Understanding the factors that drive the evolution of pathogenic fungi is central to revealing the mechanisms of virulence and host preference, as well as developing effective disease control ...measures. Prerequisite to these pursuits is the accurate delimitation of species boundaries. Colletotrichum gloeosporioides s.l. is a species complex of plant pathogens and endophytic fungi for which reliable species recognition has only recently become possible through a multi-locus phylogenetic approach. By adopting an intensive regional sampling strategy encompassing multiple hosts within and beyond agricultural zones associated with cranberry (Vaccinium macrocarpon Aiton), we have integrated North America strains of Colletotrichum gloeosporioides s.l. from these habitats into a broader phylogenetic framework. We delimit species on the basis of genealogical concordance phylogenetic species recognition (GCPSR) and quantitatively assess the monophyly of delimited species at each of four nuclear loci and in the combined data set with the genealogical sorting index (gsi). Our analysis resolved two principal lineages within the species complex. Strains isolated from cranberry and sympatric host plants are distributed across both of these lineages and belong to seven distinct species or terminal clades. Strains isolated from V. macrocarpon in commercial cranberry beds belong to four species, three of which are described here as new. Another species, C. rhexiae Ellis & Everh., is epitypified. Intensive regional sampling has revealed a combination of factors, including the host species from which a strain has been isolated, the host organ of origin, and the habitat of the host species, as useful indicators of species identity in the sampled regions. We have identified three broadly distributed temperate species, C. fructivorum , C. rhexiae , and C. nupharicola , that could be useful for understanding the microevolutionary forces that may lead to species divergence in this important complex of endophytes and plant pathogens.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Rethinking host range in Pneumocystis Babb-Biernacki, Spenser J; Esselstyn, Jacob A; Doyle, Vinson P
PLoS pathogens,
09/2020, Letnik:
16, Številka:
9
Journal Article
Recenzirano
Odprti dostop
About the Authors: Spenser J. Babb-Biernacki * E-mail: sbiern1@lsu.edu Affiliation: Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, ...Louisiana, United States of America ORCID logo http://orcid.org/0000-0002-1915-1541 Jacob A. Esselstyn Affiliation: Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America Vinson P. Doyle Affiliation: Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, Louisiana, United States of America Introduction Fungi in the genus Pneumocystis are obligate biotrophs and opportunistic pathogens of mammal lungs. Genealogical concordance phylogenetic species recognition (GCPSR), which interprets transitions between concordance and discordance of multiple gene trees as species boundaries 3, is a widely applied, well-supported method to recognize fungal species. Genetic distances (expressed as percentages) of mtLSU and mtSSU between Pneumocystis from closely related hosts. https://doi.org/10.1371/journal.ppat.1008824.t001 Expected divergence at Pneumocystis barcodes As previously mentioned, the difficulty of sequencing nuclear loci from Pneumocystis in wild animals has prevented robust study of species boundaries. ...we must critically examine how mtLSU and mtSSU variation has been used to understand species boundaries in Pneumocystis.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Aerial blight, caused by the fungus
anastomosis group (AG) 1-IA, is an economically important soybean disease in the mid-Southern United States. Management has relied on fungicide applications during ...the season, but there is an increasing prevalence of resistance to commonly used strobilurin fungicides and an urgent need to identify soybean varieties resistant to aerial blight. Because the patchy distribution of the pathogen complicates field variety screening, the present study aimed to develop a greenhouse screening protocol to identify soybean varieties resistant to aerial blight. For this, 88 pathogen isolates were collected from commercial fields and research farms across five Louisiana parishes, and 77% were confirmed to be
AG1-IA. Three polymorphic codominant microsatellite markers were used to explore the genetic diversity of 43
AG1-IA isolates, which showed high genetic diversity, with 35 haplotypes in total and only two haplotypes common to two other locations. Six genetically diverse isolates were chosen and characterized for their virulence and fungicide sensitivity. The isolate AC2 was identified as the most virulent and was resistant to both active ingredients, azoxystrobin and pyraclostrobin, tested. The six isolates were used in greenhouse variety screening trials using a millet inoculation protocol. Of the 31 varieties screened, only Armor 48-D25 was classified as moderately resistant, and plant height to the first node influenced final disease severity. The study provides short-term solutions for growers to choose less susceptible varieties for planting and lays the foundation to characterize host resistance against this important soybean pathogen.
Plant pathogenic fungi produce toxins as virulence factors in many plant diseases. In Cercospora leaf blight (CLB) of soybean caused by
cf.
, symptoms are a consequence of the production of a ...perylenequinone toxin, cercosporin, which is light-activated to produce damaging reactive oxygen species (ROS). Cercosporin is universally toxic to cells, except to the cells of the producer. The current model of self-resistance to cercosporin is largely attributed to the maintenance of cercosporin in a chemically-reduced state inside hyphae, unassociated with cellular organelles. However, in another perylenequinone-producing fungus,
sp., the toxin was specifically sequestered inside lipid droplets (LDs) to prevent ROS production. This study hypothesized that LD-based sequestration of cercosporin occurred in
. cf.
and that lipid-inhibiting fungicides could inhibit toxin production. Confocal microscopy using light-cultured
. cf.
indicated that 3-day old hyphae contained two forms of cercosporin distributed in two types of hyphae. Reduced cercosporin was uniformly distributed in the cytoplasm of thick, primary hyphae, and contrary to previous studies, active cercosporin was observed specifically in LDs of thin, secondary hyphae. The production of hyphae of two different thicknesses, a characteristic of hemibiotrophic plant pathogens, has not been documented in
. cf.
. No correlation was observed between cercosporin production and total lipid extracted, and two lipid-inhibiting fungicides had little effect on fungal growth in growth-inhibition assays. The study lays a foundation to explore the importance of pathogen lifestyle, toxin production, and LD content in pathogenicity and symptomology of Cercospora.
Cercospora janseana causes narrow brown leaf spot of rice. A nearly complete telomere-to-telomere reference genome was assembled with a combination of Oxford Nanopore and Illumina sequences. The ...genome assembly has a total length of 39,075,509 bp and consists of 15 chromosomes, 14 of which have telomeric repeats at both ends. The assembly N50 is 2.97 Mb and the L50 is 5 contigs. RNAseq-mediated gene annotation identified 10,850 genes, including 955 predicted secreted proteins and 361 predicted effector proteins. This highly contiguous and almost complete C. janseana reference genome will be a vital resource for further investigation of host-pathogen interactions and genome evolution within this pathosystem.
Resolving deep divergences in the tree of life is challenging even for analyses of genome-scale phylogenetic data sets. Relationships between Basidiomycota subphyla, the rusts and allies ...(Pucciniomycotina), smuts and allies (Ustilaginomycotina), and mushroom-forming fungi and allies (Agaricomycotina) were found particularly recalcitrant both to traditional multigene and genome-scale phylogenetics. Here, we address basal Basidiomycota relationships using concatenated and gene tree-based analyses of various phylogenomic data sets to examine the contribution of several potential sources of bias. We evaluate the contribution of biological causes (hard polytomy, incomplete lineage sorting) versus unmodeled evolutionary processes and factors that exacerbate their effects (e.g., fast-evolving sites and long-branch taxa) to inferences of basal Basidiomycota relationships. Bayesian Markov Chain Monte Carlo and likelihood mapping analyses reject the hard polytomy with confidence. In concatenated analyses, fast-evolving sites and oversimplified models of amino acid substitution favored the grouping of smuts with mushroom-forming fungi, often leading to maximal bootstrap support in both concatenation and coalescent analyses. On the contrary, the most conserved data subsets grouped rusts and allies with mushroom-forming fungi, although this relationship proved labile, sensitive to model choice, to different data subsets and to missing data. Excluding putative long-branch taxa, genes with high proportions of missing data and/or with strong signal failed to reveal a consistent trend toward one or the other topology, suggesting that additional sources of conflict are at play. While concatenated analyses yielded strong but conflicting support, individual gene trees mostly provided poor support for any resolution of rusts, smuts, and mushroom-forming fungi, suggesting that the true Basidiomycota tree might be in a part of tree space that is difficult to access using both concatenation and gene tree-based approaches. Inference-based assessments of absolute model fit strongly reject best-fit models for the vast majority of genes, indicating a poor fit of even the most commonly used models. While this is consistent with previous assessments of site-homogenous models of amino acid evolution, this does not appear to be the sole source of confounding signal. Our analyses suggest that topologies uniting smuts with mushroom-forming fungi can arise as a result of inappropriate modeling of amino acid sites that might be prone to systematic bias. We speculate that improved models of sequence evolution could shed more light on basal splits in the Basidiomycota, which, for now, remain unresolved despite the use of whole genome data.
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BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Apple bitter rot caused by Colletotrichum species is a growing problem worldwide. Colletotrichum spp. are economically important but taxonomically un-resolved. Identification of Colletotrichum spp. ...is critical due to potential species-level differences in pathogenicity-related characteristics. A 400-isolate collection from New York apple orchards were morphologically assorted to two groups, C. acutatum species complex (CASC) and C. gloeosporioides species complex (CGSC). A sub-sample of 44 representative isolates, spanning the geographical distribution and apple varieties, were assigned to species based on multi-locus phylogenetic analyses of nrITS, GAPDH and TUB2 for CASC, and ITS, GAPDH, CAL, ACT, TUB2, APN2, ApMat and GS genes for CGSC. The dominant species was C. fioriniae, followed by C. chrysophilum and a novel species, C. noveboracense, described in this study. This study represents the first report of C. chrysophilum and C. noveboracense as pathogens of apple. We assessed the enzyme activity and fungicide sensitivity for isolates identified in New York. All isolates showed amylolytic, cellulolytic and lipolytic, but not proteolytic activity. C. chrysophilum showed the highest cellulase and the lowest lipase activity, while C. noveboracense had the highest amylase activity. Fungicide assays showed that C. fioriniae was sensitive to benzovindiflupyr and thiabendazole, while C. chrysophilum and C. noveboracense were sensitive to fludioxonil, pyraclostrobin and difenoconazole. All species were pathogenic on apple fruit with varying lesion sizes. Our findings of differing pathogenicity-related characteristics among the three species demonstrate the importance of accurate species identification for any downstream investigations of Colletotrichum spp. in major apple growing regions.
Topological heterogeneity among gene trees is widely observed in phylogenomic analyses and some of this variation is likely caused by systematic error in gene tree estimation. Systematic error can be ...mitigated by improving models of sequence evolution to account for all evolutionary processes relevant to each gene or identifying those genes whose evolution best conforms to existing models. However, the best method for identifying such genes is not well established. Here, we ask if filtering genes according to their clock-likeness or posterior predictive effect size (PPES, an inference-based measure of model violation) improves phylogenetic reliability and congruence. We compared these approaches to each other, and to the common practice of filtering based on rate of evolution, using two different metrics. First, we compared gene-tree topologies to accepted reference topologies. Second, we examined topological similarity among gene trees in filtered sets. Our results suggest that filtering genes based on clock-likeness and PPES can yield a collection of genes with more reliable phylogenetic signal. For the two exemplar data sets we explored, from yeast and amniotes, clock-likeness and PPES outperformed rate-based filtering in both congruence and reliability.
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BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Cercospora leaf blight (CLB) of soybean was believed to be caused only by
Cercospora kikuchii
worldwide. However, recent studies that include molecular phylogenetic analyses reveal that several ...cryptic species within
Cercospora
are associated with the disease. In a previous study, following a survey of commercial soybean fields in Santa Cruz, Bolivia,
Cercospora
spp. strains were isolated and identified as
Cercospora
cf.
nicotianae
based on morphological characteristics and by sequencing parts of the calmodulin, histone H3, and translation elongation factor 1-α genes and placing into a multilocus phylogeny. In the present study, pathogenicity tests were carried out in greenhouse assays on eleven soybean varieties which confirmed the infection and reproduction of the symptoms originally observed in the field. All the inoculated varieties were infected and showed CLB symptoms. Isolates were recovered from all soybean varieties tested and monoconidial cultures resembled original inoculum, completing Koch’s postulates. Thus, we confirm that according to the morphology of the conidia and cultures, pathogenicity tests, and molecular identification,
C.
cf.
nicotianae
is a causal agent of CLB of soybean.
Anthracnose is one of the most important plant diseases globally, occurring on a wide range of cultivated and wild host species. This study aimed to identify the Colletotrichum species associated ...with cashew anthracnose in Brazil, determine their phylogenetic relationships and geographical distribution, and provide some insight into the factors that may be influencing community composition. Colletotrichum isolates collected from symptomatic leaves, stems, inflorescences, and fruit of cultivated and wild cashew, across four Brazilian biomes, were identified as Colletotrichum chrysophilum, Colletotrichum fragariae, Colletotrichum fructicola, Colletotrichum gloeosporioides sensu stricto, Colletotrichum queenslandicum, Colletotrichum siamense and Colletotrichum tropicale. Colletotrichum siamense was the most dominant species. The greatest species richness was associated with cultivated cashew; leaves harbored more species than the other organs; the Atlantic Forest encompassed more species than the other biomes; and Pernambuco was the most species-rich location. However, accounting for the relative abundance of Colletotrichum species and differences in sample size across strata, the interpretation of which community is most diverse depends on how species are delimited. The present study provides valuable information about the Colletotrichum/cashew pathosystem, sheds light on the causal agents identification,and highlights the impact that species delimitation can have on ecological studies of fungi.
Display omitted
•Several Colletotrichum species are associated with cashew anthracnose in Brazil.•Interpretation of Colletotrichum community diversity depends on how species are delimited.•Colletotrichum gloeosporioides was rare, while Colletotrichum siamense was the dominant species.•The cultivated cashew and leaves were the most diverse host-associated strata.•The Atlantic Forest and Pernambuco were the most diverse geographical strata.
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