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dc.contributor.author | Kanzi, Aquillah M.![]() |
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dc.contributor.author | Trollip, Conrad![]() |
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dc.contributor.author | Wingfield, Michael J.![]() |
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dc.contributor.author | Barnes, Irene![]() |
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dc.contributor.author | Van der Nest, Magrieta Aletta![]() |
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dc.contributor.author | Wingfield, Brenda D.![]() |
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dc.date.accessioned | 2020-10-22T06:48:50Z | |
dc.date.available | 2020-10-22T06:48:50Z | |
dc.date.issued | 2020-05 | |
dc.description | Additional file 1: Figure S1. Pie chart summarizing the biological processes of the shared BUSCO genes in the analysed Ceratocystidaceae. The numbers in brackets represent the number of GO (Gene Ontology) annotations. | en_ZA |
dc.description | Additional file 2: Figure S2. (A) MetaTree analysis of 1121 amino acid ML gene trees. The amino acid ML gene trees clustered showing major star-like radiation indicating a lack of phylogenetic resolution. (B) MetaTree analysis of 1121 nucleotide ML gene trees. The highlighted cluster shows the consensus trees of the C. fimbriata, C. manginecans and C. eucalypticola clade representing approximately 72% of all ML gene trees. The remaining clusters are supported by small numbers of the remaining ML gene trees. | en_ZA |
dc.description | Additional file 3: Figure S3. The three main consensus topologies of the DensiTree analysis of the 1069 nucleotide ML gene trees including all 17 Ceratocystidaceae genomes analysed. Topology 1 representing 17% of all gene trees is coloured in blue, topology 2 representing 16.5% of all ML gene trees is coloured in red, and topology 3 representing 16% of all ML gene trees is coloured in green. See Table 1 in main article for full species names. | en_ZA |
dc.description | Additional file 4: Figure S4. A Bayesian species tree for the Ceratocystidaceae species analysed. The GTR model with gamma distribution and one million generations in two runs were used. A burnin of 25% was applied when summarising the trees. All other parameters were set to default. The average standard deviation of tree splits was zero and the species tree nodes were absolutely supported with posterior probabilities of 1. | en_ZA |
dc.description.abstract | BACKGROUND: The taxonomic history of Ceratocystis, a genus in the Ceratocystidaceae, has been beset with questions and debate. This is due to many of the commonly used species recognition concepts (e.g., morphological and biological species concepts) providing different bases for interpretation of taxonomic boundaries. Species delineation in Ceratocystis primarily relied on genealogical concordance phylogenetic species recognition (GCPSR) using multiple standard molecular markers. RESULTS: Questions have arisen regarding the utility of these markers e.g., ITS, BT and TEF1-α due to evidence of intragenomic variation in the ITS, as well as genealogical incongruence, especially for isolates residing in a group referred to as the Latin-American clade (LAC) of the species. This study applied a phylogenomics approach to investigate the extent of phylogenetic incongruence in Ceratocystis. Phylogenomic analyses of a total of 1121 shared BUSCO genes revealed widespread incongruence within Ceratocystis, particularly within the LAC, which was typified by three equally represented topologies. Comparative analyses of the individual gene trees revealed evolutionary patterns indicative of hybridization. The maximum likelihood phylogenetic tree generated from the concatenated dataset comprised of 1069 shared BUSCO genes provided improved phylogenetic resolution suggesting the need for multiple gene markers in the phylogeny of Ceratocystis. CONCLUSION: The incongruence observed among single gene phylogenies in this study call into question the utility of single or a few molecular markers for species delineation. Although this study provides evidence of interspecific hybridization, the role of hybridization as the source of discordance will require further research because the results could also be explained by high levels of shared ancestral polymorphism in this recently diverged lineage. This study also highlights the utility of BUSCO genes as a set of multiple orthologous genes for phylogenomic studies | en_ZA |
dc.description.department | Biochemistry | en_ZA |
dc.description.department | Forestry and Agricultural Biotechnology Institute (FABI) | en_ZA |
dc.description.department | Genetics | en_ZA |
dc.description.department | Microbiology and Plant Pathology | en_ZA |
dc.description.librarian | pm2020 | en_ZA |
dc.description.sponsorship | The South African National Research Foundation (NRF); The University of Pretoria, Genomics Research Institute (GRI) and South African DST-NRF SARChI Chair in Fungal Genomics. | en_ZA |
dc.description.uri | http://www.biomedcentral.com/bmcgenomics | en_ZA |
dc.identifier.citation | Kanzi, A.M., Trollip, C., Wingfield, M.J. et al. 2020, 'Phylogenomic incongruence in Ceratocystis: a clue to speciation?', BMC Genomics, vol. 21, no. 1, art. 362, pp. 1-11. | en_ZA |
dc.identifier.issn | 1471-2164 (online) | |
dc.identifier.other | 10.1186/s12864-020-6772-0 | |
dc.identifier.uri | http://hdl.handle.net/2263/76566 | |
dc.language.iso | en | en_ZA |
dc.publisher | BioMed Central | en_ZA |
dc.rights | © The Author(s). 2020 Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License. | en_ZA |
dc.subject | Ceratocystis | en_ZA |
dc.subject | Incongruence | en_ZA |
dc.subject | Hybridisation | en_ZA |
dc.subject | Phylogenomics | en_ZA |
dc.subject | Genealogical concordance phylogenetic species recognition (GCPSR) | en_ZA |
dc.title | Phylogenomic incongruence in Ceratocystis : a clue to speciation? | en_ZA |
dc.type | Article | en_ZA |