scholarly journals Biases in the metabarcoding of plant pathogens using rust fungi as a model system

2018 ◽  
Vol 8 (7) ◽  
Author(s):  
Andreas Makiola ◽  
Ian A. Dickie ◽  
Robert J. Holdaway ◽  
Jamie R. Wood ◽  
Kate H. Orwin ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Model System ◽  
Rust Fungi

scholarly journals Higher Variability in Fungi Compared to Bacteria in the Foraging Honey Bee Gut

2020 ◽  
Author(s):  
Leslie E. Decker ◽  
Priscilla A. San Juan ◽  
Magdalena L. Warren ◽  
Cory E. Duckworth ◽  
Cheng Gao ◽  
...  
Keyword(s):  
Species Composition ◽  
Microbial Communities ◽  
Honey Bee ◽  
Honey Bees ◽  
Plant Pathogens ◽  
Distribution Patterns ◽  
Model System ◽  
Pathogen Transmission ◽  
Host Health ◽  
Gut Symbionts

AbstractMicrobial communities in the honey bee gut have emerged as a model system to understand the effects of host-associated microbes on animals and plants. The specific distribution patterns of bacterial associates among honey bee gut regions remains a key finding within the field. The mid- and hindgut of foraging bees house a deterministic set of core species that affect host health. In contrast, the crop, or honey stomach, contains a more diverse set of bacteria that is highly variable in composition among individual bees. Whether this contrast between the two gut regions also applies to fungi, another major group of gut-associated microbes, remains unclear despite their potential influence on host health. In honey bees caught foraging at four sites across the San Francisco Peninsula, we found that fungi were much less distinct in species composition between the crop and the mid- and hindgut than bacteria. Unlike bacteria, fungi were highly variable in composition throughout the gut, and much of this variation was attributable to bee collection site. These patterns suggest that the fungi may be passengers rather than functionally significant gut symbionts. However, many of the fungi we found in the bees have been recognized as plant pathogens. Assuming that some fungi remain viable after passage through the gut, the distribution patterns we report here point to the potential importance of honey bees as vectors of fungal pathogens and suggest a more prominent role of honey bees in plant pathogen transmission than generally thought.Importance (Nontechnical explanation of why the work was undertaken)Along with bacteria, fungi make up a significant portion of animal- and plant-associated microbial communities. However, we have only begun to describe these fungi, much less examine their effects on most animals and plants. The honey bee, Apis mellifera, has emerged as a model system for studying host-associated microbes. Honey bees contain well-characterized bacteria specialized to inhabit different regions of the gut. Fungi also exist in the honey bee gut, but their composition and function remain largely undescribed. Here we show that, unlike bacteria, fungi vary substantially in species composition throughout the honey bee gut, contingent on where the bees are sampled. This observation suggests that fungi may be transient passengers and therefore unimportant as gut symbionts. However, our findings also indicate that honey bees could be major vectors of infectious plant diseases as many of the fungi we found in the honey bee gut are recognized as plant pathogens.

scholarly journals Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Si-Qi Tao ◽  
Bin Cao ◽  
Emmanuelle Morin ◽  
Ying-Mei Liang ◽  
Sébastien Duplessis
Keyword(s):  
Life Cycle ◽  
Host Plant ◽  
Plant Pathogens ◽  
Life Stage ◽  
Rust Fungi ◽  
Comparative Transcriptomics ◽  
Genetic Program ◽  
Rust Disease ◽  
General Role ◽  
Fungal Plant Pathogens

Abstract Background Gymnosporangium spp. are fungal plant pathogens causing rust disease and most of them are known to infect two different host plants (heteroecious) with four spore stages (demicyclic). In the present study, we sequenced the transcriptome of G. japonicum teliospores on its host plant Juniperus chinensis and we performed comparison to the transcriptomes of G. yamadae and G. asiaticum at the same life stage, that happens in the same host but on different organs. Results Functional annotation for the three Gymnosporangium species showed the expression of a conserved genetic program with the top abundant cellular categories corresponding to energy, translation and signal transduction processes, indicating that this life stage is particularly active. Moreover, the survey of predicted secretomes in the three Gymnosporangium transcriptomes revealed shared and specific genes encoding carbohydrate active enzymes and secreted proteins of unknown function that could represent candidate pathogenesis effectors. A transcript encoding a hemicellulase of the glycoside hydrolase 26 family, previously identified in other rust fungi, was particularly highly expressed suggesting a general role in rust fungi. The comparison between the transcriptomes of the three Gymnosporangium spp. and selected Pucciniales species in different taxonomical families allowed to identify lineage-specific protein families that may relate to the biology of teliospores in rust fungi. Among clustered gene families, 205, 200 and 152 proteins were specifically identified in G. japonicum, G. yamadae and G. asiaticum, respectively, including candidate effectors expressed in teliospores. Conclusions This comprehensive comparative transcriptomics study of three Gymnosporangium spp. identified gene functions and metabolic pathways particularly expressed in teliospores, a stage of the life cycle that is mostly overlooked in rust fungi. Secreted protein encoding transcripts expressed in teliospores may reveal new candidate effectors related to pathogenesis. Although this spore stage is not involved in host plant infection but in the production of basidiospores infecting plants in the Amygdaloideae, we speculate that candidate effectors may be expressed as early as the teliospore stage for preparing further infection by basidiospores.

scholarly journals The potential occurrence of Puccinia asparagi in New Zealand

2006 ◽  
Vol 59 ◽  
pp. 137-140
Author(s):  
S.L.H. Viljanen-Rollinson ◽  
Y. Deng ◽  
M.V. Marroni ◽  
L-H Cheah
Keyword(s):  
New Zealand ◽  
Plant Pathogens ◽  
Rust Fungi ◽  
Wind Dispersal

Wind dispersal of plant pathogens is one of the pathways of entry for rust fungi into New Zealand from Australia Asparagus rust (caused by Puccinia asparagi) has already caused damage to asparagus crops in Australia It poses a serious risk to New Zealands biosecurity and the 2000 ha asparagus industry CLIMEX Match Climates simulations showed that climates in locations where asparagus rust is already present are similar to New Zealand climates

scholarly journals Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle

2019 ◽  
Author(s):  
Si-Qi Tao ◽  
Bin Cao ◽  
Emmanuelle Morin ◽  
Ying-Mei Liang ◽  
Sébastien Duplessis
Keyword(s):  
Life Cycle ◽  
Host Plant ◽  
Plant Pathogens ◽  
Life Stage ◽  
Rust Fungi ◽  
Comparative Transcriptomics ◽  
Genetic Program ◽  
Rust Disease ◽  
General Role ◽  
Fungal Plant Pathogens

Abstract Background: Gymnosporangium spp. are fungal plant pathogens causing rust disease and most of them are known to infect two different host plants (heteroecious) with four spore stages (demicyclic). In the present study, we sequenced the transcriptome of G. japonicum teliospores on its host plant Juniperus chinensis and we performed comparison to the transcriptomes of G. yamadae and G. asiaticum at the same life stage, that happens in the same host but on different organs. Results: Functional annotation for the three Gymnosporangium species showed the expression of a conserved genetic program with the top abundant cellular categories corresponding to energy, translation and signal transduction processes, indicating that this life stage is particularly active. Moreover, the survey of predicted secretomes in the three Gymnosporangium transcriptomes revealed shared and specific genes encoding carbohydrate active enzymes and secreted proteins of unknown function that could represent candidate pathogenesis effectors. A transcript encoding a hemicellulase of the glycoside hydrolase 26 family, previously identified in other rust fungi, was particularly highly expressed suggesting a general role in rust fungi. The comparison between the transcriptomes of the three Gymnosporangium spp. and selected Pucciniales species in different taxonomical families allowed to identify lineage-specific protein families that may relate to the biology of teliospores in rust fungi. Among clustered gene families, 205, 200 and 152 proteins were specifically identified in G. japonicum , G. yamadae and G. asiaticum , respectively, including candidate effectors expressed in teliospores. Conclusions: This comprehensive comparative transcriptomics study of three Gymnosporangium spp. identified gene functions and metabolic pathways particularly expressed in teliospores, a stage of the life cycle that is mostly overlooked in rust fungi. Secreted protein encoding transcripts expressed in teliospores may reveal new candidate effectors related to pathogenesis. Although this spore stage is not involved in host plant infection but in the production of basidiospores infecting plants in the Amygdaloideae, we speculate that candidate effectors may be expressed as early as the teliospore stage for preparing further infection by basidiospores.

scholarly journals Differential alteration of plant functions by homologous fungal candidate effectors

2020 ◽  
Author(s):  
Karen Cristine Goncalves dos Santos ◽  
Gervais Pelletier ◽  
Armand Séguin ◽  
François Guillemette ◽  
Jeffrey Hawkes ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Sequence Similarity ◽  
Mapk Signaling ◽  
Rust Fungi ◽  
Control Line ◽  
Hormone Response ◽  
Kegg Pathways ◽  
Correlated Patterns ◽  
Transgenic Lines ◽  
Plant Pathogen Interaction

AbstractRust fungi are plant pathogens that cause epidemics that threaten the production of important plant species, such as wheat, soy, coffee and poplar. Melampsora larici-populina (Mlp) causes the poplar rust and encodes at least 1 184 candidate effectors (CEs), however their functions are poorly known. In this study, we used Arabidopsis plants constitutively expressing CEs of Mlp to discover processes targeted by these fungal proteins. For this purpose, we sequenced the transcriptome and used mass spectrometry to analyse the metabolome of Arabidopsis plants expressing individually one of the 14 selected CEs and of a control line. We found 2 299 deregulated genes across the experiment. Among the down-regulated genes, the KEGG pathways “MAPK signaling pathway” and “Plant-pathogen interaction” were respectively over-represented in six and five of the 14 transgenic lines. Moreover, genes related to hormone response and defense were down-regulated across all transgenic lines are. We further observed that there were 680 metabolites deregulated in at least one CE-expressing transgenic line, with highly unsaturated and phenolic compounds enriched in up-regulated metabolites and peptides enriched among down-regulated metabolites. Interestingly, we found that transgenic lines expressing unrelated CEs had correlated patterns of gene and metabolite deregulation, while expression of CEs belonging to the same family deregulated different genes and metabolites. Taken together, our results indicate that the sequence of effectors and their belonging to families may not be a good predictor of their impact on the plant.ImportanceRust fungi are plant pathogens that threaten the production of important crops, including wheat, soy, coffee and poplar. Effectors are used by pathogens to control the host, however in the case of Melampsora larici-populina, the causal agent of the poplar rust, and other rust fungi these proteins are poorly known. We used Arabidopsis plants expressing candidate effectors (CEs) of Mlp to better understand the interaction between this pathogen and its hosts. We found that expression of unrelated CEs led to similar patterns of gene and metabolite deregulation, while transgenic lines expressing CEs belonging to the same family showed different groups of different genes and metabolites deregulated. Thus, our results suggest that functional annotation of effectors based on sequence similarity may be misleading.

scholarly journals Comparative secretomics identifies conserved WAxR motif-containing effectors in rust fungi that suppress cell death in plants

2021 ◽  
Author(s):  
Rajdeep Jaswal ◽  
Himanshu Dubey ◽  
Kanti Kiran ◽  
Hukam Rawal ◽  
Sivasubramanian Rajarammohan ◽  
...  
Keyword(s):  
Cell Death ◽  
Plant Pathogen ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Rust Fungi ◽  
Cell Wall Degrading Enzymes ◽  
Conserved Motifs ◽  
Large Numbers ◽  
Biotrophic Pathogens ◽  
Plant Pathogen Interaction

Identification of novel effectors with conserved features has always remained a challenge in plant-pathogen interaction studies. The introduction of the genomics era in plant-pathogen studies has led to the identification of significant candidate effectors with novel motifs such as RxLR and dEER motifs. However, in the case of fungal pathogens, limited conserved motifs associated with effectors have been discovered yet. In the present study, we have performed comparative secretome analysis for major plant pathogens of diverse nutrition mechanisms with the aim of dissecting the features underlying their corresponding secretome and conserved motifs. We showed that rust fungi possess the lowest Cell wall degrading enzymes (CWDEs) consortium lower than other biotrophic pathogens. We also showed rust fungi possess the highest secretory superoxide dismutase (SOD) than other studied plant pathogens. Further, we prioritized the candidate secretory effectors proteins (CSEPs) of all the studied pathogens by combining various effector mining parameters to highlight the candidates with potential effector features. A novel WAxR motif in conjugation with the Y/F/WxC (FGC) motif was identified in the effectors of various P. striiformis races present globally. The WAxR/WAxR like motifs ( WxxR, WAxx, xAxR) containing effectors were also found in the secretome of other rust fungi. Further, the functional validation of two candidate effectors with WAxR motif from P. striiformis Yr9 showed that these effectors localize to the nucleus as well as cytoplasm, and are able to suppress BAX induced cell death in Nicotiana benthamiana. The mutation analysis of individual residues of the WAxR motif (W, A, R ) however did not affect the cell death suppression nor subcellular localization of these effectors. Overall, the current study reports the presence of novel motifs in large numbers of effectors of rust fungi with cell death suppression features.

scholarly journals Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle

2019 ◽  
Author(s):  
Si-Qi Tao ◽  
Bin Cao ◽  
Emmanuelle Morin ◽  
Ying-Mei Liang ◽  
Sébastien Duplessis
Keyword(s):  
Life Cycle ◽  
Host Plant ◽  
Plant Pathogens ◽  
Life Stage ◽  
Rust Fungi ◽  
Comparative Transcriptomics ◽  
Genetic Program ◽  
Rust Disease ◽  
General Role ◽  
Fungal Plant Pathogens

Abstract Background Gymnosporangium spp. are fungal plant pathogens causing rust disease and most of them are known to infect two different host plants (heteroecious) with four spore stages (demicyclic). In the present study, we sequenced the transcriptome of 
G. japonicum teliospores on its host plant Juniperus chinensis and we performed comparison to the transcriptomes of G. yamadae and G. asiaticum at the same life stage, that happens in the same host but on different organs. Results Functional annotation for the three Gymnosporangium species showed the expression of a conserved genetic program with the top abundant cellular categories corresponding to energy, translation and signal transduction processes, indicating that this life stage is particularly active. Moreover, the survey of predicted secretomes in the three Gymnosporangium transcriptomes revealed shared and specific genes encoding carbohydrate active enzymes and secreted proteins of unknown function that could represent candidate pathogenesis effectors. A transcript encoding a hemicellulose of the glycoside hydrolase 26 family, previously identified in other rust fungi, was particularly highly expressed suggesting a general role in rust fungi. The comparison between the transcriptomes of the three Gymnosporangium spp. and selected Pucciniales species in different taxonomical families allowed to identify lineage-specific protein families that may relate to the biology of rust fungi. Among clustered gene families, 205, 200 and 152 proteins were specifically identified in G. japonicum, G. yamadae and G. asiaticum, respectively, including candidate effectors expressed in teliospores. Conclusions This comprehensive comparative transcriptomics study of three Gymnosporangium spp. identified gene functions and metabolic pathways particularly expressed in teliospores, a stage of the life cycle that is mostly overlooked in rust fungi. Secreted protein encoding transcripts expressed in teliospores may reveal new candidate effectors related to pathogenesis. Although this spore stage is not involved in host plant infection but in the production of basidiospores infecting plants in the Amygdaloideae, we speculate that candidate effectors may be expressed as early as the teliospore stage for preparing further infection by basidiospores.

scholarly journals Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle

2019 ◽  
Author(s):  
Si-Qi Tao ◽  
Bin Cao ◽  
Emmanuelle Morin ◽  
Ying-Mei Liang ◽  
Sébastien Duplessis
Keyword(s):  
Life Cycle ◽  
Host Plant ◽  
Plant Pathogens ◽  
Life Stage ◽  
Rust Fungi ◽  
Comparative Transcriptomics ◽  
Genetic Program ◽  
Rust Disease ◽  
General Role ◽  
Fungal Plant Pathogens

Abstract Background: Gymnosporangium spp. are fungal plant pathogens causing rust disease and most of them are known to infect two different host plants (heteroecious) with four spore stages (demicyclic). In the present study, we sequenced the transcriptome of G. japonicum teliospores on its host plant Juniperus chinensis and we performed comparison to the transcriptomes of G. yamadae and G. asiaticum at the same life stage, that happens in the same host but on different organs. Results: Functional annotation for the three Gymnosporangium species showed the expression of a conserved genetic program with the top abundant cellular categories corresponding to energy, translation and signal transduction processes, indicating that this life stage is particularly active. Moreover, the survey of predicted secretomes in the three Gymnosporangium transcriptomes revealed shared and specific genes encoding carbohydrate active enzymes and secreted proteins of unknown function that could represent candidate pathogenesis effectors. A transcript encoding a hemicellulase of the glycoside hydrolase 26 family, previously identified in other rust fungi, was particularly highly expressed suggesting a general role in rust fungi. The comparison between the transcriptomes of the three Gymnosporangium spp. and selected Pucciniales species in different taxonomical families allowed to identify lineage-specific protein families that may relate to the biology of teliospores in rust fungi. Among clustered gene families, 205, 200 and 152 proteins were specifically identified in G. japonicum , G. yamadae and G. asiaticum , respectively, including candidate effectors expressed in teliospores. Conclusions: This comprehensive comparative transcriptomics study of three Gymnosporangium spp. identified gene functions and metabolic pathways particularly expressed in teliospores, a stage of the life cycle that is mostly overlooked in rust fungi. Secreted protein encoding transcripts expressed in teliospores may reveal new candidate effectors related to pathogenesis. Although this spore stage is not involved in host plant infection but in the production of basidiospores infecting plants in the Amygdaloideae, we speculate that candidate effectors may be expressed as early as the teliospore stage for preparing further infection by basidiospores.

scholarly journals Differential Microbial Diversity inDrosophila melanogaster: Are Fruit Flies Potential Vectors of Opportunistic Pathogens?

2017 ◽  
Vol 2017 ◽  
pp. 1-6 ◽  
Author(s):  
Luis A. Ramírez-Camejo ◽  
Génesis Maldonado-Morales ◽  
Paul Bayman
Keyword(s):  
Plant Pathogens ◽  
Klebsiella Oxytoca ◽  
Geotrichum Candidum ◽  
Alcaligenes Faecalis ◽  
Model System ◽  
Microbial Pathogens ◽  
Tropical Fruits ◽  
Opportunistic Pathogens ◽  
Microbial Composition ◽  
Fusarium Equiseti

Drosophila melanogasterhas become a model system to study interactions between innate immunity and microbial pathogens, yet many aspects regarding its microbial community and interactions with pathogens remain unclear. In this study wildD. melanogasterwere collected from tropical fruits in Puerto Rico to test how the microbiota is distributed and to compare the culturable diversity of fungi and bacteria. Additionally, we investigated whether flies are potential vectors of human and plant pathogens. Eighteen species of fungi and twelve species of bacteria were isolated from wild flies. The most abundant microorganisms identified were the yeastCandida inconspicuaand the bacteriumKlebsiellasp. The yeastIssatchenkia hanoiensiswas significantly more common internally than externally in flies. Species richness was higher in fungi than in bacteria, but diversity was lower in fungi than in bacteria. The microbial composition of flies was similar internally and externally. We identified a variety of opportunistic human and plant pathogens in flies such asAlcaligenes faecalis,Aspergillus flavus,A. fumigatus,A. niger,Fusarium equiseti/oxysporum, Geotrichum candidum,Klebsiella oxytoca,Microbacterium oxydans, andStenotrophomonas maltophilia. Despite its utility as a model system,D. melanogastercan be a vector of microorganisms that represent a potential risk to plant and public health.

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