttp://hdl.handle.net/2263/67339
dc.language.isoenen_ZA
dc.publisherElsevieren_ZA
dc.rights© 2018 British Mycological Society. Published by Elsevier Ltd. All rights reserved. Notice : this is the author’s version of a work that was accepted for publication in Fungal Biology. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. A definitive version was subsequently published in Fungal Biology, vol. 122, no. 12, pp. 1201-1214, 2018. doi : 10.1016/j.funbio.2018.10.001.en_ZA
dc.subjectCompetitionen_ZA
dc.subjectGenomesen_ZA
dc.subjectInteractionsen_ZA
dc.subjectKnoxdaviesiaen_ZA
dc.subjectSecretomeen_ZA
dc.titleGenomic overview of closely related fungi with different Protea host rangesen_ZA
dc.typePostprint Articleen_ZA

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