scholarly journals Shifts in diversification rates and host jump frequencies shaped the diversity of host range amongSclerotiniaceaefungal plant pathogens

2017 ◽  
Author(s):  
Olivier Navaud ◽  
Adelin Barbacci ◽  
Andrew Taylor ◽  
John P. Clarkson ◽  
Sylvain Raffaele

AbstractThe range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within theSclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite co-phylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in theSclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events, and the highest proportion of broad host range species. Consistent with previous reports on oomycete parasites, our findings suggest that host jump and radiation, possibly combined with low speciation rates, could associate with the emergence of generalist pathogens. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.

2018 ◽  
Vol 27 (5) ◽  
pp. 1309-1323 ◽  
Author(s):  
Olivier Navaud ◽  
Adelin Barbacci ◽  
Andrew Taylor ◽  
John P. Clarkson ◽  
Sylvain Raffaele

1990 ◽  
Vol 4 (3) ◽  
pp. 471-474 ◽  
Author(s):  
David C. Sands ◽  
Eugene J. Ford ◽  
R. Vincent Miller

Few plant pathogens are both lethal and specific enough to be effective weed control agents. In short, highly specific organisms seldom kill. Two genetic approaches to overcome this problem are to delimit the host range of lethal pathogens or to enhance the efficacy of host-specific ones. Narrowing the virulence or survival of a deadly pathogen seems more plausible than imparting new characters to a nonlethal organism. Our approach has been to genetically restrict the host range or to decrease the survival and/or spread ofSclerotinia sclerotiorum(Lib.) de Bary, a highly virulent and aggressive pathogen of several weeds. Working with this fungus, three classes of induced mutants which meet criteria for delimitation were obtained: auxotrophic mutants that only attack plants when applied concomitantly with an exogenous source of the required nutrient; mutants unable to form sclerotia, structures required for long-term survival and precursors to fruiting bodies; and mutants with reduced virulence and/or host ranges. These studies demonstrate the validity of genetically improving bioherbicides and greatly expanding the number of fungi that may be useful as bioherbicides.


MycoKeys ◽  
2021 ◽  
Vol 85 ◽  
pp. 57-71
Author(s):  
Taichang Mu ◽  
Zhaoxue Zhang ◽  
Rongyu Liu ◽  
Shubin Liu ◽  
Zhuang Li ◽  
...  

Colletotrichum has numerous host range and distribution. Its species are important plant pathogens, endophytes and saprobes. Colletotrichum can cause regular or irregular depressions and necrotic lesions in the epidermal tissues of plants. During this research Colletotrichum specimens were collected from Mengyin County, Shandong Province, China. A multi-locus phylogenetic analysis of ITS, GAPDH, CHS-1, ACT, TUB2, CAL and GS sequence data combined with morphology, revealed a new species and two known species, viz. C. mengyinense sp. nov., C. gloeosporioides and C. pandanicola, belonging to the C. gloeosporioides species complex. The new species is described and illustrated in this paper and compared with taxa in the C. gloeosporioides species complex.


2019 ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G Kamphuis ◽  
Mark Derbyshire

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.


2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
A Bianco ◽  
L Cavicchio ◽  
A Fusaro ◽  
G Rizzo ◽  
A Milani ◽  
...  

Abstract Influenza D virus (IDV) is a new viral genus identified within the Orthomyxoviridae family, showing 50 per cent amino acid identity with human influenza C virus. Similar to human influenza viruses of the C genus, IDV also harbors 7 genomic segments and uses 9-O-acetylated sialic acids as cell receptors. This newly emerged virus exhibits a broad host range and is capable of infecting swine, cattle, sheep, goats, ferrets, and guinea pigs. In Italy, IDV was first detected in archived samples collected between 2014 and 2015 from cattle and swine in the Po Valley area. Here, we report the genetic characterization of IDV viruses detected in an extensive area of northern Italy, namely Veneto, Lombardy, and Piedmont, through passive surveillance between September 2015 and October 2017. A total of 482 samples, including nasal swabs, lungs, and bronchoalveolar lavage fluid, collected from 309 cattle farms were tested. Thirty cattle herds turned out to be positive, for a total of 40 samples positive by Real Time RT-PCR targeting the PB2 gene. Representative IDV positive swabs were sequenced on an Illumina Miseq platform, and phylogenetic analyses were performed for each genome segment. The analyses of the seven gene segments demonstrated that the viruses identified in the north of Italy clearly grouped within a genetic cluster of IDV sequences previously described in Italy and in the USA, thus suggesting a common origin for these viruses. Interestingly, the IDVs identified in Italy presented a low similarity (96.1% to 98.8% for the seven gene segments) to the French IDVs, which is the only other European country where this pathogen has been identified and characterized so far. The wide IDV host range and the ability of this virus to reassort are a matter of concern. Results of this study indicate that IDV is extensively circulating among bovine herds in Northern Italy and suggest a potential role of IDV in the bovine respiratory disease complex, highlighting the need to perform surveillance on an ongoing basis to track its spread and evolution.


eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Thomas Badet ◽  
Remi Peyraud ◽  
Malick Mbengue ◽  
Olivier Navaud ◽  
Mark Derbyshire ◽  
...  

The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom. At the species level, biased patterns of synonymous substitutions underpin increased codon optimization in a generalist but not a specialist fungal pathogen. Virulence genes were consistently enriched in highly codon-optimized genes of generalist but not specialist species. We conclude that codon optimization is related to the capacity of parasites to colonize multiple hosts. Our results link genome evolution and translational regulation to the long-term persistence of generalist parasitism.


Plant Disease ◽  
2021 ◽  
Author(s):  
Reid Frederick ◽  
Craig Cavin ◽  
Jami L Thomas ◽  
William L. Bruckart ◽  
Matthew A. Tancos

Japanese hop (Humulus scandens) is a non-native, invasive plant that colonizes disturbed riparian areas throughout the eastern United States and Canada, forming dense, monocultural stands that displace native plant communities due to a high reproductive rate, rapid growth, climbing bines, and dense shading (Balogh and Dancza 2008). It is capable of serving as a reservoir for agronomically important plant pathogens, such as the Tomato spotted wilt virus and powdery mildew species that infect commercial hemp and hop fields (Yoon et al. 2018; Weldon et al. 2020). In the spring of 2016, diseased populations of H. scandens were observed along the Monocacy River in Frederick County, Maryland with severe chlorotic and necrotic leaf lesions. Symptomatic leaves were surface sterilized and placed in moist chambers at 25°C for sporulation. Sporulating acervuli, lacking setae, developed on irregular, tan necrotic leaf lesions following 7 to 12 days in a moist chamber (Figure 1). Conidia were hyaline, aseptate, smooth-walled, fusiform to cylindrical with both ends acute (Figure 1B). Conidia measured (n = 100) [L x W; Average (+ Std. Err), range]: 12.42 µm (± 0.10), 8.41 – 14.48 µm; x 3.91 µm (±0.03), 3.03 – 4.91 µm. Monoconidial fungal cultures were obtained by transferring conidia with a sterile glass needle to acidified potato dextrose agar and incubated at 25°C for 2 to 3 days. Based on phenotypic characteristics and conidial morphology and size, the pathogen appeared to belong to the Colletotrichum acutatum complex (Damm et al. 2012). Therefore, six loci (ITS, GADPH, CHS1, HIS3, ACT, and TUB2) were amplified and sequenced from a representative isolate, 16-008, for species characterization (GenBank accessions MW023070 to MW023075) (Damm et al. 2012). For the ITS region and ACT, GADPH, and CHS1 loci, isolate 16-008 was 100% identical to C. fioriniae and shared 99% similarity to TUB2 and HIS3 for multiple accessions of C. fioriniae in GenBank. Gene sequences were aligned, trimmed, concatenated, and analyzed against 32 reference strains, within the C. acutatum complex (Damm et al. 2012). Concatenated loci were used to generate a maximum likelihood phylogeny using W-IQ-TREE (Trifinopoulos et al. 2016). Results from the phylogenetic analysis demonstrated that isolate 16-008 was most genetically similar to C. fioriniae with a bootstrap support of 100% (Figure 2). Based on phenotypic and sequence analyses, isolate 16-008 was identified as C. fioriniae. Humulus scandens seedlings from Maryland (n = 3) were inoculated with a conidia suspension (107 conidia mL-1) with 0.125% Tween 20® and applied with an atomizer until runoff. Inoculated plants were placed in a dew chamber at 25°C for 2 days. Experimental plants were distributed in a mist tent at 25°C with 14 h of light and monitored for 2 weeks. Negative control plants (n = 2) were sprayed with a sterile 0.125% Tween 20® water solution. All inoculated plants were symptomatic by 12 days post inoculation. No symptoms were observed on the mock-inoculated plants. Symptoms were identical to disease field samples. Inoculations were repeated with the same results. Colletotrichum fioriniae was reisolated and confirmed from excised leaf lesions via ITS and ACT sequencing. To our knowledge, this is the first report of C. fioriniae naturally infecting H. scandens within the United States (Farr and Rossman 2020). Future studies will evaluate the host range of this isolate due to the species broad host range and the weed’s extensive distribution.


BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G. Kamphuis ◽  
Mark C. Derbyshire

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes. Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes. Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.


2011 ◽  
Vol 77 (22) ◽  
pp. 7975-7983 ◽  
Author(s):  
Diya Sen ◽  
Geraldine A. Van der Auwera ◽  
Linda M. Rogers ◽  
Christopher M. Thomas ◽  
Celeste J. Brown ◽  
...  

ABSTRACTBroad-host-range plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to antibiotics and heavy metals or degradation of pollutants. Although some broad-host-range plasmids have been extensively studied, their evolutionary history and genetic diversity remain largely unknown. The goal of this study was to analyze and compare the genomes of 12 broad-host-range plasmids that were previously isolated from Norwegian soils by exogenous plasmid isolation and that encode mercury resistance. Complete nucleotide sequencing followed by phylogenetic analyses based on the relaxase genetraIshowed that all the plasmids belong to one of two subgroups (β and ε) of the well-studied incompatibility group IncP-1. A diverse array of accessory genes was found to be involved in resistance to antimicrobials (streptomycin, spectinomycin, and sulfonamides), degradation of herbicides (2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenoxypropionic acid), and a putative new catabolic pathway. Intramolecular transposition of insertion sequences followed by deletion was found to contribute to the diversity of some of these plasmids. The previous observation that the insertion sites of a Tn501-related element are identical in four IncP-1β plasmids (pJP4, pB10, R906, and R772) was further extended to three more IncP-1β plasmids (pAKD15, pAKD18, and pAKD29). We proposed a hypothesis for the evolution of these Tn501-bearing IncP-1β plasmids that predicts recent diversification followed by worldwide spread. Our study increases the available collection of complete IncP-1 plasmid genome sequences by 50% and will aid future studies to enhance our understanding of the evolution and function of this important plasmid family.


2019 ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G Kamphuis ◽  
Mark Derbyshire

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes. Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence absence polymorphisms and exhibited a significantly higher sequence diversity than other genes. Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.


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