Species boundaries in plant pathogenic fungi : a Colletotrichum case study

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dc.contributor.author Liu, Fang
dc.contributor.author Wang, Mei
dc.contributor.author Damm, Urlike
dc.contributor.author Crous, Pedro W.
dc.contributor.author Cai, Lei
dc.date.accessioned 2016-06-09T07:34:23Z
dc.date.available 2016-06-09T07:34:23Z
dc.date.issued 2016-04-14
dc.description Additional file 1: Figure S1. Phylograms of C. siamense s. lat. resulted from the RAxML analyses based on the seven single loci, five-locus and eight-locus alignments, only bootstrap support value > 50 % are shown. Each isolate was marked with the’clade’ number that corresponds to the ApMat tree (Fig. 1). en_ZA
dc.description Additional file 2: Table S1. Pairwise homoplasy index (PHI) of paired clades in C. siamense s. lat. en_ZA
dc.description Additional file 3: Figure S2. Super-network obtained from the combined analyses of single-gene ML trees (ApMat, CAL, GAPDH, GS, ITS, TUB2). The scale indicates the mean distance obtained from the analysis of single-gene trees. en_ZA
dc.description Additional file 4: Figure S3. Ultrametric gene genealogy and clusters recognized by the single-threshold method of GMYC (Coalescent model). Putative species clusters are indicated using transitions between blackcolored to red-colored branches. The inter- and intraspecific portions of the tree are divided with a vertical line. en_ZA
dc.description Additional file 5: Figure S4. Ultrametric gene genealogy and clusters recognized by the multi-threshold method of GMYC (Coalescent model). Putative species clusters are indicated using transitions between blackcolored to red-colored branches. The inter- and intraspecific portions of the tree are divided with a vertical line. en_ZA
dc.description Additional file 6: Figure S5. Results of the PTP analysis based on the BI and ML topologies. Putative species clusters are indicated using transitions between blue-colored to red-colored branches. en_ZA
dc.description Additional file 7: Figure S6. Development of sexual structures through the interaction of isolates LC2937 × LC2875. a. mature perithecia. b, c. Asci and ascospores. Scale bars: b–c = 10 μm. ( en_ZA
dc.description Additional file 8: Table S2. Sexual compatibility between isolates of C. siamense s. lat. en_ZA
dc.description Additional file 9: Figure S7. Dendrogram resulted from the hierarchical clustering analysis with the Ward’s method showing the distribution of mean spore lengths and widths of isolatesof C. siamense s. lat. en_ZA
dc.description Additional file 10: Figure S8. Discordance between genes trees of ApMat (left) and 5-locus (CAL, GAPDH, GS, ITS, TUB2) (right) constructed with a maximum likelihood analysis by running RAxML v.7.0.3. The RAxML bootstrap support values (ML, >50) and Bayesian posterior probabilities (PP, >0.95) are displayed at the nodes (ML/PP). Ex-type cultures of described species within in C. siamense s. lat. indicated with red color. en_ZA
dc.description Additional file 11: Table S3. Details of isolates included in the phylogenetic analyses and species delimitation. en_ZA
dc.description Additional file 12: Table S4 Primers used in this study, with sequences and sources. en_ZA
dc.description.abstract BACKGROUND : Accurate delimitation of plant pathogenic fungi is critical for the establishment of quarantine regulations, screening for genetic resistance to plant pathogens, and the study of ecosystem function. Concatenation analysis of multi-locus DNA sequence data represents a powerful and commonly used approach to recognizing evolutionary independent lineages in fungi. It is however possible to mask the discordance between individual gene trees, thus the speciation events might be erroneously estimated if one simply recognizes well supported clades as distinct species without implementing a careful examination of species boundary. To investigate this phenomenon, we studied Colletotrichum siamense s. lat., which is a cosmopolitan pathogen causing serious diseases on many economically important plant hosts. Presently there are significant disagreements among mycologists as to what constitutes a species in C. siamense s. lat., with the number of accepted species ranging from one to seven. RESULTS : In this study, multiple approaches were used to test the null hypothesis “C. siamense is a species complex”, using a global strain collection. Results of molecular analyses based on the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and coalescent methods (e.g. Generalized Mixed Yule-coalescent and Poisson Tree Processes) do not support the recognition of any independent evolutionary lineages within C. siamense s. lat. as distinct species, thus rejecting the null hypothesis. This conclusion is reinforced by the recognition of genetic recombination, cross fertility, and the comparison of ecological and morphological characters. Our results indicate that reproductive isolation, geographic and host plant barriers to gene flow are absent in C. siamense s. lat. CONCLUSIONS : This discovery emphasized the importance of a polyphasic approach when describing novel species in morphologically conserved genera of plant pathogenic fungi. en_ZA
dc.description.department Microbiology and Plant Pathology en_ZA
dc.description.librarian am2016 en_ZA
dc.description.sponsorship This work was supported by the National Natural Science Foundation of China (NSFC 31400017 & 31322001). Fang Liu acknowledges the External Cooperation Program of the Chinese Academy of Sciences (GJHZ1310) to support her visit to CBS. Pedro W. Crous acknowledges program NSFC 31070020 to support his visit to IMCAS. en_ZA
dc.description.uri http://www.biomedcentral.com/bmcevolbiol en_ZA
dc.identifier.citation Liu, F, Wang, M, Damm, U, Crous, PW & Cai, L 2016, 'Species boundaries in plant pathogenic fungi : a Colletotrichum case study', BMC Evolutionary Biology, vol. 16, art. no. 649, pp. 1-14. en_ZA
dc.identifier.issn 1471-2148
dc.identifier.other 10.1186/s12862-016-0649-5
dc.identifier.uri http://hdl.handle.net/2263/52919
dc.language.iso en en_ZA
dc.publisher BioMed Central en_ZA
dc.rights © 2016 Liu et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License. en_ZA
dc.subject Coalescent en_ZA
dc.subject Mating test en_ZA
dc.subject Phylogeny en_ZA
dc.subject Species delimitation en_ZA
dc.subject Genealogical concordance phylogenetic species recognition (GCPSR) en_ZA
dc.title Species boundaries in plant pathogenic fungi : a Colletotrichum case study en_ZA
dc.type Article en_ZA


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