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Plant J: Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations (...

Plant J: Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations (... | Plant Pathogenomics | Scoop.it

RenSeq is a NB-LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB-LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB-LRRs and can be accessed through a genome browser that we provide. We compared these NB-LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum ‘Heinz 1706’ extended the NB-LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi-ber2) and S. ruiz-ceballosii (Rpi-rzc1), we were able to apply RenSeq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines.

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bioRxiv: Interactions Between Genome Architecture and Virulence Genes in Pseudomonas syringae, strain CC1557 as a model (2013)

bioRxiv: Interactions Between Genome Architecture and Virulence Genes in Pseudomonas syringae, strain CC1557 as a model (2013) | Plant Pathogenomics | Scoop.it

Both type III effector proteins and non-ribosomal peptide toxins play important roles for Pseudomonas syringae pathogenicity in host plants, but if and how these virulence pathways interact to promote infection remains unclear. Genomic evidence from one clade of P. syringae suggests a tradeoff between the total number of type III effector proteins and presence of syringomycin, syringopeptin, and syringolin A toxins. Here we report the complete genome sequence from P. syringae CC1557, which contains the lowest number of known type III effectors to date and has also acquired a highly similar toxin to syringomycin through horizontal transfer. We demonstrate that this strain is pathogenic on Nicotiana benthamiana and that both the type III secretion system and a new type III effector family, hopBJ1, contribute to virulence. Taken together, our results provide independent evolutionary confirmation of a negative correlation between type III effector repertoires and some non-ribosomal peptide toxins while also highlighting how genomic synteny can be used to identify novel virulence proteins.

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PLOS ONE: Comparative Genomics of Multiple Strains of Pseudomonas cannabina pv. alisalensis, a Potential Model Pathogen of Both Monocots and Dicots (2013)

PLOS ONE: Comparative Genomics of Multiple Strains of Pseudomonas cannabina pv. alisalensis, a Potential Model Pathogen of Both Monocots and Dicots (2013) | Plant Pathogenomics | Scoop.it

Comparative genomics of closely related pathogens that differ in host range can provide insights into mechanisms of host-pathogen interactions and host adaptation. Furthermore, sequencing of multiple strains with the same host range reveals information concerning pathogen diversity and the molecular basis of virulence. Here we present a comparative analysis of draft genome sequences for four strains of Pseudomonas cannabina pathovaralisalensis (Pcal), which is pathogenic on a range of monocotyledonous and dicotyledonous plants. These draft genome sequences provide a foundation for understanding host range evolution across the monocot-dicot divide. Like other phytopathogenic pseudomonads, Pcalstrains harboured a hrp/hrc gene cluster that codes for a type III secretion system. Phylogenetic analysis based on the hrp/hrc cluster genes/proteins, suggests localized recombination and functional divergence within the hrp/hrc cluster. Despite significant conservation of overall genetic content across Pcal genomes, comparison of type III effector repertoires reinforced previous molecular data suggesting the existence of two distinct lineages within this pathovar. Furthermore, all Pcal strains analyzed harbored two distinct genomic islands predicted to code for type VI secretion systems (T6SSs). While one of these systems was orthologous to known P. syringae T6SSs, the other more closely resembled a T6SS found within P. aeruginosa. In summary, our study provides a foundation to unravel Pcal adaptation to both monocot and dicot hosts and provides genetic insights into the mechanisms underlying pathogenicity.

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Nature Communications: High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus (2013)

Nature Communications: High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus (2013) | Plant Pathogenomics | Scoop.it

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat. Here we report a 110-Mb draft sequence of Pst isolate CY32, obtained using a ‘fosmid-to-fosmid’ strategy, to better understand its race evolution and pathogenesis. The Pst genome is highly heterozygous and contains 25,288 protein-coding genes. Compared with non-obligate fungal pathogens, Pst has a more diverse gene composition and more genes encoding secreted proteins. Re-sequencing analysis indicates significant genetic variation among six isolates collected from different continents. Approximately 35% of SNPs are in the coding sequence regions, and half of them are non-synonymous. High genetic diversity in Pst suggests that sexual reproduction has an important role in the origin of different regional races. Our results show the effectiveness of the ‘fosmid-to-fosmid’ strategy for sequencing dikaryotic genomes and the feasibility of genome analysis to understand race evolution in Pst and other obligate pathogens.

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PLOS ONE: Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes (2013)

PLOS ONE: Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes (2013) | Plant Pathogenomics | Scoop.it

The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including Phytophthora, Pythium and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six Pythium genomes and comparison with other stramenopiles including photosynthetic diatoms, and other plant pathogenic oomycetes such as Phytophthora species, Hyaloperonospora arabidopsidis, andPythium ultimum var. ultimum. Novel features of the oomycete genomes include an expansion of genes encoding secreted effectors and plant cell wall degrading enzymes in Phytophthoraspecies and an over-representation of genes involved in proteolytic degradation and signal transduction in Pythium species. A complete lack of classical RxLR effectors was observed in the seven surveyed Pythium genomes along with an overall reduction of pathogenesis-related gene families in H. arabidopsidis. Comparative analyses revealed fewer genes encoding enzymes involved in carbohydrate metabolism in Pythium species and H. arabidopsidis as compared to Phytophthora species, suggesting variation in virulence mechanisms within plant pathogenic oomycete species. Shared features between the oomycetes and diatoms revealed common mechanisms of intracellular signaling and transportation. Our analyses demonstrate the value of comparative genome analyses for exploring the evolution of pathogenesis and survival mechanisms in the oomycetes. The comparative analyses of seven Pythium species with the closely related oomycetes, Phytophthora species and H. arabidopsidis, and distantly related diatoms provide insight into genes that underlie virulence.

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Trends in Microbiology: Epigenetics and the evolution of virulence (2013)

Trends in Microbiology: Epigenetics and the evolution of virulence (2013) | Plant Pathogenomics | Scoop.it
Pathogens must evolve rapidly in response to host or environmental challenges.Clonal and invasive species adapt quickly despite a lack of genetic diversity.Evasion of host immunity can result from silencing of relevant effectors.Epigenetic reprogramming of gene expression can aid in pathogen adaptation.

 

A feature of pathogenic and invasive organisms is their adaptability when confronted with host and environmental challenges. Recent studies have demonstrated that plant pathogens rely on epigenetic processes for this purpose. Epiallelic variation of effector genes that results in evasion of host immunity is one emerging phenomenon. Another is the epigenetically induced reprogramming and diversification of transcriptional patterns by de-repression of transposable elements. These observations indicate that epigenetic control of gene expression provides a versatile means of generating phenotypic diversity that is adaptable and heritable across generations.

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#BTG13 Tweets: Beyond the Genome 2013, San Francisco, USA. (with images, tweets)

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PeerJ: Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology (2013)

PeerJ: Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology (2013) | Plant Pathogenomics | Scoop.it

The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of “effector” proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen’s predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology.

 

This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols.

 

The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu).

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julien levy's curator insight, September 23, 2013 12:24 PM

Iplant or Galaxy webbased ?

 

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PLOS ONE: Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation (2013)

PLOS ONE: Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation (2013) | Plant Pathogenomics | Scoop.it

Carbohydrate-active enzymes (CAZymes) are involved in the metabolism of glycoconjugates, oligosaccharides, and polysaccharides and, in the case of plant pathogens, in the degradation of the host cell wall and storage compounds. We performed an in silico analysis of CAZymes predicted from the genomes of seven Pythium species (Py. aphanidermatum, Py. arrhenomanes, Py. irregulare, Py. iwayamai, Py. ultimum var. ultimum,Py. ultimum var. sporangiiferum and Py. vexans) using the “CAZymes Analysis Toolkit” and “Database for Automated Carbohydrate-active Enzyme Annotation” and compared them to previously published oomycete genomes. Growth of Pythium spp. was assessed in a minimal medium containing selected carbon sources that are usually present in plants. Thein silico analyses, coupled with our in vitro growth assays, suggest that most of the predicted CAZymes are involved in the metabolism of the oomycete cell wall with starch and sucrose serving as the main carbohydrate sources for growth of these plant pathogens. The genomes of Pythium spp. also encode pectinases and cellulases that facilitate degradation of the plant cell wall and are important in hyphal penetration; however, the species examined in this study lack the requisite genes for the complete saccharification of these carbohydrates for use as a carbon source. Genes encoding for xylan, xyloglucan, (galacto)(gluco)mannan and cutin degradation were absent or infrequent in Pythium spp.. Comparative analyses of predicted CAZymes in oomycetes indicated distinct evolutionary histories. Furthermore, CAZyme gene families among Pythium spp. were not uniformly distributed in the genomes, suggesting independent gene loss events, reflective of the polyphyletic relationships among some of the species.

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J Zhejiang Univ Sci B: Genomic organization and sequence dynamics of the AvrPiz-t locus in Magnaporthe oryzae (2012)

J Zhejiang Univ Sci B: Genomic organization and sequence dynamics of the AvrPiz-t locus in Magnaporthe oryzae (2012) | Plant Pathogenomics | Scoop.it

Plants utilize multiple layers of defense mechanisms to fight against the invasion of diverse pathogens. The R gene mediates resistance, in most cases, dependent on the co-existence of its cognate pathogen-derived avirulence (Avr) gene. The rice blast R gene Piz-t corresponds in gene-for-gene fashion to the Magnaporthe oryzae Avr gene AvrPiz-t. In this study, we determined and compared the genomic sequences surrounding the AvrPiz-t gene in both avirulent and virulent isolates, designating as AvrPiz-t-ZB15 and avrPiz-t-70-15 regions, respectively. The sequence of the AvrPiz-t-ZB15 region is 120 966 bp whereas avrPiz-t-70-15 is 146 292 bp in length. The extreme sequence similarity and good synteny in gene order and content along with the absence of two predicted genes in the avrPiz-t-70-15 region were observed in the predicted protein-coding regions in the AvrPiz-t locus. Nevertheless, frequent presence/absence and highly dynamic organization of transposable elements (TEs) were identified, representing the major variation of the AvrPiz-t locus between different isolates. Moreover, TEs constitute 27.3% and 43.2% of the genomic contents of the AvrPiz-t-ZB15 and avrPiz-t-70-15 regions, respectively, indicating that TEs contribute largely to the organization and evolution of AvrPiz-t locus. The findings of this study suggest that M. oryzae could benefit in an evolutionary sense from the presence of active TEs in genes conferring avirulence and provide an ability to rapidly change and thus to overcome host R genes.

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EMBO Conference on Comparative Genomics of Eukaryotic Microorganisms: Complexity Patterns in Eukaryotic Genomes. 19 – 24 October 2013 | Sant Feliu de Guixols, Spain

EMBO Conference on Comparative Genomics of Eukaryotic Microorganisms: Complexity Patterns in Eukaryotic Genomes. 19 – 24 October 2013 | Sant Feliu de Guixols, Spain | Plant Pathogenomics | Scoop.it
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Nature Genetics: The wheat powdery mildew genome shows the unique evolution of an obligate biotroph (2013)

Nature Genetics: The wheat powdery mildew genome shows the unique evolution of an obligate biotroph (2013) | Plant Pathogenomics | Scoop.it

Wheat powdery mildew, Blumeria graminis forma specialis tritici, is a devastating fungal pathogen with a poorly understood evolutionary history. Here we report the draft genome sequence of wheat powdery mildew, the resequencing of three additional isolates from different geographic regions and comparative analyses with the barley powdery mildew genome. Our comparative genomic analyses identified 602 candidate effector genes, with many showing evidence of positive selection. We characterize patterns of genetic diversity and suggest that mildew genomes are mosaics of ancient haplogroups that existed before wheat domestication. The patterns of diversity in modern isolates suggest that there was no pronounced loss of genetic diversity upon formation of the new host bread wheat 10,000 years ago. We conclude that the ready adaptation of B. graminis f.sp. tritici to the new host species was based on a diverse haplotype pool that provided great genetic potential for pathogen variation.

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Genome Announcements: Several plant pathogen genomes published in the issue of May/June 2013

Draft Genome Sequence of Botrytis cinerea BcDW1, Inoculum for Noble Rot of Grape Berries

Barbara Blanco-Ulate, Greg Allen, Ann L. T. Powell, and Dario CantuGenome Announc. May/June 2013 1:e00252-13; doi:10.1128/genomeA.00252-13http://genomea.asm.org/content/1/3/e00252-13.abstract.html

 

Draft Genome Sequence of the Grapevine Dieback Fungus Eutypa lata UCR-EL1

Barbara Blanco-Ulate, Philippe E. Rolshausen, and Dario CantuGenome Announc. May/June 2013 1:e00228-13; doi:10.1128/genomeA.00228-13http://genomea.asm.org/content/1/3/e00228-13.abstract.html

 

Draft Genome Sequence of Neofusicoccum parvum Isolate UCR-NP2, a Fungal Vascular Pathogen Associated with Grapevine Cankers

Barbara Blanco-Ulate, Philippe Rolshausen, and Dario CantuGenome Announc. May/June 2013 1:e00339-13; doi:10.1128/genomeA.00339-13http://genomea.asm.org/content/1/3/e00339-13.abstract.html

 

Draft Genome Sequence of the Ascomycete Phaeoacremonium aleophilum Strain UCR-PA7, a Causal Agent of the Esca Disease Complex in Grapevines

Barbara Blanco-Ulate, Philippe Rolshausen, and Dario CantuGenome Announc. May/June 2013 1:e00390-13; doi:10.1128/genomeA.00390-13http://genomea.asm.org/content/1/3/e00390-13.abstract.html

 

Genome Sequencing of Ralstonia solanacearum FQY_4, Isolated from a Bacterial Wilt Nursery Used for Breeding Crop Resistance

Yi Cao, Baoyu Tian, Yanxia Liu, Liuti Cai, Hancheng Wang, Ning Lu, Maosheng Wang, Shenghua Shang, Zhengyou Luo, and Junxiong ShiGenome Announc. May/June 2013 1:e00125-13; doi:10.1128/genomeA.00125-13http://genomea.asm.org/content/1/3/e00125-13.abstract.html

 

Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi

Daniel Passos da Silva, Giulia Devescovi, Konrad Paszkiewicz, Chiaraluce Moretti, Roberto Buonaurio, David J. Studholme, and Vittorio VenturiGenome Announc. May/June 2013 1:e00205-13; doi:10.1128/genomeA.00205-13http://genomea.asm.org/content/1/3/e00205-13.abstract.html

 

Genome Sequences of Pseudomonas spp. Isolated from Cereal CropsDonald M. Gardiner, Jiri Stiller, Lorenzo Covarelli, Magdalen Lindeberg, Roger G. Shivas, and John M. MannersGenome Announc. May/June 2013 1:e00209-13; doi:10.1128/genomeA.00209-13http://genomea.asm.org/content/1/3/e00209-13.abstract.html

 

Complete Genome Sequence of Xanthomonas citri subsp. citri Strain Aw12879, a Restricted-Host-Range Citrus Canker-Causing Bacterium

Neha Jalan, Dibyendu Kumar, Fahong Yu, Jeffrey B. Jones, James H. Graham, and Nian WangGenome Announc. May/June 2013 1:e00235-13; doi:10.1128/genomeA.00235-13http://genomea.asm.org/content/1/3/e00235-13.abstract.html

 

Genome Sequence of Xanthomonas arboricola pv. Corylina, Isolated from Turkish Filbert in Colorado

Jorge Ibarra Caballero, Marcelo M. Zerillo, Jacob Snelling, Christina Boucher, and Ned TisseratGenome Announc. May/June 2013 1:e00246-13; doi:10.1128/genomeA.00246-13http://genomea.asm.org/content/1/3/e00246-13.abstract.html

 

Genome Sequence of the Banana Pathogen Dickeya zeae Strain MS1, Which Causes Bacterial Soft Rot

Jing-Xin Zhang, Bi-Run Lin, Hui-Fang Shen, and Xiao-Ming PuGenome Announc. May/June 2013 1:e00317-13; doi:10.1128/genomeA.00317-13http://genomea.asm.org/content/1/3/e00317-13.abstract.html

 

Genome Sequence of the Pectobacterium atrosepticum Strain CFBP6276, Causing Blackleg and Soft Rot Diseases on Potato Plants and Tubers

Anthony Kwasiborski, Samuel Mondy, Amélie Beury-Cirou, and Denis FaureGenome Announc. May/June 2013 1:e00374-13; doi:10.1128/genomeA.00374-13http://genomea.asm.org/content/1/3/e00374-13.abstract.html

 

Complete Genome Sequences of Two Sweet Potato Chlorotic Stunt Virus Isolates from China

Yanhong Qin, Zhenchen Zhang, Qi Qiao, Desheng Zhang, Yuting Tian, Yongjiang Wang, and Shuang WangGenome Announc. May/June 2013 1:e00218-13; doi:10.1128/genomeA.00218-13http://genomea.asm.org/content/1/3/e00218-13.abstract.html


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Resource: Wheat Yellow Rust Genomics data now available (2013)

Resource: Wheat Yellow Rust Genomics data now available (2013) | Plant Pathogenomics | Scoop.it

We have been working with colleagues in India, Kenya, Ethiopia, Denmark and the UK to develop wheat yellow rust genomics through the re-sequencing of isolates from different continents. Our project also includes traditional field trials of a common set of germplasm which has been evaluated in these countries. One of our goals is to make the genomic data of wheat yellow rust isolates and phenotypic data (Yr, Sr, Lr) from the wheat Watkins landraces rapidly and broadly available to the scientific community, as stated at the BGRI workshop 2013.


We hope that this data will be of use to others in the community and we have made this information available (open access) through our project website (www.yellowrust.com). It is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analyses. We strongly believe that as a global research community we can have a greater impact in our common goals if data is shared openly and used responsibly.


Diane Saunders and Cristobal Uauy on behalf of SCPRID project partners

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PLOS Pathogens: Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining (2013)

PLOS Pathogens: Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining (2013) | Plant Pathogenomics | Scoop.it

Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when silenced, constitute promising targets for the development of more specific and safer control means.

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Arjen ten Have's curator insight, November 20, 2013 4:13 PM

My guess this is a rather stringent protocol. There will be many cool targets at intermediate levels of the filtration flow! But obviously a great piece of work. Love its simplicity! (likely much of the work actually performed is not shown).

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PLOS ONE: Evolution of RXLR-Class Effectors in the Oomycete Plant Pathogen Phytophthora ramorum (2013)

PLOS ONE: Evolution of RXLR-Class Effectors in the Oomycete Plant Pathogen Phytophthora ramorum (2013) | Plant Pathogenomics | Scoop.it

Phytophthora plant pathogens contain many hundreds of effectors potentially involved in infection of host plants. Comparative genomic analyses have shown that these effectors evolve rapidly and have been subject to recent expansions. We examined the recent sequence evolution of RXLR-class effector gene families in the sudden oak death pathogen, P. ramorum. We found that P. ramorum RXLR effectors have taken multiple evolutionary paths, including loss or gain of repeated domains, recombination or gene conversion among paralogs, and selection on point mutations. Sequencing of homologs from two subfamilies in P. ramorum’s closest known relatives revealed repeated gene duplication and divergence since speciation with P. lateralis. One family showed strong signatures of recombination while the other family has evolved primarily by point mutation. Comparison of a small number of the hundreds of RXLR-class effectors across three clonal lineages of P. ramorum shows striking divergence in alleles among lineages, suggesting the potential for functional differences between lineages. Our results suggest future avenues for examination of rapidly evolving effectors in P. ramorum, including investigation of the functional and coevolutionary significance of the patterns of sequence evolution that we observed.


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Niklaus Grunwald's curator insight, November 8, 2013 4:07 PM

Our paper on evoution of RXLR effectors in the sudden oak death pathogen Phytophthora ramorum describing loss or gain of repeated domains, recombination or gene conversion among paralogs, and selection on point mutations and more.

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PLOS ONE: Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs (2013)

PLOS ONE: Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs (2013) | Plant Pathogenomics | Scoop.it

In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.

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PNAS: A transposable element is domesticated for service in the plant immune system (2013)

PNAS: A transposable element is domesticated for service in the plant immune system (2013) | Plant Pathogenomics | Scoop.it

Genomes continue to surprise us with the diversity of mechanisms involved in gene regulation. Sequencing of the Arabidopsis genome 13 y ago revealed transposable elements (TEs) distributed throughout the genome. TEs were characterized nearly 70 y ago by maize geneticist Barbara McClintock, who named them “controlling elements” for their activity in regulating aleurone color genes and chromosomal breakage (1). TEs are rife in plant genomes; their necessary inactivation via heterochromatin formation is an epigenetic phenomenon that can spill over into adjacent chromosomal regions. Although many TEs appear inert, some retain primary or vestigial functions, and others have even been adapted to confer novel functions. In PNAS, Tsuchiya and Eulgem (2) provide a fascinating example of how a retrotransposon has been domesticated to control expression of a plant immune system surveillance gene and highlight a unique mode of action through which TEs can regulate activity of protein-coding genes.

 

This story focuses on the Arabidopsis RPP7 gene [resistance to Hyaloperonsopora arabidopsidis (Hpa), a downy mildew pathogen]. RPP7 is polymorphic, with alleles for resistance and susceptibility in variousArabidopsis accessions. This natural variation is a hallmark of plant disease resistance genes (R genes) that have been exploited for decades in breeding programs. RPP7 (along with most other R genes) encodes an NLR protein comprised of a nucleotide-binding domain and leucine-rich repeats (3). The function for NLR proteins is immune surveillance, in which they detect pathogen effector proteins that are secreted into the interior of plant cells and then activate signaling networks that control cellular immune responses.

 

See original paper by Tsuchiya and Eulgem http://www.pnas.org/content/110/37/E3535.abstract

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Book: The Ecological Genomics of Fungi (2013)

Book: The Ecological Genomics of Fungi (2013) | Plant Pathogenomics | Scoop.it

This unique book covers a broad diversity of fungal systems and provides unique insight into the functions of those fungi in various ecosystems - from soil, to plant, to human. Bringing together fungal genomic information on a variety of lifestyles and traits, the book covers saprotrophism, pathogenesis (including biotrophs, hemibiotrophs, necrotrophs) and symbiosis. Advances in high-throughput sequencing now offer unprecedented opportunities for identification of novel key molecular mechanisms controlling plant-microbe interactions, evolution of fungi and developmentally- and ecologically-relevant traits, this book explores how these massive streams of fungal sequences can be exploited to gain a deeper understanding of the evolution of fungi and their ecological role.

 

Although tremendous progress has been made in recent years in fungal genomics, thanks to the sequencing of over one hundred fungal genomes, until now no book has used this information to bridge fungal genomics, molecular ecology and ecology. Edited by a recognized leader in fungal genomics and soil metagenomics with over a decade of experience, Genomics & Metagenomics for Harnessing the Ecology of Fungi will be a useful resource for the experienced as well as the new researchers entering the field.

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J Biotechnology: Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14 (2013)

J Biotechnology: Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14 (2013) | Plant Pathogenomics | Scoop.it

Anastomosis group AG1-IB isolates of the anamorphic basidiomycetous fungus Rhizoctonia solani Kühn affect various agricultural and horticultural important crops including bean, rice, soybean, figs, hortensia, cabbage and lettuce. To gain insights into the genome structure and content, the first draft genome sequence of R. solani AG1-IB isolate 7/3/14 was established. Four complete runs on the Genome Sequencer (GS) FLX platform (Roche Applied Science) yielding approx. a 25-fold coverage of the R. solani genome were accomplished. Assembly of the sequence reads by means of the gsAssembler software version 2.6 applying the heterozygotic mode resulted in numerous contigs and scaffolds and a predicted size of 87.1 Mb for the diploid status of the genome. ‘Contig-length vs. read-count’ analysis revealed that the assembled contigs can be classified into five different groups. Detailed BLAST-analysis revealed that most contigs of group II feature high-scoring matches to other contigs of the same group suggesting that distinguishable allelic variants exist for many genes. Due to the supposed diploid and heterokaryotic nature of R. solani AG1-IB 7/3/14, this result has been anticipated. However, the heterokaryotic character of the isolate is not really supported by sequencing data obtained for the isolate R. solani AG1-IB 7/3/14. Coverage of group III contigs is twice as high as for group II contigs which can also be explained by the diploid status of the genome and indistinguishable alleles on homologous chromosomes. Assembly of sequence data led to the identification of the rRNA unit (group V contigs) and the mitochondrial (mt) genome (group IV contigs) which is a circular molecule of 162,751 bp in size featuring a GC-content of 36.4%. The R. solani 7/3/14 mt-genome is one of the largest fungal mitochondrial genomes known to date. Its large size essentially is due to the presence of numerous non-conserved hypothetical ORFs and introns. Gene prediction for the R. solani AG1-IB 7/3/14 genome was conducted by the Augustus Gene Prediction Software for Eukaryotes (version 2.6.) applying the parameter set for the fungus Coprinopsis cinerea okayama 7#130. Gene prediction and annotation provided first insights into the R. solani AG1-IB 7/3/14 gene structure and content. In total, 12,422 genes were predicted. The average number of exons per gene is five. Exons have a mean length of 214 bp, whereas introns on average are 66 bp in length. Annotation of the genome revealed that 4169 of 12,422 genes could be assigned to KOG functional categories.

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Annual Review of Microbiology: Fusarium Pathogenomics (2013)

Annual Review of Microbiology: Fusarium Pathogenomics (2013) | Plant Pathogenomics | Scoop.it

Comparative analyses have revealed that the Fusarium genome is compartmentalized into regions responsible for primary metabolism and reproduction (core genome), and pathogen virulence, host specialization, and possibly other functions (adaptive genome). Genes involved in virulence and host specialization are located on pathogenicity chromosomes within strains pathogenic to tomato (Fusarium oxysporum f. sp. lycopersici) and pea (Fusarium ‘solani’ f. sp.pisi). The experimental transfer of pathogenicity chromosomes from F. oxysporum f. sp. lycopersici into a nonpathogen transformed the latter into a tomato pathogen. Thus, horizontal transfer may explain the polyphyletic origins of host specificity within the genus. Additional genome-scale comparative and functional studies are needed to elucidate the evolution and diversity of pathogenicity mechanisms, which may help inform novel disease management strategies against fusarial pathogens.


Via Bradford Condon, Niklaus Grunwald, Alejandro Rojas
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Nature Reviews Microbiology: Horizontal gene transfer in osmotrophs: playing with public goods (2013)

Nature Reviews Microbiology: Horizontal gene transfer in osmotrophs: playing with public goods (2013) | Plant Pathogenomics | Scoop.it

Osmotrophic microorganisms, such as fungi and oomycetes, feed by secreting depolymerizing enzymes to process complex food sources in the extracellular environment, and taking up the resulting simple sugars, micronutrients and amino acids. As a consequence of this lifestyle, osmotrophs engage in the acquisition and protection of public goods. In this Opinion article, we propose that horizontal gene transfer (HGT) has played a key part in shaping both the repertoire of proteins required for osmotrophy and the nature of public goods interactions in which eukaryotic microorganisms engage.

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Jie Wang's comment, September 18, 2013 11:43 PM
Good paper
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PLOS Genetics: Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae (2012)

PLOS Genetics: Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae (2012) | Plant Pathogenomics | Scoop.it

Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide. The fungal pathogen is notorious for its ability to overcome host resistance. To better understand its genetic variation in nature, we sequenced the genomes of two field isolates, Y34 and P131. In comparison with the previously sequenced laboratory strain 70-15, both field isolates had a similar genome size but slightly more genes. Sequences from the field isolates were used to improve genome assembly and gene prediction of 70-15. Although the overall genome structure is similar, a number of gene families that are likely involved in plant-fungal interactions are expanded in the field isolates. Genome-wide analysis on asynonymous to synonymous nucleotide substitution rates revealed that many infection-related genes underwent diversifying selection. The field isolates also have hundreds of isolate-specific genes and a number of isolate-specific gene duplication events. Functional characterization of randomly selected isolate-specific genes revealed that they play diverse roles, some of which affect virulence. Furthermore, each genome contains thousands of loci of transposon-like elements, but less than 30% of them are conserved among different isolates, suggesting active transposition events in M. oryzae. A total of approximately 200 genes were disrupted in these three strains by transposable elements. Interestingly, transposon-like elements tend to be associated with isolate-specific or duplicated sequences. Overall, our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus.

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PLOS Pathogens: Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease (2013)

PLOS Pathogens: Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease (2013) | Plant Pathogenomics | Scoop.it

The origins of crop diseases are linked to domestication of plants. Most crops were domesticated centuries – even millennia – ago, thus limiting opportunity to understand the concomitant emergence of disease. Kiwifruit (Actinidia spp.) is an exception: domestication began in the 1930s with outbreaks of canker disease caused by P. syringae pv. actinidiae(Psa) first recorded in the 1980s. Based on SNP analyses of two circularized and 34 draft genomes, we show that Psa is comprised of distinct clades exhibiting negligible within-clade diversity, consistent with disease arising by independent samplings from a source population. Three clades correspond to their geographical source of isolation; a fourth, encompassing thePsa-V lineage responsible for the 2008 outbreak, is now globally distributed. Psa has an overall clonal population structure, however, genomes carry a marked signature of within-pathovar recombination. SNP analysis of Psa-V reveals hundreds of polymorphisms; however, most reside within PPHGI-1-like conjugative elements whose evolution is unlinked to the core genome. Removal of SNPs due to recombination yields an uninformative (star-like) phylogeny consistent with diversification of Psa-V from a single clone within the last ten years. Growth assays provide evidence of cultivar specificity, with rapid systemic movement of Psa-V inActinidia chinensis. Genomic comparisons show a dynamic genome with evidence of positive selection on type III effectors and other candidate virulence genes. Each clade has highly varied complements of accessory genes encoding effectors and toxins with evidence of gain and loss via multiple genetic routes. Genes with orthologs in vascular pathogens were found exclusively within Psa-V. Our analyses capture a pathogen in the early stages of emergence from a predicted source population associated with wild Actinidia species. In addition to candidate genes as targets for resistance breeding programs, our findings highlight the importance of the source population as a reservoir of new disease.

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Nature Communications: Reconstructing genome evolution in historic samples of the Irish potato famine pathogen (2013)

Nature Communications: Reconstructing genome evolution in historic samples of the Irish potato famine pathogen (2013) | Plant Pathogenomics | Scoop.it

Responsible for the Irish potato famine of 1845–49, the oomycete pathogen Phytophthora infestanscaused persistent, devastating outbreaks of potato late blight across Europe in the 19th century. Despite continued interest in the history and spread of the pathogen, the genome of the famine-era strain remains entirely unknown. Here we characterize temporal genomic changes in introduced P. infestans. We shotgun sequence five 19th-century European strains from archival herbarium samples—including the oldest known European specimen, collected in 1845 from the first reported source of introduction. We then compare their genomes to those of extant isolates. We report multiple distinct genotypes in historical Europe and a suite of infection-related genes different from modern strains. At virulence-related loci, several now-ubiquitous genotypes were absent from the historical gene pool. At least one of these genotypes encodes a virulent phenotype in modern strains, which helps explain the 20th century’s episodic replacements of European P. infestanslineages.

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