Plant Pathogenomics
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MPMI: A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research (2012)

MPMI: A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research (2012) | Plant Pathogenomics | Scoop.it

Nicotiana benthamiana is a widely used model plant species for the study of fundamental questions in molecular plant-microbe interactions and other areas of plant biology. This popularity derives from its well-characterized susceptibility to diverse pathogens and especially its amenability to virus-induced gene silencing (VIGS) and transient protein expression methods. Here we report the generation of a 63-fold coverage draft genome sequence of N. benthamiana and its availability on the Sol Genomics Network (http://solgenomics.net/) for both BLAST searches and for downloading to local servers. The estimated genome size of N. benthamiana is ~3 gigabases (Gb). The current assembly consists of ~141,000 scaffolds, spanning 2.6 Gb of which >50% are longer than 89 kilobases. Of the ~16,000 N. benthamiana unigenes available in GenBank, >90% are represented in the assembly. The usefulness of the sequence was demonstrated by the retrieval of N. benthamiana orthologs for 24 immunity-associated genes from other species including Ago2, Ago7, Bak1, Bik1, Crt1, Fls2, Pto, Prf, Rar1 and MAP kinases. The sequence will also be useful for comparative genomics in the Solanaceae as shown here by the discovery of microsynteny between N. benthamiana and tomato in the region encompassing the Pto/Prf genes.

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bioRxiv: Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss (2017)

bioRxiv: Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss (2017) | Plant Pathogenomics | Scoop.it

The fungal genus Verticillium contains ten species, some of which are notorious plant pathogens causing vascular wilt diseases in host plants, while others are known as saprophytes and opportunistic plant pathogens. Whereas the genome of V. dahliae, the most notorious plan pathogen of the genus, has been well characterized, evolution and speciation of other members of the genus received little attention thus far. Here, we sequenced the genomes of the nine haploid Verticillium spp. to study evolutionary trajectories of their divergence from a last common ancestor. Frequent occurrence of chromosomal rearrangement and gene family loss was identified. In addition to ~11,000 core genes that are shared among all species, only 200-600 species-specific genes occur. Intriguingly, these species-specific genes show different features than core genes.

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Genome Biology and Evolution: Complete Genome Sequence of the Phytopathogenic Fungus Sclerotinia sclerotiorum Reveals Insights into the Genome Architecture of Broad Host Range Pathogens (2017)

Genome Biology and Evolution: Complete Genome Sequence of the Phytopathogenic Fungus  Sclerotinia sclerotiorum  Reveals Insights into the Genome Architecture of Broad Host Range Pathogens (2017) | Plant Pathogenomics | Scoop.it

Sclerotinia sclerotiorum is a phytopathogenic fungus with over 400 hosts including numerous economically important cultivated species. This contrasts many economically destructive pathogens that only exhibit a single or very few hosts. Many plant pathogens exhibit a “two-speed” genome. So described because their genomes contain alternating gene rich, repeat sparse and gene poor, repeat-rich regions. In fungi, the repeat-rich regions may be subjected to a process termed repeat-induced point mutation (RIP). Both repeat activity and RIP are thought to play a significant role in evolution of secreted virulence proteins, termed effectors. We present a complete genome sequence of S. sclerotiorum generated using Single Molecule Real-Time Sequencing technology with highly accurate annotations produced using an extensive RNA sequencing data set. We identified 70 effector candidates and have highlighted their in planta expression profiles. Furthermore, we characterized the genome architecture of S. sclerotiorum in comparison to plant pathogens that exhibit “two-speed” genomes. We show that there is a significant association between positions of secreted proteins and regions with a high RIP index in S. sclerotiorum but we did not detect a correlation between secreted protein proportion and GC content. Neither did we detect a negative correlation between CDS content and secreted protein proportion across the S. sclerotiorumgenome. We conclude that S. sclerotiorum exhibits subtle signatures of enhanced mutation of secreted proteins in specific genomic compartments as a result of transposition and RIP activity. However, these signatures are not observable at the whole-genome scale.

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Storify: #pathpopgen Population Genomics of Fungal and Oomycete Diseases of Animals and Plants, Ascona, 7-11 May 2017

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mBio: The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat (2016)

mBio: The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat (2016) | Plant Pathogenomics | Scoop.it

Fungal plant pathogens rapidly evolve virulence on resistant hosts through mutations in genes encoding proteins that modulate the host immune responses. The mutational spectrum likely includes chromosomal rearrangements responsible for gains or losses of entire genes. However, the mechanisms creating adaptive structural variation in fungal pathogen populations are poorly understood. We used complete genome assemblies to quantify structural variants segregating in the highly polymorphic fungal wheat pathogen Zymoseptoria tritici. The genetic basis of virulence in Z. tritici is complex, and populations harbor significant genetic variation for virulence; hence, we aimed to identify whether structural variation led to functional differences. We combined single-molecule real-time sequencing, genetic maps, and transcriptomics data to generate a fully assembled and annotated genome of the highly virulent field isolate 3D7. Comparative genomics analyses against the complete reference genome IPO323 identified large chromosomal inversions and the complete gain or loss of transposable-element clusters, explaining the extensive chromosomal-length polymorphisms found in this species. Both the 3D7 and IPO323 genomes harbored long tracts of sequences exclusive to one of the two genomes. These orphan regions contained 296 genes unique to the 3D7 genome and not previously known for this species. These orphan genes tended to be organized in clusters and showed evidence of mutational decay. Moreover, the orphan genes were enriched in genes encoding putative effectors and included a gene that is one of the most upregulated putative effector genes during wheat infection. Our study showed that this pathogen species harbored extensive chromosomal structure polymorphism that may drive the evolution of virulence.

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MPP: High‐resolution mapping of the recombination landscape of the phytopathogen Fusarium graminearum suggests two‐speed genome evolution (2017)

MPP: High‐resolution mapping of the recombination landscape of the phytopathogen Fusarium graminearum suggests two‐speed genome evolution (2017) | Plant Pathogenomics | Scoop.it

Recombination is a major evolutionary force, increasing genetic diversity and permitting efficient coevolution of fungal pathogen(s) with their host(s). The ascomycete Fusarium graminearum is a devastating pathogen of cereal crops, and can contaminate food and feed with harmful mycotoxins. Previous studies have suggested a high adaptive potential of this pathogen, illustrated by an increase in pathogenicity and resistance to fungicides. In this study, we provide the first detailed picture of the crossover events occurring during meiosis and discuss the role of recombination in pathogen evolution. An experimental recombinant population (n = 88) was created and genotyped using 1306 polymorphic markers obtained from restriction site-associated DNA sequencing (RAD-seq) and aligned to the reference genome. The construction of a high-density linkage map, anchoring 99% of the total length of the reference genome, allowed the identification of 1451 putative crossovers, positioned at a median resolution of 24 kb. The majority of crossovers (87.2%) occurred in a relatively small portion of the genome (30%). All chromosomes demonstrated recombination-active sections, which had a near 15-fold higher crossover rate than non-active recombinant sections. The recombination rate showed a strong positive correlation with nucleotide diversity, and recombination-active regions were enriched for genes with a putative role in host–pathogen interaction, as well as putative diversifying genes. Our results confirm the preliminary analysis observed in other F. graminearum strains and suggest a conserved ‘two-speed’ recombination landscape. The consequences with regard to the evolutionary potential of this major fungal pathogen are also discussed.

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BMC Biology: Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae (2016)

BMC Biology: Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae (2016) | Plant Pathogenomics | Scoop.it

Background. In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated wheat area in Bangladesh, with yield losses reaching up to 100 %. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields.

Results. Reinoculation of seedlings with strains isolated from infected wheat grains showed wheat blast symptoms on leaves of wheat but not rice. Our phylogenomic and population genomic analyses revealed that the wheat blast outbreak in Bangladesh was most likely caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae.

Conclusion. Our findings suggest that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent.

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bioRxiv: Multiple reference genome sequences of hot pepper reveal the massive evolution of plant disease resistance genes by retroduplication (2017)

bioRxiv: Multiple reference genome sequences of hot pepper reveal the massive evolution of plant disease resistance genes by retroduplication (2017) | Plant Pathogenomics | Scoop.it

Transposable elements (TEs) provide major evolutionary forces leading to new genome structure and species diversification. However, the role of TEs in the expansion of disease resistance gene families has been unexplored in plants. Here, we report high-quality de novo genomes for two peppers (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum). Dynamic genome rearrangements involving translocations among chromosome 3, 5 and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs exhibited great abundance across the angiosperms, with most cases lineage-specific and thus recent events. Our study revealed that retroduplication has played key roles in the emergence of new disease-resistance genes in plants.

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eLife: Codon optimization underpins generalist parasitism in fungi (2017)

eLife: Codon optimization underpins generalist parasitism in fungi (2017) | Plant Pathogenomics | Scoop.it

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 parasite. 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.

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Arjen ten Have's curator insight, February 15, 9:39 AM
Does this suggest specialists do not have the time to evolve codon optimization? Evolution does not cease to surprise me!
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Genome Biol Evol: Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms (2017)

Genome Biol Evol: Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms (2017) | Plant Pathogenomics | Scoop.it

Phytophthora megakarya (Pmeg) and P. palmivora (Ppal) are closely related species causing cacao black pod rot. While Ppal is a cosmopolitan pathogen, cacao is the only known host of economic importance for Pmeg. Pmeg is more virulent on cacao than Ppal. We sequenced and compared the Pmeg and Ppal genomes and identified virulence-related putative gene models (PGeneM) that may be responsible for their differences in host specificities and virulence. Pmeg and Ppal have estimated genome sizes of 126.88 and 151.23 Mb and PGeneM numbers of 42,036 and 44,327, respectively. The evolutionary histories of Pmeg and Ppal appear quite different. Post-speciation, Ppal underwent whole-genome duplication whereas Pmeg has undergone selective increases in PGeneM numbers, likely through accelerated transposable element driven duplications. Many PGeneMs in both species failed to match transcripts and may represent pseudogenes or cryptic genetic reservoirs. Pmeg appears to have amplified specific gene families, some of which are virulence-related. Analysis of mycelium, zoospore and in planta transcriptome expression profiles using neural network self-organizing map analysis generated 24 multi-variate and non-linear self-organizing map classes. Many members of the RxLR, NPP, and pectinase genes families were specifically induced in planta. Pmeg displays a diverse virulence-related gene complement similar in size to and potentially of greater diversity than Ppal but it remains likely that the specific functions of the genes determine each species’ unique characteristics as pathogens.

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Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens (2016)

Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens (2016) | Plant Pathogenomics | Scoop.it

An organism’s adaptation to changing environments is fueled by its genetic variability, which is established by mechanisms ranging from single-nucleotide polymorphisms to large-scale structural variations, all of which affect chromosomal shape, organization, and gene content [1]. These processes are particularly relevant for pathogens that must respond to continual selection pressure arising from host immune systems that evolved to detect the presence or activity of potential microbial pathogens through a variety of invasion patterns [2]. In their adaptive response, pathogens evolve strategies, often involving secreted effector molecules, to overcome host immunity and support host colonization [3]. Thus, it can be anticipated that this coevolutionary arms race leads to highly specific interactions between adapted pathogens and their specific hosts. Paradoxically, particular pathogens successfully colonize a broad range of hosts, yet how such pathogens cope in arms races with such a diversity of hosts remains unknown.

 

A structured genome drives adaptive evolution. It has been proposed that filamentous fungal and oomycete plant pathogens often evolved structured genomes with two distinct types of genomic regions: (1) gene-rich regions containing slowly evolving genes that mediate general physiology and (2) gene-poor regions that are dynamic and enriched for repetitive DNA such as transposable elements (TEs) and virulence-related genes that often display signs of accelerated evolution [4,5]. Extensive structural variation often occurs in these fast-evolving regions, leading to translocation, duplication, or loss of genetic material [1,4,5]. The highly dynamic regions can either be embedded within the core chromosomes or be located on separate chromosomes that often display presence/absence variations within a population, known as conditionally dispensable or accessory chromosomes [4,6]. The common occurrence of these bipartite genomes led to the “two-speed” model for pathogen genome evolution [4], suggesting that specific regions form sites of rapid genomic diversification to facilitate coevolution during host interactions [1,4,5].

 

Transposable elements shape “two-speed” genomes. It is generally observed that the dynamic regions of two-speed genomes are enriched in TEs, yet it remains undemonstrated how they mechanistically contribute to genome variability [1,4,5]. Recently, the contribution of TEs towards the evolution of the two-speed genome in the vascular wilt pathogen Verticillium dahliae was reported [7]. Extensive genome rearrangements are generated by double-strand repair pathways that erroneously utilize stretches of homologous sequence at an unlinked locus, the majority of which occur around TEs simply as a consequence of their abundance and sequence similarity (Fig 1A) [7]. Genomic rearrangements often occur at dynamic regions that are enriched for recent segmental duplications, generating genetic material subject to evolutionary diversification, e.g., by reciprocal gene loss (Fig 1A) [7,8]. Furthermore, these dynamic regions are enriched in in planta induced effectors [8] and evolutionary young and “active” TEs (Fig 1B). These TEs likely contribute to accelerated genomic diversification of dynamic effector regions [7].

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BMC Genomics: Diversity, evolution and expression profiles of histone acetyltransferases and deacetylases in oomycetes (2016)

BMC Genomics: Diversity, evolution and expression profiles of histone acetyltransferases and deacetylases in oomycetes (2016) | Plant Pathogenomics | Scoop.it

Background - Oomycetes are a group of fungus-like eukaryotes with diverse microorganisms living in marine, freshwater and terrestrial environments. Many of them are important pathogens of plants and animals, causing severe economic losses. Based on previous study, gene expression in eukaryotic cells is regulated by epigenetic mechanisms such as DNA methylation and histone modification. However, little is known about epigenetic mechanisms of oomycetes.

 

Results - In this study, we investigated the candidate genes in regulating histone acetylation in oomycetes genomes through bioinformatics approaches and identified a group of diverse histone acetyltransferases (HATs) and histone deacetylases (HDACs), along with three putative novel HATs. Phylogenetic analyses suggested that most of these oomycetes HATs and HDACs derived from distinct evolutionary ancestors. Phylogenetic based analysis revealed the complex and distinct patterns of duplications and losses of HATs and HDACs in oomycetes. Moreover, gene expression analysis unveiled the specific expression patterns of the 33 HATs and 11 HDACs of Phytophthora infestans during the stages of development, infection and stress response.

 

Conclusions - In this study, we reveal the structure, diversity and the phylogeny of HATs and HDACs of oomycetes. By analyzing the expression data, we provide an overview of the specific biological stages of these genes involved. Our datasets provide useful inputs to help explore the epigenetic mechanisms and the relationship between genomes and phenotypes of oomycetes.

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Genome Biology and Evolution: A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi (2016)

Genome Biology and Evolution: A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi (2016) | Plant Pathogenomics | Scoop.it

Smut fungi are plant pathogens mostly parasitizing wild species of grasses as well as domesticated cereal crops. Genome analysis of several smut fungi including Ustilago maydis revealed a singular clustered organization of genes encoding secreted effectors. In U. maydis, many of these clusters have a role in virulence. Reconstructing the evolutionary history of clusters of effector genes is difficult because of their intrinsically fast evolution, which erodes the phylogenetic signal and homology relationships. Here, we describe the use of comparative evolutionary analyses of quality draft assemblies of genomes to study the mechanisms of this evolution. We report the genome sequence of a South African isolate of Sporisorium scitamineum, a smut fungus parasitizing sugar cane with a phylogenetic position intermediate to the two previously sequenced species U. maydisand Sporisorium reilianum. We show that the genome of S. scitamineumcontains more and larger gene clusters encoding secreted effectors than any previously described species in this group. We trace back the origin of the clusters and find that their evolution is mainly driven by tandem gene duplication. In addition, transposable elements play a major role in the evolution of the clustered genes. Transposable elements are significantly associated with clusters of genes encoding fast evolving secreted effectors. This suggests that such clusters represent a case of genome compartmentalization that restrains the activity of transposable elements on genes under diversifying selection for which this activity is potentially beneficial, while protecting the rest of the genome from its deleterious effect.

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Bridget Barker's curator insight, February 2, 11:17 AM
Using this for my microbial ecology course
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PLOS ONE: Hidden Genetic Diversity in an Asexually Reproducing Lichen Forming Fungal Group (2016)

PLOS ONE: Hidden Genetic Diversity in an Asexually Reproducing Lichen Forming Fungal Group (2016) | Plant Pathogenomics | Scoop.it

Asexual species with vegetative propagation of both symbiont partners (soredia) in lichens may harbor lower species diversity because they may indeed represent evolutionary dead ends or clones. In this study we aim to critically examine species boundaries in the sorediate lichen forming fungi Parmotrema reticulatum–Parmotrema pseudoreticulatum complex applying coalescent-based approaches and other recently developed DNA-based methods. To this end, we gathered 180 samples from Africa, Asia, Australasia, Europe, North and South America and generated sequences of internal transcribed spacer of nuclear ribosomal DNA (ITS) and DNA replication licensing factor MCM7 (MCM7). The dataset was analysed using different approaches such as traditional phylogeny–maximum likelihood and Bayesian–genetic distances, automatic barcode gap discovery and coalescent-based methods–PTP, GMYC, spedeSTEM and *Beast–in order to test congruence among results. Additionally, the divergence times were also estimated to elucidate diversification events. Delimitations inferred from the different analyses are comparable with only minor differences, and following a conservative approach we propose that the sampled specimens of the PreticulatumPpseudoreticulatum complex belong to at least eight distinct species-level lineages. Seven are currently classified under Preticulatum and one as Ppseudoreticulatum. In this work we discuss one of only few examples of cryptic species that have so far been found in sorediate reproducing lichen forming fungi. Additionally our estimates suggest a recent origin of the species complex–during the Miocene. Consequently, the wide distribution of several of the cryptic species has to be explained by intercontinental long-distance dispersal events.

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bioRxiv: Gene flow between divergent cereal- and grass-specific lineages of the rice blast fungus Magnaporthe oryzae (2017)

bioRxiv: Gene flow between divergent cereal- and grass-specific lineages of the rice blast fungus Magnaporthe oryzae (2017) | Plant Pathogenomics | Scoop.it

Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity, and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multi-host pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae, and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously-used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae. These findings provide greater understanding of the eco-evolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multi-host pathogen.

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BMC Biology: Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors (2017)

BMC Biology: Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors (2017) | Plant Pathogenomics | Scoop.it

Background. Plant-pathogenic oomycetes are responsible for economically important losses in crops worldwide. Phytophthora palmivora, a tropical relative of the potato late blight pathogen, causes rotting diseases in many tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus.

 

Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped in understanding how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce.

 

Results. We employed the model plant Nicotiana benthamiana to study the P. palmivora root infections at the cellular and molecular levels. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features.

 

Conclusions. These results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection-relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.

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Genetics: Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae (2015)

Genetics: Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae (2015) | Plant Pathogenomics | Scoop.it

Sex chromosomes in plants and animals and fungal mating-type chromosomes often show exceptional genome features, with extensive suppression of homologous recombination and cytological differentiation between members of the diploid chromosome pair. Despite strong interest in the genetics of these chromosomes, their large regions of suppressed recombination often are enriched in transposable elements and therefore can be challenging to assemble. Here we show that the latest improvements of the PacBio sequencing yield assembly of the whole genome of the anther-smut fungus, Microbotryum lychnidis-dioicae (the pathogenic fungus causing anther-smut disease of Silene latifolia), into finished chromosomes or chromosome arms, even for the repeat-rich mating-type chromosomes and centromeres. Suppressed recombination of the mating-type chromosomes is revealed to span nearly 90% of their lengths, with extreme levels of rearrangements, transposable element accumulation, and differentiation between the two mating types. We observed no correlation between allelic divergence and physical position in the nonrecombining regions of the mating-type chromosomes. This may result from gene conversion or from rearrangements of ancient evolutionary strata, i.e., successive steps of suppressed recombination. Centromeres were found to be composed mainly of copia-like transposable elements and to possess specific minisatellite repeats identical between the different chromosomes. We also identified subtelomeric motifs. In addition, extensive signs of degeneration were detected in the nonrecombining regions in the form of transposable element accumulation and of hundreds of gene losses on each mating-type chromosome. Furthermore, our study highlights the potential of the latest breakthrough PacBio chemistry to resolve complex genome architectures.

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Frontiers: Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution (2017)

Frontiers: Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution (2017) | Plant Pathogenomics | Scoop.it

Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution.

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#PlantPathogenomics Training School of the COST Action SUSTAIN, 2017 (with images, tweets)

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bioRxiv: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2017)

bioRxiv: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2017) | Plant Pathogenomics | Scoop.it

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are an expanding threat to crops, wild animals and natural ecosystems (Fisher et al. 2012, Kupferschmidt 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl and Thomma 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 (Cooke et al. 2012, Yoshida et al. 2013, Yoshida et al. 2014). Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by compared sibling strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Forbes et al. 1997, Oyarzun et al. 1998, Delgado et al. 2013, Yoshida et al. 2013, Yoshida et al. 2014). We detected numerous examples of structural variation, nucleotide polymorphisms and gene conversion within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. These results highlight the exceptional genetic and phenotypic plasticity that underpins host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen.

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bioRxiv: Ancient duplication and horizontal transfer of a toxin gene cluster reveals novel mechanisms in the cercosporin biosynthesis pathway (2017)

bioRxiv: Ancient duplication and horizontal transfer of a toxin gene cluster reveals novel mechanisms in the cercosporin biosynthesis pathway (2017) | Plant Pathogenomics | Scoop.it

Cercospora species have a global distribution and are best known as the causal agents of leaf spot diseases of many crops. Cercospora leaf spot (CLS) is an economically devastating disease of sugar beet caused by C. beticola. The C. beticola genome encodes 63 biosynthetic gene clusters, including the cercosporin toxin biosynthesis (CTB) cluster. Studies spanning nearly 60 years have shown that cercosporin is photo-activated, critical for disease development, and toxic to most organisms except Cercospora spp. themselves, which exhibit cercosporin auto-resistance. We show that the CTB gene cluster has experienced an unprecedented number of duplications, losses, and horizontal transfers across a spectrum of plant pathogenic fungi. Although cercosporin biosynthesis has been widely assumed to rely on the eight gene CTB cluster, our comparative genomic analysis revealed extensive gene collinearity adjacent to the established cluster in all CTB cluster-harboring species. We demonstrate that the CTB cluster is larger than previously recognized and includes the extracellular proteins fasciclin and laccase required for cercosporin biosynthesis and the final pathway enzyme that installs the unusual cercosporin methylenedioxy bridge. Additionally, the expanded cluster contains CFP, which contributes to cercosporin auto-resistance in C. beticola. Together, our results give new insight on the intricate evolution of the CTB cluster.

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Genome Biology: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species (2017)

Genome Biology: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species (2017) | Plant Pathogenomics | Scoop.it

Background. The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species.


Results. To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes.


Conclusions. Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution.

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bioRxiv: Time-resolved dual root-microbe transcriptomics reveals early induced Nicotiana benthamiana genes and conserved infection-promoting Phytophthora palmivora effectors (2017)

bioRxiv: Time-resolved dual root-microbe transcriptomics reveals early induced Nicotiana benthamiana genes and conserved infection-promoting Phytophthora palmivora effectors (2017) | Plant Pathogenomics | Scoop.it

Background. Plant-pathogenic oomycetes are responsible for economically important losses on crops worldwide. Phytophthora palmivora, a broad-host-range tropical relative of the potato late blight pathogen, causes rotting diseases in many important tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus. Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped understanding of how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce.

 

Results. We employed the model plant Nicotiana benthamiana to study the P. palmivora root infections at the cellular and molecular level. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features.

Conclusions. These results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.

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MPMI: Changing ploidy as a strategy; the Irish potato Famine pathogen shifts ploidy in relation to its sexuality (2016)

MPMI: Changing ploidy as a strategy; the Irish potato Famine pathogen shifts ploidy in relation to its sexuality (2016) | Plant Pathogenomics | Scoop.it

The oomycete Phytophthora infestans was the causal agent of the Irish Great Famine and is a recurring threat to global food security. The pathogen can reproduce both sexually and asexually, with high potential to adapt to various environments and great risk to break disease resistance genes in potato. As other oomycetes, P. infestans is regarded to be diploid during the vegetative phase of its life cycle, although some studies reported trisomy, and polyploidy. Using microsatellite fingerprinting, genome-wide assessment of SNP polymorphism, nuclear DNA quantification, and microscopic counting of chromosome numbers we assessed the ploidy level of isolates. All progeny from sexual populations of P. infestans in nature were found to be diploid, in contrast nearly all dominant asexual lineages, including the most important pandemic clonal lineages US-1 and 13_A2 were triploid. Such triploids possess significantly more allelic variation than diploids. We observed that triploid genotype can change to a diploid genome constitution when exposed to artificial stress conditions. This study reveals that fluctuations in the ploidy level maybe a key factor in the adaptation process of this notorious plant destroyer and imposes an extra challenge to control this disease.

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Bridget Barker's curator insight, February 15, 10:42 AM
Ploidy and sexual recombination have implications for pathogenesis 
Rescooped by Kamoun Lab @ TSL from plant microbe interaction genomics
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bioRxiv: The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only (2016)

bioRxiv: The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only (2016) | Plant Pathogenomics | Scoop.it

The ability to quickly obtain accurate genome sequences of eukaryotic pathogens at low costs provides a tremendous opportunity to identify novel targets for therapeutics, develop pesticides with increased target specificity and breed for resistance in food crops. Here, we present the first report of the ~54 MB eukaryotic genome sequence of Rhizoctonia solani, an important pathogenic fungal species of maize, using nanopore technology. Moreover, we show that optimizing the strategy for wet-lab procedures aimed to isolate high quality and ultra-pure high molecular weight (HMW) DNA results in increased read length distribution and thereby allowing generation of the most contiguous genome assembly for R. solani to date. We further determined sequencing accuracy and compared the assembly to short-read technologies. With the current sequencing technology and bioinformatics tool set, we are able to deliver an eukaryotic fungal genome at low cost within a week. With further improvements of the sequencing technology and increased throughput of the PromethION sequencer we aim to generate near-finished assemblies of large and repetitive plant genomes and cost-efficiently perform de novo sequencing of large collections of microbial pathogens and the microbial communities that surround our crops.


Via Steve Marek, Jessie Uehling
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Scientific Reports: Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment (2016)

Scientific Reports: Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment (2016) | Plant Pathogenomics | Scoop.it

Understanding the processes that shaped contemporary pathogen populations in agricultural landscapes is quite important to define appropriate management strategies and to support crop improvement efforts. Here, we took advantage of an historical record to examine the adaptation pathway of the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo) in a semi-isolated environment represented in the Philippine archipelago. By comparing genomes of key Xoo groups we showed that modern populations derived from three Asian lineages. We also showed that diversification of virulence factors occurred within each lineage, most likely driven by host adaptation, and it was essential to shape contemporary pathogen races. This finding is particularly important because it expands our understanding of pathogen adaptation to modern agriculture.


Via dromius
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