Plant Pathogenomics
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Trends in Genetics: Transposable Elements Direct The Coevolution between Plants and Microbes (2016)

Trends in Genetics: Transposable Elements Direct The Coevolution between Plants and Microbes (2016) | Plant Pathogenomics | Scoop.it

Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as ‘selfish’ genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host–microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a ‘two-speed’ genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.

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eLife: Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management (2018)

eLife: Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management (2018) | Plant Pathogenomics | Scoop.it

Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses.

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bioRxiv: Re-annotated Nicotiana benthamiana gene models for enhanced proteomics and reverse genetics (2018)

bioRxiv: Re-annotated Nicotiana benthamiana gene models for enhanced proteomics and reverse genetics (2018) | Plant Pathogenomics | Scoop.it

Nicotiana benthamiana is an important model organism and representative of the Solanaceae (Nightshade) family. N. benthamiana has a complex ancient allopolyploid genome with 19 chromosomes, and an estimated genome size of 3.1Gb. Several draft assemblies of the N. benthamiana genome have been generated, however, many of the gene-models in these draft assemblies appear incorrect. Here we present a nearly non-redundant database of improved N. benthamiana gene-models based on gene annotations from well-annotated genomes in the Nicotiana genus. We show that the new predicted proteome is more complete than the previous proteomes and more sensitive and accurate in proteomics applications, while maintaining a reasonable low gene number (~43,000). As a proof-of-concept we use this proteome to compare the leaf extracellular (apoplastic) proteome to a total extract of leaves. Several gene families are more abundant in the apoplast. For one of these apoplastic protein families, the subtilases, we present a phylogenetic analysis illustrating the utility of this database. Besides proteome annotation, this database will aid the research community with improved target gene selection for genome editing and off-target prediction for gene silencing.

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BMC Series blog: Phenotypic plasticity in a pandemic lineage of the Irish potato famine pathogen (2018)

BMC Series blog: Phenotypic plasticity in a pandemic lineage of the Irish potato famine pathogen (2018) | Plant Pathogenomics | Scoop.it

What did you find?

We studied two different races of the Irish potato famine pathogen, and we discovered that the difference invirulence between these races could not be ascribed to a genetic difference but rather to a difference in the expression of the underlying virulence gene. This adds to our knowledge of how this important scourge on world agriculture evolves to evade plant immunity.

 

Why is this work important?

As our colleague Mark Gijzen tweeted, “is this a rare and unusual curiosity or another example of a widespread biological phenomenon?” Indeed, there are few other examples in related plant pathogens, including the soybean root rot pathogen that Mark studies. This finding has far reaching implications. It indicates that these pathogens can evolve even more rapidly than anticipated thus counteracting the efforts of plant breeders to deploy disease resistant crops.

 

Are potato varieties resistant to the pathogen available?

Yes, there are. But there are several examples of potato cultivars that were initially resistant to late blight when farmers started to grow them, but succumbed to the disease a few years later. The ability to switch on and off virulence genes such as we found in this research may partly explain why the pathogen is so effective at overcoming the plants defense barriers.

 

What is currently done to control the disease?

Susceptible potato cultivars must be protected by repeated applications of fungicides. If left unchecked, the disease will destroy the leaves and stems in a matter of days as in the pictured trial plot of potato varieties in the highlands of Peru.

Is chemical protection the only way to control late blight?

In nature, there are wild relatives of the cultivated potato and many of them can withstand the disease (see image of potato variety field trial). Breeders identify the genes in these plants and introduce them to cultivated potato through crosses or genetic transformation.

 

How did you put this project together?

We studied an Andean lineage of the Irish potato famine pathogen known as EC-1 so the project had an international flavor from day one. Ours was a wide reaching multinational collaboration bringing together scientists based in the UK, Japan, Netherlands, USA, Philippines, and Peru. It’s how science often goes on these days. Experts from all over the world team up to solve problems, make new discoveries and advance our knowledge.

 

Anything you would have done differently?

DNA sequencing technology develops so fast that by the time the paper gets published you wish you could apply a different method. It also takes more time to analyze the data, write up the paper etc. than to generate the sequence data. This can be frustrating.

 

You posted the paper in bioRxiv before submission. Why?

Why not? Posting the article on bioRxiv enabled us to share our findings with our colleagues and hear about it from the community as soon as possible. The tweet by Mark Gijzen we referred to above is an example of such feedback. Posting a preprint relieves some of the delays associated with publishing. It’s a liberating feeling to finish writing up a paper and immediately share it with anyone who’s interested.

 

Authors

 

Dr. Vivianne Vleeshouwers is assistant professor in Wageningen University & Research, the Netherlands. Her research is dedicated to understand the molecular interaction between the potato late blight pathogen Phytophthora infestans and potato, and exploit this knowledge to achieve a better and more durable disease resistance.

 

Dr. Hannele Lindqvist-Kreuze works as a Molecular Breeder at the International Potato Center (CIP) in Lima, Peru. Her current work focuses on the discovery and application of molecular markers in the potato and sweet potato breeding programs of CIP. She describes her work as a Haiku: Searching for Hidden Patterns, Coded in the DNA, Unknowingly selected.

 

Dr. Sophien Kamoun is a Senior Scientist at The Sainsbury Laboratory and a Professor of Biology at the University of East Anglia in Norwich, UK. He studies the interactions between plants and filamentous pathogens, notably the Irish potato famine pathogen and the rice and wheat blast fungus. He’s known for saying “Don’t bet against the pathogen.”

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bioRxiv: Comparative genomic analysis revealed rapid differentiation in the pathogenicity-related gene repertoires between Pyricularia oryzae and Pyricularia penniseti isolated from a Pennisetum gr...

bioRxiv: Comparative genomic analysis revealed rapid differentiation in the pathogenicity-related gene repertoires between Pyricularia oryzae and Pyricularia penniseti isolated from a Pennisetum gr... | Plant Pathogenomics | Scoop.it

Backgrounds: Pyricularia is a multispecies complex that could infect and cause severe blast disease on diverse hosts, including rice, wheat and many other grasses. Although the genome size of this fungal complex is small [~40 Mbp for Pyricularia oryzae (syn. Magnaporthe oryzae), and ~45 Mbp for P. grisea], the genome plasticity allows the fungus to jump and adapt to new hosts. Therefore, deciphering the genome basis of individual species could facilitate the evolutionary and genetic study of this fungus. However, except for the P. oryzae subgroup, many other species isolated from diverse hosts, such as the Pennisetum grasses, remain largely uncovered genetically. Results: Here, we report the genome sequence of a pyriform-shaped fungal strain P. penniseti P1609 isolated from a Pennisetum grass (JUJUNCAO) using PacBio SMRT sequencing technology. We performed a phylogenomic analysis of 28 Magnaporthales species and 5 non-Magnaporthales species and addressed P1609 into a Pyricularia subclade that is distant from P. oryzae. Comparative genomic analysis revealed that the pathogenicity-related gene repertoires were fairly different between P1609 and the P. oryzae strain 70-15, including the cloned avirulence genes, other putative secreted proteins, as well as some other predicted Pathogen-Host Interaction (PHI) genes. Genomic sequence comparison also identified many genomic rearrangements. Conclusion: Taken together, our results suggested that the genomic sequence of the P. penniseti P1609 could be a useful resource for the genetic study of the Pennisetum-infecting Pyricularia species.

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bioRxiv: Subfamily-specific functionalization of diversified immune receptors in wild barley (2018)

bioRxiv: Subfamily-specific functionalization of diversified immune receptors in wild barley (2018) | Plant Pathogenomics | Scoop.it

Gene-for-gene immunity between plants and host-adapted pathogens is often linked to population-level diversification of immune receptors encoded by disease resistance (R) genes. The complex barley (Hordeum vulgare L.) R gene locus Mildew Locus A (Mla) provides isolate-specific resistance against the powdery mildew fungus Blumeria graminis f. sp. hordei (Bgh) and has been introgressed into modern barley cultivars from diverse germplasms, including the wild relative H. spontaneum. Known Mla disease resistance specificities to Bgh appear to encode allelic variants of the R Gene Homolog 1 (RGH1) family of nucleotide-binding domain and leucine-rich repeat (NLR) proteins. To gain insights into Mla diversity in wild barley populations, we here sequenced and assembled the transcriptomes of 50 accessions of H. spontaneum representing nine populations distributed throughout the Fertile Crescent. The assembled Mla transcripts exhibited rich sequence diversity, which is linked neither to geographic origin nor population structure. Mla transcripts in the tested H. spontaneum accessions could be grouped into two similar-sized subfamilies based on two major N-terminal coiled-coil signaling domains that are both capable of eliciting cell death. The presence of positively selected sites, located mainly in the C-terminal leucine-rich repeats of both MLA subfamilies, together with the fact that both coiled-coil signaling domains mediate cell death, implies that the two subfamilies are actively maintained in the host population. Unexpectedly, known MLA receptor variants that confer Bgh resistance belong exclusively to one subfamily. Thus, signaling domain divergence, potentially to distinct pathogen populations, is an evolutionary signature of functional diversification of an immune receptor.

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New Phytologist: Comparative genomics of Pseudomonas syringae reveals convergent gene gain and loss associated with specialization onto cherry (Prunus avium) (2018)

New Phytologist: Comparative genomics of Pseudomonas syringae reveals convergent gene gain and loss associated with specialization onto cherry (Prunus avium) (2018) | Plant Pathogenomics | Scoop.it
  • Genome‐wide analyses of the effector‐ and toxin‐encoding genes were used to examine the phylogenetics and evolution of pathogenicity amongst diverse strains of Pseudomonas syringae causing bacterial canker of cherry (Prunus avium), including pathovars P. syringae pv morsprunorum (Psm) races 1 and 2, P. syringae pv syringae(Pss) and P. syringae pv avii.
  • Phylogenetic analyses revealed Psm races and P. syringae pv avii clades were distinct and were each monophyletic, whereas cherry‐pathogenic strains of Pss were interspersed amongst strains from other host species.
  • A maximum likelihood approach was used to predict effectors associated with pathogenicity on cherry. Pss possesses a smaller repertoire of type III effectors but has more toxin biosynthesis clusters than Psm and P. syringae pv avii. Evolution of cherry pathogenicity was correlated with gain of genes such as hopAR1 and hopBB1through putative phage transfer and horizontal transfer respectively. By contrast, loss of the avrPto/hopAB redundant effector group was observed in cherry‐pathogenic clades. Ectopic expression of hopAB and hopC1 triggered the hypersensitive reaction in cherry leaves, confirming computational predictions.
  • Cherry canker provides a fascinating example of convergent evolution of pathogenicity that is explained by the mix of effector and toxin repertoires acting on a common host.
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mBio: The Blast Fungus Decoded: Genomes in Flux (2018)

mBio: The Blast Fungus Decoded: Genomes in Flux (2018) | Plant Pathogenomics | Scoop.it

Plant disease outbreaks caused by fungi are a chronic threat to global food security. A prime case is blast disease, which is caused by the ascomycete fungus Magnaporthe oryzae (syn. Pyricularia oryzae), which is infamous as the most destructive disease of the staple crop rice. However, despite its Linnaean binomial name, M. oryzae is a multihost pathogen that infects more than 50 species of grasses. A timely study by P. Gladieux and colleagues (mBio 9:e01219-17, 2018, https://doi.org/10.1128/mBio.01219-17) reports the most extensive population genomic analysis of the blast fungus thus far. M. oryzae consists of an assemblage of differentiated lineages that tend to be associated with particular host genera. Nonetheless, there is clear evidence of gene flow between lineages consistent with maintaining M. oryzae as a single species. Here, we discuss these findings with an emphasis on the ecologic and genetic mechanisms underpinning gene flow. This work also bears practical implications for diagnostics, surveillance, and management of blast diseases.

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Current Opinion Microbiology: The birth and death of effectors in rapidly evolving filamentous pathogen genomes (2018)

Current Opinion Microbiology: The birth and death of effectors in rapidly evolving filamentous pathogen genomes (2018) | Plant Pathogenomics | Scoop.it
• Plant pathogens produce effectors to interfere with host defences and metabolism.
• Effector genes are among the most rapidly evolving genes in pathogen populations.
• Transcriptional control evolved in tandem with the chromosomal location of effectors.
• Chromosomal rearrangements are at the origin of high effector gain and loss rates.

Plant pathogenic fungi and oomycetes are major risks to food security due to their evolutionary success in overcoming plant defences. Pathogens produce effectors to interfere with host defences and metabolism. These effectors are often encoded in rapidly evolving compartments of the genome. We review how effector genes emerged and were lost in pathogen genomes drawing on the links between effector evolution and chromosomal rearrangements. Some new effectors entered pathogen genomes via horizontal transfer or introgression. However, new effector functions also arose through gene duplication or from previously non-coding sequences. The evolutionary success of an effector is tightly linked to its transcriptional regulation during host colonization. Some effectors converged on an epigenetic control of expression imposed by genomic defences against transposable elements. Transposable elements were also drivers of effector diversification and loss that led to mosaics in effector presence–absence variation. Such effector mosaics within species was the foundation for rapid pathogen adaptation.

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bioRxiv: Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen (2018)

bioRxiv: Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen (2018) | Plant Pathogenomics | Scoop.it

Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare). The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes (SPs) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SP clusters nor TEs are enriched in specific genomic regions. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs, but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome. The characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of compartmentalization) are consistent with a 'one-speed' genome that differs in its architecture and (co-)evolutionary pattern from the 'two-speed' genomes reported for several other filamentous phytopathogens.

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Molecular Plant Pathology: Signatures of selection and host-adapted gene expression of the Phytophthora infestans RNA silencing suppressor PSR2 (2016)

Molecular Plant Pathology: Signatures of selection and host-adapted gene expression of the Phytophthora infestans RNA silencing suppressor PSR2 (2016) | Plant Pathogenomics | Scoop.it

Phytophthora infestans is a devastating pathogen in agricultural systems. Recently, an RNA silencing suppressor (PSR2, ‘Phytophthora suppressor of RNA silencing 2’) has been described in P. infestans. PSR2 has been shown to increase the virulence of Phytophthora pathogens on their hosts. This gene is one of the few effectors present in many economically important Phytophthora species. In this study, we investigated: (i) the evolutionary history of PSR2 within and between species of Phytophthora; and (ii) the interaction between sequence variation, gene expression and virulence. In P. infestans, the highest PiPSR2 expression was correlated with decreased symptom expression. The highest gene expression was observed in the biotrophic phase of the pathogen, suggesting that PSR2 is important during early infection. Protein sequence conservation was negatively correlated with host range, suggesting host range as a driver of PSR2 evolution. Within species, we detected elevated amino acid variation, as observed for other effectors; however, the frequency spectrum of the mutations was inconsistent with strong balancing selection. This evolutionary pattern may be related to the conservation of the host target(s) of PSR2 and the absence of known corresponding R genes. In summary, our study indicates that PSR2 is a conserved effector that acts as a master switch to modify plant gene regulation early during infection for the pathogen's benefit. The conservation of PSR2 and its important role in virulence make it a promising target for pathogen management.

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ISMEJ: A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements (2017)

ISMEJ: A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements (2017) | Plant Pathogenomics | Scoop.it

Fungal pathogens can rapidly evolve virulence towards resistant crops in agricultural ecosystems. Gains in virulence are often mediated by the mutation or deletion of a gene encoding a protein recognized by the plant immune system. However, the loci and the mechanisms of genome evolution enabling rapid virulence evolution are poorly understood. We performed genome-wide association mapping on a global collection of 106 strains of Zymoseptoria tritici, the most damaging pathogen of wheat in Europe, to identify polymorphisms linked to virulence on two wheat varieties. We found 25 distinct genomic loci associated with reproductive success of the pathogen. However, no locus was shared between the host genotypes, suggesting host specialization. The main locus associated with virulence encoded a highly expressed, small secreted protein. Population genomic analyses showed that the gain in virulence was explained by a segregating gene deletion polymorphism. The deletion was likely adaptive by preventing detection of the encoded protein. Comparative genomics of closely related species showed that the locus emerged de novo since speciation. A large cluster of transposable elements in direct proximity to the locus generated extensive rearrangements leading to multiple independent gene losses. Our study demonstrates that rapid turnover in the chromosomal structure of a pathogen can drive host specialization.

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Journal of Experimental Botany: Modulation of R-gene expression across environments (2016)

Journal of Experimental Botany: Modulation of R-gene expression across environments (2016) | Plant Pathogenomics | Scoop.it

Some environments are more conducive to pathogen growth than others, and, as a consequence, plants might be expected to invest more in resistance when pathogen growth is favored. Resistance (R-) genes in Arabidopsis thaliana have unusually extensive variation in basal expression when comparing the same R-gene among accessions collected from different environments. R-gene expression variation was characterized to explore whether R-gene expression is up-regulated in environments favoring pathogen proliferation and down-regulated when risks of infection are low; down-regulation would follow if costs of R-gene expression negatively impact plant fitness in the absence of disease. Quantitative reverse transcription-PCR was used to quantify the expression of 13 R-gene loci in plants grown in eight environmental conditions for each of 12 A. thaliana accessions, and large effects of the environment on R-gene expression were found. Surprisingly, almost every change in the environment--be it a change in biotic or abiotic conditions--led to an increase in R-gene expression, a response that was distinct from the average transcriptome response and from that of other stress response genes. These changes in expression are functional in that environmental change prior to infection affected levels of specific disease resistance to isolates of Pseudomonas syringae. In addition, there are strong latitudinal clines in basal R-gene expression and clines in R-gene expression plasticity correlated with drought and high temperatures. These results suggest that variation in R-gene expression across environments may be shaped by natural selection to reduce fitness costs of R-gene expression in permissive or predictable environments.

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Trends in Genetics: Transposable Elements Direct The Coevolution between Plants and Microbes (2016)

Trends in Genetics: Transposable Elements Direct The Coevolution between Plants and Microbes (2016) | Plant Pathogenomics | Scoop.it

Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as ‘selfish’ genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host–microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a ‘two-speed’ genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.

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MMBR: The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species (2018)

MMBR: The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species (2018) | Plant Pathogenomics | Scoop.it

The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.

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BMC Evolutionary Biology: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2018)

BMC Evolutionary Biology: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2018) | Plant Pathogenomics | Scoop.it

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186–194, 2012; Kupferschmidt K, Science 337:636–638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335–345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591–11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans.


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bioRxiv: Tracking disease resistance deployment in potato breeding by enrichment sequencing (2018)

bioRxiv: Tracking disease resistance deployment in potato breeding by enrichment sequencing (2018) | Plant Pathogenomics | Scoop.it

Following the molecular characterisation of functional disease resistance genes in recent years, methods to track and verify the integrity of multiple genes in varieties are needed for crop improvement through resistance stacking. Diagnostic resistance gene enrichment sequencing (dRenSeq) enables the high-confidence identification and complete sequence validation of known functional resistance genes in crops. As demonstrated for tetraploid potato varieties, the methodology is more robust and cost-effective in monitoring resistances than whole-genome sequencing and can be used to appraise (trans)gene integrity efficiently. All currently known NB-LRRs effective against viruses, nematodes and the late blight pathogen Phytophthora infestans can be tracked with dRenSeq in potato and hitherto unknown polymorphisms have been identified. The methodology provides a means to improve the speed and efficiency of future disease resistance breeding in crops by directing parental and progeny selection towards effective combinations of resistance genes.

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bioRxiv: Effector Gene Reshuffling Involves Dispensable Mini-chromosomes in the Wheat Blast Fungus (2018)

bioRxiv: Effector Gene Reshuffling Involves Dispensable Mini-chromosomes in the Wheat Blast Fungus (2018) | Plant Pathogenomics | Scoop.it

Newly emerged wheat blast disease is a serious threat to global wheat production. Wheat blast is caused by a distinct, exceptionally diverse lineage of the fungus causing rice blast disease. To understand genetic diversity in wheat-infecting strains, we report a near-finished reference genome of a recent field isolate generated using long read sequencing and a novel scaffolding approach with long-distance paired genomic sequences. The genome assemblage includes seven core chromosomes and sequences from a dispensable mini-chromosome that harbors effector genes normally found on the ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and two mini-chromosomes from another field isolate each contain different effector homologous genes and core chromosome end sequences. The mini-chromosome is highly repetitive and is enriched in transposons occurring most frequently at core chromosome ends. Additionally, transposons in mini-chromosomes lack the characteristic signature for inactivation by repeat-induced point (RIP) mutation genome defenses. Our results, collectively, indicate that dispensable mini-chromosomes and non-dispensable core chromosomes undergo divergent evolutionary trajectories, and mini-chromosomes and core chromosome ends are coupled as a mobile, fast-evolving effector compartment in the wheat pathogen genome.

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Nature Plants: Oak genome reveals facets of long lifespan (2018)

Nature Plants: Oak genome reveals facets of long lifespan (2018) | Plant Pathogenomics | Scoop.it

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

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bioRxiv: Extraordinary genome instability and widespread chromosome rearrangements during vegetative growth (2018)

bioRxiv: Extraordinary genome instability and widespread chromosome rearrangements during vegetative growth (2018) | Plant Pathogenomics | Scoop.it

The haploid genome of the pathogenic fungus Zymoseptoria tritici is contained on “core” and “accessory” chromosomes. While 13 core chromosomes are found in all strains, as many as eight accessory chromosomes show presence/absence variation and rearrangements among field isolates. We investigated chromosome stability using experimental evolution, karyotyping and genome sequencing. We report extremely high and variable rates of accessory chromosome loss during mitotic propagation in vitro and in planta. Spontaneous chromosome loss was observed in 2 to >50 % of cells during four weeks of incubation. Similar rates of chromosome loss in the closely related Z. ardabiliae suggest that this extreme chromosome dynamic is a conserved phenomenon in the genus. Elevating the incubation temperature greatly increases instability of accessory and even core chromosomes, causing severe rearrangements involving telomere fusion and chromosome breakage. Chromosome losses do not impact the fitness of Z. tritici in vitro, but some lead to increased virulence suggesting an adaptive role of this extraordinary chromosome instability.

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ISME Journal: Population genomic analysis of the rice blast fungus reveals specific events associated with expansion of three main clades (2018)

ISME Journal: Population genomic analysis of the rice blast fungus reveals specific events associated with expansion of three main clades (2018) | Plant Pathogenomics | Scoop.it

We examined the genomes of 100 isolates of Magnaporthe oryzae (Pyricularia oryzae), the causal agent of rice blast disease. We grouped current field populations of M. oryzae into three major globally distributed groups. A genetically diverse group, clade 1, which may represent a group of closely related lineages, contains isolates of both mating types. Two well-separated clades, clades 2 and 3, appear to have arisen as clonal lineages distinct from the genetically diverse clade. Examination of genes involved in mating pathways identified clade-specific diversification of several genes with orthologs involved in mating behavior in other fungi. All isolates within each clonal lineage are of the same mating type. Clade 2 is distinguished by a unique deletion allele of a gene encoding a small cysteine-rich protein that we determined to be a virulence factor. Clade 3 isolates have a small deletion within the MFA2 pheromone precursor gene, and this allele is shared with an unusual group of isolates we placed within clade 1 that contain AVR1-CO39 alleles. These markers could be used for rapid screening of isolates and suggest specific events in evolution that shaped these populations. Our findings are consistent with the view that M. oryzae populations in Asia generate diversity through recombination and may have served as the source of the clades 2 and 3 isolates that comprise a large fraction of the global population.

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bioRxiv: A small subset of NLR genes drives local adaptation to pathogens in wild tomato (2017)

bioRxiv: A small subset of NLR genes drives local adaptation to pathogens in wild tomato (2017) | Plant Pathogenomics | Scoop.it

In plants, defence-associated genes including the NLR gene family are under constant evolutionary pressure to adapt to pathogens. It is still unknown how many NLRs contribute to adaptation, and if the involved loci vary within a species across habitats. We use a three-pronged approach to reveal and quantify selection signatures at over 90 NLR genes over 14 populations of Solanum chilense a wild tomato species endemic to Peru and Chile found in different habitats. First, we generated a de novo genome of S. chilense. Second, by whole genome resequencing of three geographically distant individuals we infer the species past demographic history of habitat colonisation. Finally, using targeted resequencing we show that a small subset of NLRs, 7%, show signs of positive or balancing selection. We demonstrate that 13 NLRs change direction of selection during the colonisation of new habitats and form a mosaic pattern of adaptation to pathogens. We estimate that the turn over time of selection (birth-and-death rate) on NLRs is 18,000 years. Finally, our work identifies new NLRs under strong selective pressure between habitats, thus providing novel opportunities for R-gene identification.

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Phytopathology: Population Structure of Mycosphaerella graminicola: From Lesions to Continents (2002)

Phytopathology: Population Structure of Mycosphaerella graminicola: From Lesions to Continents (2002) | Plant Pathogenomics | Scoop.it

The genetic structure of field populations of Mycosphaerella graminicola was determined across a hierarchy of spatial scales using restriction fragment length polymorphism markers. The hierarchical gene diversity analysis included 1,098 isolates from seven field populations. Spatial scales ranged from millimeters to thousands of kilometers, including comparisons within and among lesions, within and among fields, and within and among regions and continents. At the smallest spatial scale, microtransect sampling was used to determine the spatial distribution of 15 genotypes found among 158 isolates sampled from five individual lesions. Each lesion had two to six different genotypes including both mating types in four of the five lesions, but in most cases a lesion was composed of one or two genotypes that occupied the majority of the lesion, with other rare genotypes interspersed among the common genotypes. The majority (77%) of gene diversity was distributed within plots ranging from ≈1 to 9 m2 in size. Genotype diversity (Ĝ / N) within fields for the Swiss, Texas, and Israeli fields was high, ranging from 79 to 100% of maximum possible values. Low population differentiation was indicated by the low GST values among populations, suggesting a corresponding high degree of gene flow among these populations. At the largest spatial scale, populations from Switzerland, Israel, Oregon, and Texas were compared. Population differentiation among these populations was low (GST = 0.05), and genetic identity between populations was high. A low but significant correlation between genetic and geographic distance among populations was found (r = -0.47, P = 0.012), suggesting that these populations probably have not reached an equilibrium between gene flow and genetic drift. Gene flow on a regional level can be reduced by implementing strategies, such as improved stubble management that minimize the production of ascospores. The possibility of high levels of gene flow on a regional level indicates a significant potential risk for the regional spread of mutant alleles that enable fungicide resistance or the breakdown of resistance genes.

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Genome Biology and Evolution: Evolutionarily Dynamic, but Robust, Targeting of Resistance Genes by the miR482/2118 Gene Family in the Solanaceae (2018)

Genome Biology and Evolution: Evolutionarily Dynamic, but Robust, Targeting of Resistance Genes by the miR482/2118 Gene Family in the Solanaceae (2018) | Plant Pathogenomics | Scoop.it

Plants are exposed to pathogens around the clock. A common resistance response in plants upon pathogen detection is localized cell death. Given the irreversible nature of this response, multiple layers of negative regulation are present to prevent the untimely or misexpression of resistance genes. One layer of negative regulation is provided by a recently discovered microRNA (miRNA) gene family, miR482/2118. This family targets the transcripts of resistance genes in plants. We investigated the evolutionary history and specificity of this miRNA gene family within the Solanaceae. This plant family includes many important crop species, providing a set of well-defined resistance gene repertoires. Across 14 species from the Solanaceae, we identified eight distinct miR482/2118 gene family members. Our studies show conservation of miRNA type and number in the group of wild tomatoes and, to a lesser extent, throughout the Solanaceae. The eight orthologous miRNA gene clusters evolved under different evolutionary constraints, allowing for individual subfunctionalization of the miRNAs. Despite differences in the predicted targeting behavior of each miRNA, the miRNA–R-gene network is robust due to its high degree of interconnectivity and redundant targeting. Our data suggest that the miR482/2118 gene family acts as an evolutionary buffer for R-gene sequence diversity.

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BMC Biology: Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome (2018)

BMC Biology: Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome (2018) | Plant Pathogenomics | Scoop.it

Background. Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence.

 

Results. We constructed and analyzed the pangenome of Zymoseptoria tritici, a major pathogen of wheat that evolved host specialization by chromosomal rearrangements and gene deletions. We used single-molecule real-time sequencing and high-density genetic maps to assemble multiple genomes. We annotated the gene space based on transcriptomics data that covered the infection life cycle of each strain. Based on a total of five telomere-to-telomere genomes, we constructed a pangenome for the species and identified a core set of 9149 genes. However, an additional 6600 genes were exclusive to a subset of the isolates. The substantial accessory genome encoded on average fewer expressed genes but a larger fraction of the candidate effector genes that may interact with the host during infection. We expanded our analyses of the pangenome to a worldwide collection of 123 isolates of the same species. We confirmed that accessory genes were indeed more likely to show deletion polymorphisms and loss-of-function mutations compared to core genes.

 

Conclusions. The pangenome construction of a highly polymorphic eukaryotic pathogen showed that a single reference genome significantly underestimates the gene space of a species. The substantial accessory genome provides a cradle for adaptive evolution.

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Insect Molecular Biology: A massive incorporation of microbial genes into the genome of Tetranychus urticae, a polyphagous arthropod herbivore (2018)

Insect Molecular Biology: A massive incorporation of microbial genes into the genome of Tetranychus urticae, a polyphagous arthropod herbivore (2018) | Plant Pathogenomics | Scoop.it

A number of horizontal gene transfers (HGTs) have been identified in the spider mite Tetranychus urticae, a chelicerate herbivore. However, the genome of this mite species has at present not been thoroughly mined for the presence of HGT genes. Here, we performed a systematic screen for HGT genes in the T. urticae genome using the h-index metric. Our results not only validated previously identified HGT genes but also uncovered 25 novel HGT genes. In addition to HGT genes with a predicted biochemical function in carbohydrate, lipid and folate metabolism, we also identified the horizontal transfer of a ketopantoate hydroxymethyltransferase and a pantoate β-alanine ligase gene. In plants and bacteria, both genes are essential for vitamin B5 biosynthesis and their presence in the mite genome strongly suggests that spider mites, similar to Bemisia tabaci and nematodes, can synthesize their own vitamin B5. We further show that HGT genes were physically embedded within the mite genome and were expressed in different life stages. By screening chelicerate genomes and transcriptomes, we were able to estimate the evolutionary histories of these HGTs during chelicerate evolution. Our study suggests that HGT has made a significant and underestimated impact on the metabolic repertoire of plant-feeding spider mites.

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