- 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. - 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. - 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.. - fungi, species recognition is generally based on three commonly applied concepts i.e., the Biological Species Concept (BSC), the Morphological Species Concept (MSC) and the Phylogenetic Species Concept (PSC) [2, 3]. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - Full list of author information is available at the end of the article. - For example, in the case of the BSC and MSC, species numbers could be underestimated due to the extended time periods for changes in morphology or mating compatibility to become evident [2]. - Ceratocystis is one of numerous genera that reside in the family Ceratocystidaceae, order Microascales, and class Sordariomycetes [7]. - Application of the PSC for Ceratocystis reveals four geographically defined groups. - This is due to intragenomic variation of mul- tiple ITS gene within individual isolates of Ceratocystis [23, 24]. - Intragenomic variation in the ITS region has been as- sociated with hybridization [29, 30]. - A study on Ceratocystis manginecans to elucidate the causes of intragenomic variation in the ITS region dem- onstrated the effects of unequal crossing over, and po- tentially gene conversion, to explain the random homogenization toward a specific ITS type in culture [23]. - The results suggested that the observed polymor- phisms in the ITS region could have originated from a hybridization event.. - The overall objective was to explore the possible role of hybridization and/or introgression that might explain phylogenetic discordance in the group.. - This phylogenomic study made use of the Benchmarking Universal Single-Copy Ortho- logs tool [BUSCO] method [35] as the basis for ortholog selection.. - BUSCO analysis of the 17 Ceratocystidaceae genomes showed high levels of completeness (Table 2) with scores between 97 and 98%. - Functional annotation of the 1082 complete BUSCOs revealed that these genes were predominantly associ- ated with primary cellular functions, including cellular. - Further analysis of incongruence among the 1121 amino acid ML tree set using DensiTree revealed 448 consensus tree topologies present in the tree set (Fig. - Tree topologies showed incongruent branches through- out the dataset, including inconsistencies in the deeper nodes of the tree. - Although not a complete rep- resentation of the number of gene trees supporting each Table 1 General information and assembly statistics of the 17 Ceratocystidaceae isolates used in this study. - a Species code used in this study for identification of each isolate. - Numbers at the end of codes represent different isolates of the same species. - None of the consensus trees resolved C.. - DensiTree analysis of the nucleotide 1121 gene ML tree set showed a reduction in the number of alternative topologies (99) compared to the amino acid dataset (448). - Approximately 73% of the gene trees show incongruence occurring within C. - These topologies were supported by approximately 17% of the ML gene trees. - platani as a part of the incongruent clade, the propor- tions of support for these consensus trees was masked by other topologies.. - To better understand the levels of incongruence seen in the C. - The final dataset included 17 Cerato- cystidaceae isolates used in this study (Table 1). - concatenation and curation of the 1082 BUSCO genes shared among the expanded dataset, we inspected the alignment and removed genes that were not present in all 17 isolates leaving 1069 BUSCO genes. - For this ana- lysis only nucleotide data were considered due to the low signal caused by widespread conservation in the amino acid sequences in the initial analysis including only Ceratocystis species. - The branch lengths in the C. - Incongruence analysis of the nucleotide ML gene tree set of 1069 concatenated BUSCOs shared among the 17 Ceratocystidaceae genomes analysed using DensiTree re- vealed 977 consensus tree topologies (Fig. - There were several incongruent branches deep within the tree space, showing uncertainty in the divergence patterns of Ceratocystis. - The deep branching pattern of the LAC was distinct, but a less uniform pattern was ob- served towards the terminal nodes. - 2 DensiTree analysis of 1121 amino acid and nucleotide ML gene trees of Ceratocystis species. - DensiTree analysis revealed 448 and 99 different topologies in the amino acid (a) and nucleotide (b) maximum likelihood (ML) trees respectively drawn using default tree drawing parameters. - In contrast, the divergence of the C. - Species concepts in the phylogenetics era are however, constantly being challenged. - Results of the. - Similar in- congruence was observed between individual nucleotide and amino acid ML gene trees. - This is particularly relevant for species of Ceratocystis residing in the LAC where the branching pattern is diffi- cult to determine.. - [40] where the age of speciation events in the Cera- tocystidaceae was estimated. - 3 Maximum likelihood species phylogeny of the 17 Ceratocystidaceae isolates used in this study. - The parameters used in the ML include the GTRGAMMA model of evolution and 1000 bootstrap replicates for branch support estimation. - Bootstrap for nodes supporting isolates of the same species were below 100% as expected (not shown). - Insets A and B are zoomed in images of the C. - Both factors mani- fest in the same way when assessing tree topologies.. - The results of the present study show incongruence patterns in the LAC group of Ceratocystis, which may be expected in lineages that have undergone introgression.. - Introgression, or gene flow, is also most common in populations that constantly undergo admixture, or in populations that are in the process of divergence [6]. - Over- all, the results of the present study appear to reflect a situation in Ceratocystis where speciation is occurring and where gene flow will continue until barriers are established through absolute divergence [6].. - Closely related species of Ceratocystis such as those re- lated to C. - In this regard, species of Ceratocystis provide a useful ex- ample to explore species concepts in a fungal lineage that is currently undergoing divergence.. - However, despite the larger body of data, this approach failed to resolve the issue as to whether the isolates of Ceratocystis residing in the LAC. - 4 DensiTree analysis of phylogenetic trees of 1069 concatenated gene sequences including all 17 isolates analysed in this study. - b – DensiTree image of the consensus tree topologies drawn using the star-tree drawing option to illustrate branching patterns of the ML phylogenies. - All researchers in the field agree that C. - Results of the present study show there is greater separation be- tween C. - albifundus there is more obvious recombination than is evident than in the LAC.. - Phylogenomic analyses of representative species in Cera- tocystidaceae revealed widespread incongruence among single gene trees. - The concatenated dataset was able to re- solve some of the incongruence suggesting a phylogenomic approach could be necessary for the phyl- ogeny of these species. - As such, we recommend that fu- ture taxonomic analyses of species in the Ceratocystidaceae should apply a phylogenomic ap- proach incorporating larger populations sampled from different hosts and geographical regions to maximise genetic variability.. - Seventeen isolates representing 10 species across three genera of the Ceratocystidaceae [7], were chosen for this study (Table 1). - Characterization of the shared BUSCO genes across the Ceratocystidaceae was performed using Blast2GO’s de- fault pipeline [57–59] to identify functions possibly linked to patterns observed in the phylogenomic ana- lysis. - Individual ML gene trees were generated for each BUSCO align- ment using RAxML with 100 bootstrap replicates. - Sub- stitution models for the nucleotide ML gene trees (individual gene trees and species tree) used the GTR model as a default parameter. - The gene trees were first transformed in Figtree v1.4.2 (tree.bio.ed.ac.uk/soft- ware/figtree/) to make all branch lengths proportional, ensuring overlap for tree topology comparison in DensiTree. - Pie chart summarizing the biological processes of the shared BUSCO genes in the analysed Ceratocystidaceae.. - (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) Meta- Tree analysis of 1121 nucleotide ML gene trees. - The highlighted cluster shows the consensus trees of the 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.. - 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. - MW, BW, IB and MN were supervisors for the Masters research of CT all contributed to the idea behind the study and revisions of the final manuscript. - CT did the initial data analyses and first draft of the manuscript for his Masters research. - AK did the final analyses that appear in the manuscript as well as the final revisions. - GenBank under accession numbers listed in Table 1 and are available in the National Centre for Biotechnology Information (NCBI) GenBank database (https://www.ncbi.nlm.nih.gov/genbank. - Additional results supporting findings presented in this study are provided in the additional information section.. - Occurrence of the wattle wilt pathogen, Ceratocystis albifundus on native south African trees. - Variation in growth rates and aggressiveness of naturally occuring self-fertile and self-sterile isolates of the wilt pathogen Ceratocystis albifundus. - Phylogeny and taxonomy of the north American clade of the Ceratocystis fimbriata complex. - Intersterility, morphology and taxonomy of Ceratocystis fimbriata on sweet potato, cacao and sycamore. - Host specialization and speciation in the American wilt pathogen. - Reconsidering species boundaries in the Ceratocystis paradoxa complex, including a new species from oil palm and cacao in Cameroon. - Pathogenicity, internal transcribed spacer-rDNA variation, and human dispersal of Ceratocystis fimbriata on the family Araceae. - Species or genotypes? Reassessment of four recently described species of the Ceratocystis wilt pathogen, Ceratocystis fimbriata, on Mangifera indica. - Concerted evolution in the ribosomal RNA cistron. - Apparent recombination or gene conversion in the ribosomal ITS region of a Flammulina (Fungi, Agaricales) hybrid. - Evolution of the 5.8 S nrDNA gene and internal transcribed spacers in Carapichea ipecacuanha (Rubiaceae) within a phylogeographic context. - Intragenomic polymorphism and intergenomic recombination in the ribosomal RNA genes of strains belonging to a yeast species Pichia membranifaciens. - albifundus, an African species in the C. - Discordance of species trees with their most likely gene trees. - Genomic analysis of the aggressive tree pathogen Ceratocystis albifundus. - IMA genome-F 5: draft genome sequences of Ceratocystis eucalypticola, Chrysoporthe cubensis, C.
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