Plant Pathogenomics
51.2K views | +2 today
Follow
 
Scooped by Kamoun Lab @ TSL
onto Plant Pathogenomics
Scoop.it!

New Phytologist: Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi (2012)

New Phytologist: Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi (2012) | Plant Pathogenomics | Scoop.it

 

Hemibiotrophic fungal plant pathogens represent a group of agronomically significant disease-causing agents that grow first on living tissue and then cause host death in later, necrotrophic growth. Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes of genes in the genomes of phytopathogenic Colletotrichum, especially those associated with specific stages of hemibiotrophy, can provide insights on how these pathogens infect a large number of hosts.The genomes of Colletotrichum orbiculare, which infects cucurbits and Nicotiana benthamiana, and C. gloeosporioides, which infects a wide range of crops, were sequenced and analyzed, focusing on features with potential roles in pathogenicity. Regulation ofC. orbiculare gene expression was investigated during infection of N. benthamiana using a custom microarray.Genes expanded in both genomes compared to other fungi included sequences encoding small, secreted proteins (SSPs), secondary metabolite synthesis genes, proteases and carbohydrate-degrading enzymes. Many SSP and secondary metabolite synthesis genes were upregulated during initial stages of host colonization, whereas the necrotrophic stage of growth is characterized by upregulation of sequences encoding degradative enzymes.Hemibiotrophy in C. orbiculare is characterized by distinct stage-specific gene expression profiles of expanded classes of potential pathogenicity genes.
more...
No comment yet.
Plant Pathogenomics
Everything related to plant pathogen genomics
Your new post is loading...
Your new post is loading...
Scooped by Kamoun Lab @ TSL
Scoop.it!

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

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 Bghgenome. 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.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

BMC Genomics: Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews (2017)

BMC Genomics: Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews (2017) | Plant Pathogenomics | Scoop.it

Background. Downy mildew, caused by the oomycete pathogen Sclerospora graminicola, is an economically important disease of Gramineae crops including foxtail millet (Setaria italica). Plants infected with S. graminicola are generally stunted and often undergo a transformation of flower organs into leaves (phyllody or witches’ broom), resulting in serious yield loss. To establish the molecular basis of downy mildew disease in foxtail millet, we carried out whole-genome sequencing and an RNA-seq analysis of S. graminicola.

 

Results. Sequence reads were generated from S. graminicola using an Illumina sequencing platform and assembled de novo into a draft genome sequence comprising approximately 360 Mbp. Of this sequence, 73% comprised repetitive elements, and a total of 16,736 genes were predicted from the RNA-seq data. The predicted genes included those encoding effector-like proteins with high sequence similarity to those previously identified in other oomycete pathogens. Genes encoding jacalin-like lectin-domain-containing secreted proteins were enriched in S. graminicola compared to other oomycetes. Of a total of 1220 genes encoding putative secreted proteins, 91 significantly changed their expression levels during the infection of plant tissues compared to the sporangia and zoospore stages of the S. graminicola lifecycle.

 

Conclusions. We established the draft genome sequence of a downy mildew pathogen that infects Gramineae plants. Based on this sequence and our transcriptome analysis, we generated a catalog of in planta-induced candidate effector genes, providing a solid foundation from which to identify the effectors causing phyllody.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

Advances in Genetics: Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens (2017)

Advances in Genetics: Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens (2017) | Plant Pathogenomics | Scoop.it

An unprecedented number of pathogenic fungi are emerging and causing disease in animals and plants, putting the resilience of wild and managed ecosystems in jeopardy. While the past decades have seen an increase in the number of pathogenic fungi, they have also seen the birth of new big data technologies and analytical approaches to tackle these emerging pathogens. We review how the linked fields of genomics and epigenomics are transforming our ability to address the challenge of emerging fungal pathogens. We explore the methodologies and bioinformatic toolkits that currently exist to rapidly analyze the genomes of unknown fungi, then discuss how these data can be used to address key questions that shed light on their epidemiology. We show how genomic approaches are leading a revolution into our understanding of emerging fungal diseases and speculate on future approaches that will transform our ability to tackle this increasingly important class of emerging pathogens.

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plant Pathogens
Scoop.it!

Molecular Plant: PacBio Sequencing Reveals Transposable Element as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae (2017)

Molecular Plant: PacBio Sequencing Reveals Transposable Element as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae (2017) | Plant Pathogenomics | Scoop.it
We deployed single molecule real-time (SMRT) sequencing developed by Pacific BioSciences (PacBio), to generate near complete genome assembly for M. oryzae field isolates FJ81278 and Guy11, and evaluated the possible contribution of TEs to genomic variation events such as chromosomal translocation, gene presence/absence in LS regions and virulence-associated secreted proteins (SPs) polymorphism.

Via Philip Carella, Elsa Ballini, Yogesh Gupta
more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plant pathogenic fungi
Scoop.it!

bioRxiv: The genomic rate of adaptation in the fungal wheat pathogen Zymoseptoria tritici (2017)

bioRxiv: The genomic rate of adaptation in the fungal wheat pathogen Zymoseptoria tritici (2017) | Plant Pathogenomics | Scoop.it

Antagonistic host-pathogen co-evolution is a determining factor in the outcome of infection and shapes genetic diversity at the population level of both partners. Little is known about the overall genomic rate of evolution in pathogens or the molecular bases of rapid adaptation. Here we apply a population genomic approach to infer genome-wide patterns of selection among thirteen isolates of the fungal pathogen Zymoseptoria tritici. Based on whole genome alignments, we report extensive presence-absence polymorphisms of genes resulting from a high extent of within population karyotypic variation. We apply different test statistics based on the distribution of non-synonymous and synonymous polymorphisms (pN/pS) and substitutions (dN/dS) to estimate rates of adaptation and identify specific targets of selection. Overall we estimate that 44% of substitutions in the proteome of Z. tritici are adaptive and we find that the rate of adaptation is positively correlated with recombination rate. The proportion of adaptive amino acid substitutions in genes encoding determinants of pathogenicity is as high as 68% underlining the importance of positive selection in the evolution of virulence-associated traits. Using a maximum likelihood approach and codon models we furthermore identify a set of 786 additional genes showing signatures of diversifying selection. We furthermore addressed the effect of different parameters on adaptation using a linear model with pN/pS as response variable. Our results point to an increased effectiveness of purifying selection with increased recombination rate and high gene density. Overall we show a central role of sexual recombination in protein evolution in this important wheat pathogen.


Via Steve Marek
more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

bioRxiv: Positively selected effector genes and their contribution to virulence in the smut fungus Sporisorium reilianum (2017)

bioRxiv: Positively selected effector genes and their contribution to virulence in the smut fungus Sporisorium reilianum (2017) | Plant Pathogenomics | Scoop.it

Plants and fungi display a broad range of interactions within natural and agricultural ecosystems ranging from symbiosis to parasitism. Pathogenic interactions are governed by secreted fungal effector proteins, which are thought to coevolve with their host targets. Biotrophic smut fungi which belong to the division of Basidiomycota are well-suited to investigate the evolution of plant pathogens, because several quality draft genomes and genetic tools are available for these species. Here, we used the genomes of Sporisorium reilianum f. sp. zeae and S. reilianum f. sp. reilianum, two closely related formae speciales infecting maize and sorghum, respectively, together with the genomes of Ustilago hordei, U. maydis and S. scitamineum to identify effector genes showing signs of positive selection. The largest numbers of such genes were identified in the two pathovariants of S. reilianum and between paralogues in U. hordei, where many belong to families showing species-specific expansions. Next, we assessed the contribution to virulence of candidate effector genes in S. reilianum f. sp. zeae by deletion of individual genes in a solopathogenic strain. While eight of nine deletions mutants were unaffected in virulence, one mutant had lost virulence. This shows that despite the relatively recent divergent time of the two formae speciales, a signature of positive selection in candidate effector genes in S. reilianum is a poor indicator for the identification of genes with virulence functions.

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Adaptive Evolution and Speciation
Scoop.it!

Nature Reviews Microbiology: Evolution and genome architecture in fungal plant pathogens (2017)

Nature Reviews Microbiology: Evolution and genome architecture in fungal plant pathogens (2017) | Plant Pathogenomics | Scoop.it

The fungal kingdom comprises some of the most devastating plant pathogens. Sequencing the genomes of fungal pathogens has shown a remarkable variability in genome size and architecture. Population genomic data enable us to understand the mechanisms and the history of changes in genome size and adaptive evolution in plant pathogens. Although transposable elements predominantly have negative effects on their host, fungal pathogens provide prominent examples of advantageous associations between rapidly evolving transposable elements and virulence genes that cause variation in virulence phenotypes. By providing homogeneous environments at large regional scales, managed ecosystems, such as modern agriculture, can be conducive for the rapid evolution and dispersal of pathogens. In this Review, we summarize key examples from fungal plant pathogen genomics and discuss evolutionary processes in pathogenic fungi in the context of molecular evolution, population genomics and agriculture.


Via Ronny Kellner
more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

Genome Biology and Evolution: Evolution of Transcription Activator-Like Effectors in Xanthomonas oryzae (2017)

Genome Biology and Evolution: Evolution of Transcription Activator-Like Effectors in  Xanthomonas oryzae  (2017) | Plant Pathogenomics | Scoop.it

Transcription activator-like effectors (TALEs) are secreted by plant–pathogenic Xanthomonas bacteria into plant cells where they act as transcriptional activators and, hence, are major drivers in reprogramming the plant for the benefit of the pathogen. TALEs possess a highly repetitive DNA-binding domain of typically 34 amino acid (AA) tandem repeats, where AA 12 and 13, termed repeat variable di-residue (RVD), determine target specificity. Different Xanthomonas strains possess different repertoires of TALEs. Here, we study the evolution of TALEs from the level of RVDs determining target specificity down to the level of DNA sequence with focus on rice-pathogenic Xanthomonas oryzae pv. oryzae(Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) strains. We observe that codon pairs coding for individual RVDs are conserved to a similar degree as the flanking repeat sequence. We find strong indications that TALEs may evolve 1) by base substitutions in codon pairs coding for RVDs, 2) by recombination of N-terminal or C-terminal regions of existing TALEs, or 3) by deletion of individual TALE repeats, and we propose possible mechanisms. We find indications that the reassortment of TALE genes in clusters is mediated by an integron-like mechanism in Xoc. We finally study the effect of the presence/absence and evolutionary modifications of TALEs on transcriptional activation of putative target genes in rice, and find that even single RVD swaps may lead to considerable differences in activation. This correlation allowed a refined prediction of TALE targets, which is the crucial step to decipher their virulence activity.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

bioRxiv: Genomics-enabled analysis of the emergent disease cotton bacterial blight (2017)

bioRxiv: Genomics-enabled analysis of the emergent disease cotton bacterial blight (2017) | Plant Pathogenomics | Scoop.it

Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv. malvacearum (Xcm) strains. Illumina based draft genomes were generated for thirteen Xcm isolates and analyzed along with 4 previously published Xcm genomes. These genomes encode 24 conserved and nine variable type three effectors. Strains in the race 18 clade contain 3 to 5 more effectors than other Xcm strains. SMRT sequencing of two geographically and temporally diverse strains of Xcm yielded circular chromosomes and accompanying plasmids. These genomes encode eight and thirteen distinct transcription activator-like effector genes. RNA-sequencing revealed 52 genes induced within two cotton cultivars by both tested Xcm strains. This gene list includes a homeologous pair of genes, with homology to the known susceptibility gene, MLO. In contrast, the two strains of Xcm induce different clade III SWEET sugar transporters. Subsequent genome wide analysis revealed patterns in the overall expression of homeologous gene pairs in cotton after inoculation by Xcm. These data reveal host-pathogen specificity at the genetic level and strategies for future development of resistant cultivars.

more...
No comment yet.
Rescooped by Kamoun Lab @ TSL from Plant pathogenic fungi
Scoop.it!

Microbiology Spectrum: Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution (2017)

Microbiology Spectrum: Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution (2017) | Plant Pathogenomics | Scoop.it
The ability of an organism to replicate and segregate its genome with high fidelity is vital to its survival and for the production of future generations. Errors in either of these steps (replication or segregation) can lead to a change in ploidy or chromosome number. While these drastic genome changes can be detrimental to the organism, resulting in decreased fitness, they can also provide increased fitness during periods of stress. A change in ploidy or chromosome number can fundamentally change how a cell senses and responds to its environment. Here, we discuss current ideas in fungal biology that illuminate how eukaryotic genome size variation can impact the organism at a cellular and evolutionary level. One of the most fascinating observations from the past 2 decades of research is that some fungi have evolved the ability to tolerate large genome size changes and generate vast genomic heterogeneity without undergoing canonical meiosis.

Via Niklaus Grunwald, Steve Marek
more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

bioRxiv: Extremely flexible infection programs in a fungal plant pathogen (2017)

bioRxiv: Extremely flexible infection programs in a fungal plant pathogen (2017) | Plant Pathogenomics | Scoop.it

Filamentous plant pathogens exhibit extraordinary levels of genomic variability that is proposed to facilitate rapid adaptation to changing host environments. However, the impact of genomic variation on phenotypic differentiation in pathogen populations is largely unknown. Here, we address the extent of variability in infection phenotypes of the hemibiotrophic wheat pathogen Zymoseptoria tritici by studying three field isolates collected in Denmark, Iran, and the Netherlands. These three isolates differ extensively in genome structure and gene content, but produce similar disease symptoms in the same susceptible wheat cultivar. Using advanced confocal microscopy, staining of reactive oxygen species, and comparative analyses of infection stage-specific RNA-seq data, we demonstrate considerable variation in the temporal and spatial course of infection of the three isolates. Based on microscopic observation, we determined four core infection stages: establishment, biotrophic growth, lifestyle transition, and necrotrophic growth and asexual reproduction. Comparative analyses of the fungal transcriptomes, sequenced for every infection stage, revealed that the gene expression profiles of the isolates differed significantly, and 20% of the genes are differentially expressed between the three isolates during infection. The genes exhibiting isolate-specific expression patterns are enriched in genes encoding effector candidates that are small, secreted, cysteine-rich proteins and putative virulence determinants. Moreover, the differentially expressed genes were located significantly closer to transposable elements, which are enriched for the heterochromatin-associated histone marks H3K9me3 and H3K27me3 on the accessory chromosomes. This observation indicates that transposable elements and epigenetic regulation contribute to the infection-associated transcriptional variation between the isolates. Our findings illustrate how high genetic diversity in a pathogen population can result in highly differentiated infection and expression phenotypes that can support rapid adaptation in changing environments. Furthermore, our study reveals an exceptionally high extent of plasticity in the infection program of an important wheat pathogen and shows a substantial redundancy in infection-related gene expression.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

bioRxiv: Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions (2017)

bioRxiv: Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions (2017) | Plant Pathogenomics | Scoop.it

Filamentous plant pathogen genomes often display a bipartite architecture with gene sparse, repeat-rich compartments serving as a cradle for adaptive evolution. However, the extent to which this "two-speed" genome architecture is associated with genome-wide epigenetic modifications is unknown. Here, we show that the oomycete plant pathogens Phytophthora infestans and Phytophthora sojae possess functional adenine N6-methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine (5mC) could not be detected in the two Phytophthora species. Methylated DNA IP Sequencing (MeDIP-seq) of each species revealed that 6mA is depleted around the transcriptional starting sites (TSS) and is associated with low expressed genes, particularly transposable elements. Remarkably, genes occupying the gene-sparse regions have higher levels of 6mA compared to the remainder of both genomes, possibly implicating the methylome in adaptive evolution of Phytophthora. Among three putative adenine methyltransferases, DAMT1 and DAMT3 displayed robust enzymatic activities. Surprisingly, single knockouts of each of the 6mA methyltransferases in P. sojae significantly reduced in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the damt3 mutant revealed uneven patterns of 6mA methylation across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Our findings provide evidence that 6mA modification is an epigenetic mark of Phytophthora genomes and that complex patterns of 6mA methylation by the expanded 6mA methyltransferases may be associated with adaptive evolution in these important plant pathogens.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

Frontiers: Re-analyses of “Algal” Genes Suggest a Complex Evolutionary History of Oomycetes (2017)

Frontiers: Re-analyses of “Algal” Genes Suggest a Complex Evolutionary History of Oomycetes (2017) | Plant Pathogenomics | Scoop.it

The spread of photosynthesis is one of the most important but constantly debated topics in eukaryotic evolution. Various hypotheses have been proposed to explain the plastid distribution in extant eukaryotes. Notably, the chromalveolate hypothesis suggested that multiple eukaryotic lineages were derived from a photosynthetic ancestor that had a red algal endosymbiont. As such, genes of plastid/algal origin in aplastidic chromalveolates, such as oomycetes, were considered to be important supporting evidence. Although the chromalveolate hypothesis has been seriously challenged, some of its supporting evidence has not been carefully investigated. In this study, we re-evaluate the “algal” genes from oomycetes with a larger sampling and careful phylogenetic analyses. Our data provide no conclusive support for a common photosynthetic ancestry of stramenopiles, but show that the initial estimate of “algal” genes in oomycetes was drastically inflated due to limited genome data available then for certain eukaryotic lineages. These findings also suggest that the evolutionary histories of these “algal” genes might be attributed to complex scenarios such as differential gene loss, serial endosymbioses, or horizontal gene transfer.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

bioRxiv: De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust (2017)

bioRxiv: De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust (2017) | Plant Pathogenomics | Scoop.it

Oat crown rust, caused by the fungus Puccinia coronata f. sp. avenae (Pca), is a devastating disease that impacts worldwide oat production. For much of its life cycle, Pca is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two Pcaisolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for a total assembly length of 99.16 Mbp for 12SD80 and 777 primary contigs with a total length of 105.25 Mbp for 12NC29, and approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of co-expressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in Pca.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

bioRxiv: Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions (2017)

bioRxiv: Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions (2017) | Plant Pathogenomics | Scoop.it

The plant immune system is innate, encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes. We showed that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncovered a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events revealed that homologous receptors can be fused to diverse domains. Furthermore, we discovered a 43 amino acids long motif that was associated with this dominant integration clade and was located immediately upstream of the fusion site. Sequence analysis revealed that DNA transposition and/or ectopic recombination are the most likely mechanisms of NLR-ID formation. The identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen baits.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

bioRxiv: Coexistence of multiple endemic and pandemic lineages of the rice blast pathogen (2017)

bioRxiv: Coexistence of multiple endemic and pandemic lineages of the rice blast pathogen (2017) | Plant Pathogenomics | Scoop.it

The rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae) causes the most damaging rice disease. Yet, little is known about the genetic makeup of this important system for plant pathology. Using whole genome resequencing of a worldwide collection of isolates, we identified four major M. oryzae lineages mainly associated with Japonica or Indica rice, including one pandemic lineage on each rice subspecies. Tip-dating calibration indicated that M. oryzae lineages separated about a millenium ago, much later than the initial domestication of rice. The major lineage endemic to Southeast continental Asia displayed signatures of sexual recombination and evidence for having received DNA from multiple lineages. Tests of weak selection revealed that the pandemic spread of clonal lineages entailed an evolutionary 'cost', in terms of an accumulation of deleterious mutations. Our work reveals the coexistence of multiple endemic and pandemic lineages with contrasting population and genetic characteristics within a widely distributed pathogen.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

Molecular Biology and Evolution: Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen (2017)

Molecular Biology and Evolution: Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen (2017) | Plant Pathogenomics | Scoop.it

Differences in gene content are a significant source of variability within species and have an impact on phenotypic traits. However, little is known about the mechanisms responsible for the most recent gene gains and losses. We screened the genomes of 123 worldwide isolates of the major pathogen of wheat Zymoseptoria tritici for robust evidence of gene copy number variation. Based on orthology relationships in three closely related fungi, we identified 599 gene gains and 1,024 gene losses that have not yet reached fixation within the focal species. Our analyses of gene gains and losses segregating in populations showed that gene copy number variation arose preferentially in subtelomeres and in proximity to transposable elements. Recently lost genes were enriched in virulence factors and secondary metabolite gene clusters. In contrast, recently gained genes encoded mostly secreted protein lacking a conserved domain. We analyzed the frequency spectrum at loci segregating a gene presence–absence polymorphism in four worldwide populations. Recent gene losses showed a significant excess in low-frequency variants compared with genome-wide single nucleotide polymorphism, which is indicative of strong negative selection against gene losses. Recent gene gains were either under weak negative selection or neutral. We found evidence for strong divergent selection among populations at individual loci segregating a gene presence–absence polymorphism. Hence, gene gains and losses likely contributed to local adaptation. Our study shows that microbial eukaryotes harbor extensive copy number variation within populations and that functional differences among recently gained and lost genes led to distinct evolutionary trajectories.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

Web Resouce: AnnoTALE (2016)

Web Resouce: AnnoTALE (2016) | Plant Pathogenomics | Scoop.it

Transcription activator-like effectors (TALEs) are virulence factors of plant-pathogenic Xanthomonas spp. that function as gene activators inside plant host cells.

 

AnnoTALE is a suite of applications for identifying and analysing TALEs in Xanthomonas genomes, for clustering TALEs into classes by their RVD sequences, for assigning novel TALEs to existing classes, for proposing TALE names using a unified nomenclature, and for predicting targets of individual TALEs and TALE classes.

 

AnnoTALE is available as a JavaFX-based stand-alone application with graphical user interface for interactive analysis sessions. In addition, we provide a command line application that may be integrated into other pipelines. Both use identical code for the actual analysis, ensuring consistent results between both versions.

 

If you use AnnoTALE, please cite:

Jan Grau, Maik Reschke, Annett Erkes, Jana Streubel, Richard D. Morgan, Geoffrey G. Wilson, Ralf Koebnik and Jens Boch. AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences. Scientific Reports 6:21077, DOI: 10.1038/srep21077, 2016.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

bioRxiv: Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia (2017)

bioRxiv: Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia (2017) | Plant Pathogenomics | Scoop.it

Rhizobium nitrogen-fixing nodules are a well-known trait of legumes, but nodules also occur in other plant lineages either with rhizobium or the actinomycete Frankia as microsymbiont. The widely accepted hypothesis is that nodulation evolved independently multiple times, with only a few losses. However, insight in the evolutionary trajectory of nodulation is lacking. We conducted comparative studies using Parasponia (Cannabaceae), the only non-legume able to establish nitrogen fixing nodules with rhizobium. This revealed that Parasponia and legumes utilize a large set of orthologous symbiosis genes. Comparing genomes of Parasponia and its non-nodulating relative Trema did not reveal specific gene duplications that could explain a recent gain of nodulation in Parasponia. Rather, Trema and other non-nodulating species in the order Rosales show evidence of pseudogenization or loss of key symbiosis genes. This demonstrates that these species have lost the potential to nodulate. This finding challenges a long-standing hypothesis on evolution of nitrogen-fixing symbioses, and has profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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.

more...
No comment yet.
Scooped by Kamoun Lab @ TSL
Scoop.it!

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

Click here to edit the content

more...
No comment yet.