Species boundaries in plant pathogenic fungi : a Colletotrichum case study
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Date
Authors
Liu, Fang
Wang, Mei
Damm, Urlike
Crous, Pedro W.
Cai, Lei
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
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.
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).
Additional file 2: Table S1. Pairwise homoplasy index (PHI) of paired clades in C. siamense s. lat.
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.
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.
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.
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.
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. (
Additional file 8: Table S2. Sexual compatibility between isolates of C. siamense s. lat.
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.
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.
Additional file 11: Table S3. Details of isolates included in the phylogenetic analyses and species delimitation.
Additional file 12: Table S4 Primers used in this study, with sequences and sources.
Additional file 2: Table S1. Pairwise homoplasy index (PHI) of paired clades in C. siamense s. lat.
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.
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.
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.
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.
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. (
Additional file 8: Table S2. Sexual compatibility between isolates of C. siamense s. lat.
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.
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.
Additional file 11: Table S3. Details of isolates included in the phylogenetic analyses and species delimitation.
Additional file 12: Table S4 Primers used in this study, with sequences and sources.
Keywords
Coalescent, Mating test, Phylogeny, Species delimitation, Genealogical concordance phylogenetic species recognition (GCPSR)
Sustainable Development Goals
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.