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PLoS ONE: Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi

PLoS ONE: Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi | Publications | Scoop.it

Rust fungi are obligate biotrophic pathogens that cause considerable damage on crop plants. Puccinia graminis f. sp. tritici, the causal agent of wheat stem rust, and Melampsora larici-populina, the poplar leaf rust pathogen, have strong deleterious impacts on wheat and poplar wood production, respectively. Filamentous pathogens such as rust fungi secrete molecules called disease effectors that act as modulators of host cell physiology and can suppress or trigger host immunity. Current knowledge on effectors from other filamentous plant pathogens can be exploited for the characterisation of effectors in the genome of recently sequenced rust fungi. We designed a comprehensive in silico analysis pipeline to identify the putative effector repertoire from the genome of two plant pathogenic rust fungi. The pipeline is based on the observation that known effector proteins from filamentous pathogens have at least one of the following properties: (i) contain a secretion signal, (ii) are encoded by in planta induced genes, (iii) have similarity to haustorial proteins, (iv) are small and cysteine rich, (v) contain a known effector motif or a nuclear localization signal, (vi) are encoded by genes with long intergenic regions, (vii) contain internal repeats, and (viii) do not contain PFAM domains, except those associated with pathogenicity. We used Markov clustering and hierarchical clustering to classify protein families of rust pathogens and rank them according to their likelihood of being effectors. Using this approach, we identified eight families of candidate effectors that we consider of high value for functional characterization. This study revealed a diverse set of candidate effectors, including families of haustorial expressed secreted proteins and small cysteine-rich proteins. This comprehensive classification of candidate effectors from these devastating rust pathogens is an initial step towards probing plant germplasm for novel resistance components.

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bioRxiv: Phytophthora infestans RXLR-WY effector AVR3a associates with a Dynamin-Related Protein involved in endocytosis of a plant pattern recognition receptor (2014)

bioRxiv: Phytophthora infestans RXLR-WY effector AVR3a associates with a Dynamin-Related Protein involved in endocytosis of a plant pattern recognition receptor (2014) | Publications | Scoop.it

Perception of pathogen associated molecular patterns (PAMPs) by cell surface localized pattern recognition receptors (PPRs), activates plant basal defense responses in a process known as PAMP/PRR–triggered immunity (PTI). In turn, pathogens deploy effector proteins that interfere with different steps in PTI signaling. However, our knowledge of PTI suppression by filamentous plant pathogens, i.e. fungi and oomycetes, remains fragmentary. Previous work revealed that BAK1/SERK3, a regulatory receptor of several PRRs, contributes to basal immunity against the Irish potato famine pathogen Phytophthora infestans. Moreover BAK1/SERK3 is required for the cell death induced by P. infestans elicitin INF1, a protein with characteristics of PAMPs. The P. infestans host-translocated RXLR-WY effector AVR3a is known to supress INF1-mediated defense by binding the E3 ligase CMPG1. In contrast, AVR3aKI-Y147del, a deletion mutant of the C-terminal tyrosine of AVR3a, fails to bind CMPG1 and suppress INF1 cell death. Here we studied the extent to which AVR3a and its variants perturb additional BAK1/SERK3 dependent PTI responses using the plant PRR FLAGELLIN SENSING 2 (FLS2). We found that all tested variants of AVR3a, including AVR3aKI-Y147del, suppress early defense responses triggered by the bacterial flagellin-derived peptide flg22 and reduce internalization of activated FLS2 from the plasma membrane without disturbing its nonactivated localization. Consistent with this effect of AVR3a on FLS2 endocytosis, we discovered that AVR3a associates with the Dynamin-Related Protein DRP2, a plant GTPase implicated in receptor-mediated endocytosis. Interestingly, DRP2 is required for ligand-induced FLS2 internalization but does not affect internalization of the growth receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1). Furthermore, overexpression of DRP2 suppressed accumulation of reactive oxygen species triggered by PAMP treatment. We conclude that AVR3a associates with a key cellular trafficking and membrane-remodeling complex involved in immune receptor-mediated endocytosis and signaling. AVR3a is a multifunctional effector that can suppress BAK1/SERK3 mediated immunity through at least two different pathways.

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fundoshi's curator insight, December 22, 3:10 AM
Arabidopsis dynamin-related proteins, DRP2A and DRP2B, function coordinately in post-Golgi trafficking.

http://www.sciencedirect.com/science/article/pii/S0006291X14020956

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Video: Fifi The Oomycete (2014)

Happy holidays from the @KamounLab!


FiFi (Phytophthora) The Oomycete


(adapted from Frosty The Snowman)


Fifi the oomycete is a scary parasite,
With flagellated spores and hyphal threads
She kills crops and triggers blight.


Fifi the oomycete is a heterokont, they say,
She’s fungus-like but the scientists
Know how she had plastids one day.


There must have been some magic in those
Transposons they found.
For when they mapped ‘em on the genome
They began to jump around.


Fifi the oomycete has a big genome, they say,
Full of repeats but don’t call it junk
‘cause can be handy one day.


O, Fifi the oomycete
Was as virulent as she’s been;
and scientists say she secretes her way
Inside potatoes and bean.


Fifi the oomycete found
A resistant plant that day,
So she said, "Let's run and
There’ll be no fun
Until I mutate away."


There must have been some magic in those
Transposons they found.
For when they mapped ‘em on the genome
They began to jump around.


For Fifi the oomycete
Keeps evolving in her way,
But don’t wave her goodbye,
Don't you even try,
She’ll be back again some day.


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Mary Williams's curator insight, December 10, 12:46 PM

She's adorable (or maybe not...). Nice song though!

Easwaramurthy Rgr's curator insight, December 19, 2:37 PM

Happy holidays from the @KamounLab!

 

FiFi (Phytophthora) The Oomycete


(adapted from Frosty The Snowman),scopped by Jean Michel

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Current Opinion in Biotechnology: Editing plant genomes with CRISPR/Cas9 (2015)

Current Opinion in Biotechnology: Editing plant genomes with CRISPR/Cas9 (2015) | Publications | Scoop.it

• Cas9 is an RNA-guided DNA endonuclease innate to prokaryotic immune systems.
• CRISPR/Cas9 has recently emerged as a powerful genome editing tool.
• CRISPR/Cas9 has been successfully applied in many organisms, including model and crop plants.
• CRISPR/Cas9 is a cheap, robust and easy to implement technology.


CRISPR/Cas9 is a rapidly developing genome editing technology that has been successfully applied in many organisms, including model and crop plants. Cas9, an RNA-guided DNA endonuclease, can be targeted to specific genomic sequences by engineering a separately encoded guide RNA with which it forms a complex. As only a short RNA sequence must be synthesized to confer recognition of a new target, CRISPR/Cas9 is a relatively cheap and easy to implement technology that has proven to be extremely versatile. Remarkably, in some plant species, homozygous knockout mutants can be produced in a single generation. Together with other sequence-specific nucleases, CRISPR/Cas9 is a game-changing technology that is poised to revolutionise basic research and plant breeding.

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PLOS ONE: Variation in Capsidiol Sensitivity between Phytophthora infestans and Phytophthora capsici Is Consistent with Their Host Range (2014)

PLOS ONE: Variation in Capsidiol Sensitivity between Phytophthora infestans and Phytophthora capsici Is Consistent with Their Host Range (2014) | Publications | Scoop.it

Plants protect themselves against a variety of invading pathogenic organisms via sophisticated defence mechanisms. These responses include deployment of specialized antimicrobial compounds, such as phytoalexins, that rapidly accumulate at pathogen infection sites. However, the extent to which these compounds contribute to species-level resistance and their spectrum of action remain poorly understood. Capsidiol, a defense related phytoalexin, is produced by several solanaceous plants including pepper and tobacco during microbial attack. Interestingly, capsidiol differentially affects growth and germination of the oomycete pathogensPhytophthora infestans and Phytophthora capsici, although the underlying molecular mechanisms remain unknown. In this study we revisited the differential effect of capsidiol on P. infestans and P. capsici, using highly pure capsidiol preparations obtained from yeast engineered to express the capsidiol biosynthetic pathway. Taking advantage of transgenicPhytophthora strains expressing fluorescent markers, we developed a fluorescence-based method to determine the differential effect of capsidiol on Phytophtora growth. Using these assays, we confirm major differences in capsidiol sensitivity between P. infestans and P. capsiciand demonstrate that capsidiol alters the growth behaviour of both Phytophthora species. Finally, we report intraspecific variation within P. infestans isolates towards capsidiol tolerance pointing to an arms race between the plant and the pathogens in deployment of defence related phytoalexins.

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Steve Marek's curator insight, September 17, 3:04 PM

Pepper pathogen can handle the 'heat'

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Plant Physiology Cover — July 2014

Plant Physiology Cover  — July 2014 | Publications | Scoop.it

Filamentous plant pathogens such as the late blight pathogenPhytophthora infestans form digit-like infection structures called haustoria inside plant cells. Haustoria enable the pathogen to feed on its host, and secrete effector proteins that modulate the physiology of the host cell to facilitate infection. Haustoria are enveloped by a specialized plant-derived membrane (the extrahaustorial membrane) the biogenesis of which is poorly understood. In this issue, Bozkurt et al. http://www.plantphysiol.org/content/165/3/1005 used the plant membrane microdomain protein REMORIN1.3, known to accumulate around P. infestans haustoria, to reveal discrete extrahaustorial domains labeled by REMORIN1.3 and P. infestans effector AVRblb2. SYNAPTOTAGMIN1, another previously identified perihaustorial protein, localized to subdomains which are mainly not labeled by REMORIN1.3 and AVRblb2. Functional characterization of REMORIN1.3 revealed that it is a susceptibility factor that promotes infection by P. infestans. This activity, and REMORIN1.3 recruitment to the EHM, require REM1.3 membrane-binding domain. These results implicate REMORIN1.3 membrane microdomains in plant susceptibility to an oomycete pathogen. The cover shows Nicotiana benthamiana epidermal cells expressing fluorescently labeled REMORIN1.3 (blue) infected by P. infestans expressing the red fluorescent protein (red). Cover image credits: Sylvain Raffaele.

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New Phytologist: Multiple recognition of RXLR effectors is associated with nonhost resistance of pepper against Phytophthora infestans (2014)

New Phytologist: Multiple recognition of RXLR effectors is associated with nonhost resistance of pepper against Phytophthora infestans (2014) | Publications | Scoop.it
  • Nonhost resistance (NHR) is a plant immune response to resist most pathogens. The molecular basis of NHR is poorly understood, but recognition of pathogen effectors by immune receptors, a response known as effector-triggered immunity, has been proposed as a component of NHR.
  • We performed transient expression of 54 Phytophthora infestansRXLR effectors in pepper (Capsicum annuum) accessions. We used optimized heterologous expression methods and analyzed the inheritance of effector-induced cell death in an F2 population derived from a cross between two pepper accessions.
  • Pepper showed a localized cell death response upon inoculation with P. infestans, suggesting that recognition of effectors may contribute to NHR in this system. Pepper accessions recognized as many as 36 effectors. Among the effectors, PexRD8 and Avrblb2 induced cell death in a broad range of pepper accessions. Segregation of effector-induced cell death in an F2 population derived from a cross between two pepper accessions fit 15 : 1, 9 : 7 or 3 : 1 ratios, depending on the effector.
  • Our genetic data suggest that a single or two independent/complementary dominant genes are involved in the recognition of RXLR effectors. Multiple loci recognizing a series of effectors may underpin NHR of pepper to P. infestans and confer resistance durability.
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Plant Physiology: The plant membrane-associated REM1.3 remorin accumulates in discrete perihaustorial domains and enhances susceptibility to Phytophthora infestans (2014)

Plant Physiology: The plant membrane-associated REM1.3 remorin accumulates in discrete perihaustorial domains and enhances susceptibility to Phytophthora infestans (2014) | Publications | Scoop.it

Filamentous pathogens such as the oomycete Phytophthora infestans infect plants by developing specialized structures termed haustoria inside the host cells. Haustoria are thought to enable secretion of effector proteins into the plant cells. Haustorium biogenesis is therefore critical for pathogen accommodation in the host tissue. Haustoria are enveloped by a specialized host-derived membrane, the extrahaustorial membrane (EHM), which is distinct from the plant plasma membrane. The mechanisms underlying the biogenesis of the EHM are unknown. Remarkably, several plasma membrane localised proteins are excluded from the EHM but the remorin REM1.3 accumulates around P. infestans haustoria. Here, we used overexpression, co-localization with reporter proteins, and super-resolution microscopy in cells infected by P. infestans to reveal discrete EHM domains labelled by REM1.3 and P. infestans effector AVRblb2. Moreover, SYT1 synaptotagmin, another previously identified perihaustorial protein, localized to subdomains which are mainly not labelled by REM1.3 and AVRblb2. Functional characterization of REM1.3 revealed that it is a susceptibility factor that promotes infection by P. infestans. This activity, and REM1.3 recruitment to the EHM, require REM1.3 membrane binding domain. Our results implicate REM1.3 membrane micro-domains in plant susceptibility to an oomycete pathogen.

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Jean-Michel Ané's curator insight, May 14, 4:17 PM

I know that it is not a symbiont but... some people will guess why I am scooping this :-)

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PLOS Pathogens: Mining Herbaria for Plant Pathogen Genomes: Back to the Future (2014)

PLOS Pathogens: Mining Herbaria for Plant Pathogen Genomes: Back to the Future (2014) | Publications | Scoop.it

Since the dawn of agriculture, plant pathogens and pests have been a scourge of humanity. Yet we have come a long way since the Romans attempted to mitigate the effects of plant disease by worshipping and honoring the god Robigus. Books in the Middle Ages by Islamic and European scholars described various plant diseases and even proposed particular disease management strategies. Surprisingly, the causes of plant diseases remained a matter of debate over a long period. It took Henri-Louis Duhamel du Monceau's elegant demonstration in his 1728 “Explication Physique” paper that a “contagious” fungus was responsible for a saffron crocus disease to usher in an era of documented scientific inquiry. Confusion and debate about the exact nature of the causal agents of plant diseases continued until the 19th century, which not only saw the first detailed analyses of plant pathogens but also provided much-needed insight into the mechanisms of plant disease. An example of this is Anton de Bary's demonstration that a “fungus” is a cause, not a consequence, of plant disease. This coming of age of plant pathology was timely. In the 19th century, severe plant disease epidemics hit Europe and caused economic and social upheaval. These epidemics were not only widely covered in the press but also recognized as serious political issues by governments. Many of the diseases, including late blight of potato, powdery and downy mildew of grapevine, as well as phylloxera, were due to exotic introductions from the Americas and elsewhere. These and subsequent epidemics motivated scientific investigations into crop breeding and plant disease management that developed into modern plant pathology science over the 20th century.


Nowadays, our understanding of plant pathogens and the diseases they cause greatly benefits from molecular genetics and genomics. All aspects of plant pathology, from population biology and epidemiology to mechanistic research, are impacted. The polymerase chain reaction (PCR) first enabled access to plant pathogen DNA sequences from historical specimens deposited in herbaria. Historical records in combination with herbarium specimens have turned out to provide powerful tools for understanding the course of past plant epidemics. Recently, thanks to new developments in DNA sequencing technology, it has become possible to reconstruct the genomes of plant pathogens in herbaria. In this article, we first summarize how whole genome analysis of ancient DNA has been recently used to reconstruct the 19th-century potato-blight epidemic that rapidly spread throughout Europe and triggered the Irish potato famine. We then discuss the exciting prospects offered by the emergence of the discipline of ancient plant pathogen genomics.

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Mary Williams's curator insight, April 25, 3:02 AM

Good overview for students - very accessible and interesting!

Freddy Monteiro's comment, April 25, 4:21 AM
This is a great source of teaching materials for potato late blight. Congrats on the work behind it.
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MPMI: Single amino acid mutations in the potato immune receptor R3a expand response to Phytophthora effectors (2014)

MPMI: Single amino acid mutations in the potato immune receptor R3a expand response to Phytophthora effectors (2014) | Publications | Scoop.it

Both plants and animals rely on nucleotide-binding domain and leucine-rich repeat-containing proteins (NB-LRRs or NLRs) to respond to invading pathogens and activate immune responses. How plant NB-LRR proteins respond to pathogens is poorly understood. We undertook a gain-of-function random mutagenesis screen of the potato NB-LRR immune receptor R3a to study how this protein responds to the effector protein AVR3a from the oomycete pathogen Phytophthora infestans. R3a response can be extended to the stealthy AVR3aEM isoform of the effector while retaining recognition of AVR3aKI. Each one of 8 single amino acid mutations is sufficient to expand the R3a response to AVR3aEM and other AVR3a variants. These mutations occur across the R3a protein, from the N-terminus to different regions of the LRR domain. Further characterization of these R3a mutants revealed that at least one of them was sensitized, exhibiting a stronger response than the wild-type R3a protein to AVR3aKI. Remarkably, the N336Y mutation, near the R3a nucleotide-binding pocket, conferred response to the effector protein PcAVR3a4 from the vegetable pathogen Phytophthora capsici. This work contributes to understanding how NB-LRR receptor specificity can be modulated. Together with knowledge of pathogen effector diversity, this strategy can be exploited to develop synthetic immune receptors.

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Stephen Bolus's curator insight, March 30, 2:09 AM

I just really love the idea of synthetic immune receptors!

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Plant Cell: Phytophthora infestans RXLR Effector PexRD2 Interacts with Host MAPKKKε to Suppress Plant Immune Signaling (2014)

Plant Cell: Phytophthora infestans RXLR Effector PexRD2 Interacts with Host MAPKKKε to Suppress Plant Immune Signaling (2014) | Publications | Scoop.it

Mitogen-activated protein kinase cascades are key players in plant immune signaling pathways, transducing the perception of invading pathogens into effective defense responses. Plant pathogenic oomycetes, such as the Irish potato famine pathogen Phytophthora infestans, deliver RXLR effector proteins to plant cells to modulate host immune signaling and promote colonization. Our understanding of the molecular mechanisms by which these effectors act in plant cells is limited. Here, we report that the P. infestans RXLR effector PexRD2 interacts with the kinase domain of MAPKKKε, a positive regulator of cell death associated with plant immunity. Expression of PexRD2 or silencing MAPKKKε inNicotiana benthamiana enhances susceptibility to P. infestans. We show that PexRD2 perturbs signaling pathways triggered by or dependent on MAPKKKε. By contrast, homologs of PexRD2 from P. infestans had reduced or no interaction with MAPKKKε and did not promote disease susceptibility. Structure-led mutagenesis identified PexRD2 variants that do not interact with MAPKKKε and fail to support enhanced pathogen growth or perturb MAPKKKε signaling pathways. Our findings provide evidence that P. infestans RXLR effector PexRD2 has evolved to interact with a specific host MAPKKK to perturb plant immunity–related signaling.


Via Suayib Üstün, Kamoun Lab @ TSL
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Suayib Üstün's curator insight, March 14, 3:52 PM

What a great week for effector biology!!

Freddy Monteiro's comment, March 14, 8:42 PM
Indeed! A crazy week. You guys belong to an excellent generation of scientists.
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Science: Effector Specialization in a Lineage of the Irish Potato Famine Pathogen (2014)

Science: Effector Specialization in a Lineage of the Irish Potato Famine Pathogen (2014) | Publications | Scoop.it

Accelerated gene evolution is a hallmark of pathogen adaptation following a host jump. Here, we describe the biochemical basis of adaptation and specialization of a plant pathogen effector after its colonization of a new host. Orthologous protease inhibitor effectors from the Irish potato famine pathogen, Phytophthora infestans, and its sister species, Phytophthora mirabilis, which is responsible for infection of Mirabilis jalapa, are adapted to protease targets unique to their respective host plants. Amino acid polymorphisms in both the inhibitors and their target proteases underpin this biochemical specialization. Our results link effector specialization to diversification and speciation of this plant pathogen.

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Nature Genetics: A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity (2013)

Nature Genetics: A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity (2013) | Publications | Scoop.it

Most fruits in our daily diet are the products of domestication and breeding. Here we report a map of genome variation for a major fruit that encompasses ~3.6 million variants, generated by deep resequencing of 115 cucumber lines sampled from 3,342 accessions worldwide. Comparative analysis suggests that fruit crops underwent narrower bottlenecks during domestication than grain crops. We identified 112 putative domestication sweeps; 1 of these regions contains a gene involved in the loss of bitterness in fruits, an essential domestication trait of cucumber. We also investigated the genomic basis of divergence among the cultivated populations and discovered a natural genetic variant in a β-carotene hydroxylase gene that could be used to breed cucumbers with enhanced nutritional value. The genomic history of cucumber evolution uncovered here provides the basis for future genomics-enabled breeding.

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Plant Methods: Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system (2013)

Plant Methods: Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system (2013) | Publications | Scoop.it

Targeted genome engineering (also known as genome editing) has emerged as an alternative to classical plant breeding and transgenic (GMO) methods to improve crop plants. Until recently, available tools for introducing site-specific double strand DNA breaks were restricted to zinc finger nucleases (ZFNs) and TAL effector nucleases (TALENs). However, these technologies have not been widely adopted by the plant research community due to complicated design and laborious assembly of specific DNA binding proteins for each target gene. Recently, an easier method has emerged based on the bacterial type II CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) immune system. The CRISPR/Cas system allows targeted cleavage of genomic DNA guided by a customizable small noncoding RNA, resulting in gene modifications by both non-homologous end joining (NHEJ) and homology-directed repair (HDR) mechanisms. In this review we summarize and discuss recent applications of the CRISPR/Cas technology in plants.

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New Phytologist: Meetings - A snapshot of molecular plant–microbe interaction research (2014)

New Phytologist: Meetings - A snapshot of molecular plant–microbe interaction research (2014) | Publications | Scoop.it

Plants and microbes are in a continuous arms race to maintain their predominance within their particular niche. Understanding the complexity of these plant–microbe interactions is of utmost importance as it can provide new insights into the mechanisms mediating disease processes and in turn inspire new plant breeding strategies. The International Society for Molecular Plant–Microbe Interactions (IS-MPMI) invited scientists from around the world to share their findings during the XVI International Congress on Molecular Plant–Microbe Interactions, which was held on the beautiful island of Rhodes in Greece. The congress was organized by the Agricultural University of Athens, the Hellenic Phytopathology Society, and the Hellenic Society of Phytiatry and provided over 1100 participants from 55 countries with the opportunity to present and discuss their current and future research. A great number of talks and posters were presented, however our aim within this report is to provide a snapshot of the discipline by focusing on just some of the exciting research and discussions which took place. The key topics discussed were virulence factors, epigenetic regulation, hormones, symbiosis factors, toxins, signaling pathways, microbe recognition, immunity, and pathogen diagnostics. Effector biology was also a recurrent theme in many plenary and concurrent sessions, indicating the importance of a topic that was also highlighted recently by a Virtual Special Issue in New Phytologist (see Kuhn & Panstruga, 2014). In addition to this, throughout the meeting next generation sequencing (NGS) techniques were described and shown to be shedding new light on long-standing issues in microbial ecology.

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Traffic: Rerouting of plant late endocytic trafficking towards a pathogen interface (2014)

Traffic: Rerouting of plant late endocytic trafficking towards a pathogen interface (2014) | Publications | Scoop.it

The biogenesis and functions of the extrahaustorial membrane (EHM), an intimate interface between plants and filamentous pathogens, are poorly understood. One long-standing puzzle is why several membrane proteins, such as some cell surface receptors, are missing from the EHM. We gained a significant insight into how the EHM is formed and made an important step in understanding why certain membrane proteins are missing from the EHM. We discovered that late endosomes targeted to the vacuoles are rerouted to the EHM. This process is dynamic because, upon activation, a cell surface immune receptor traffics to this compartment. We propose a model in which some cell surface receptors that undergo ligand induced endocytosis and traffic to late endosomes get sorted to the host pathogen interface, instead of taking the default route to the vacuole as in uninfected cells.


--- A number of plant pathogenic and symbiotic microbes produce specialized cellular structures that invade host cells where they remain enveloped by host-derived membranes. The mechanisms underlying the biogenesis and functions of host-microbe interfaces are poorly understood. Here, we show that plant late endocytic trafficking is diverted towards the extrahaustorial membrane; a host-pathogen interface that develops in plant cells invaded by Irish potato famine pathogen Phytophthora infestans. A late endosome and tonoplast marker protein Rab7 GTPase RabG3c, but not a tonoplast-localized sucrose transporter, is recruited to the extrahaustorial membrane suggesting specific rerouting of vacuole targeted late endosomes to a host pathogen interface. We revealed the dynamic nature of this process by showing that, upon activation, a cell surface immune receptor traffics towards the haustorial interface. Our work provides insight into the biogenesis of the extrahaustorial membrane and reveals dynamic processes that recruit membrane compartments and immune receptors to this host-pathogen interface.

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Plant Physiology: Efficient gene editing in tomato in the first generation using the CRISPR/Cas9 system (2014)

Plant Physiology: Efficient gene editing in tomato in the first generation using the CRISPR/Cas9 system (2014) | Publications | Scoop.it

To test the efficacy of CRISPR/Cas9 in tomato, we chose to target a gene that, when function was disrupted, would result in a distinctive, immediately recognizable phenotype early in the plant tissue culture phase of Agrobacterium-mediated transformation. A CRISPR/Cas9 construct was designed to target neighboring sequences in the second exon of the tomato homolog of Arabidopsis ARGONAUTE7 (SlAGO7), because loss-of-function mutations are recessive and result in plants whose typical compound flat leaves become needle-like, or “wiry” (Fig. 1) (Lesley, 1928; Yifhar et al., 2012). SlAGO7 is required for the biogenesis of a class of small RNAs known as trans-acting short interfering RNAs (ta-siRNAs), which regulate organ polarity through post-transcriptional silencing of AUXIN RESPONSE FACTOR (ARF) genes (Husbands et al., 2009). Strong alleles of slago7 thus produce lower levels of ta-siRNAs and reduced ARF mRNA degradation, resulting in the first leaves of mutant plants having leaflets without petioles, and later formed leaves lacking laminae (Fig. 1C). These distinctive phenotypes allowed us to immediately identify first generation transformed (T0) plants in which both alleles of SlAGO7 might be mutated.

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Molecular Plant Pathology: The Top 10 oomycete pathogens in molecular plant pathology (2014)

Molecular Plant Pathology: The Top 10 oomycete pathogens in molecular plant pathology (2014) | Publications | Scoop.it

Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens that threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. The article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.


See also [link below]:


Top 10 plant-parasitic nematodes in molecular plant pathology
Top 10 plant viruses in molecular plant pathology
Top 10 plant pathogenic bacteria in molecular plant pathology
The Top 10 fungal pathogens in molecular plant pathology


http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1364-3703/homepage/free_poster.htm

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PLOS Biology: New Horizons for Plant Translational Research (2014)

PLOS Biology: New Horizons for Plant Translational Research (2014) | Publications | Scoop.it

The world's human population continues to expand and is predicted to reach ~9 billion by 2040, up from its current level of just over 7 billion. Some estimate that with this rate of population growth, accommodating the increased demand for food will require the world's agricultural production to increase 50% by 2030. The planet's water resources are also under pressure. As Pamela Ronald highlights in her accompanying Essay, the amount of fresh water available per person has decreased 4-fold in the last 60 years and of the water that is available, ~70% is already used for agriculture. Thus, agricultural production must be intensified to feed more people with less water on the same amount of land (given that little undeveloped arable land remains and what does is being lost to urbanization, desertification, and environmental damage). Furthermore, pathogens that cause devastating crop losses continue to spread in the face of increased global commerce and climate change. Given these challenges, there is a pressing need for plant research to produce solutions to ensure food security in a sustainable and safe way. The need is acute in both developed countries and in the less developed parts of the world, where many people endure chronic malnutrition and suffer the long term consequences on their health and well being. Plant scientists, therefore, urgently need to increase the productivity, pathogen resistance, and sustainability of existing crops, and are challenged to domesticate new crops.

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PlantVillage: Keeping Up With The Plant Destroyers (2014)

PlantVillage: Keeping Up With The Plant Destroyers (2014) | Publications | Scoop.it

Readers of PlantVillage who visited popular pages like the one on tomato late blight would have come across the term “oomycetes” and probably wondered what in the world is an oomycete? It’s the taxon of microbes that groups many plant pathogens such as Phytophthora, Pythium, and the downy mildews. These are destructive pathogens of plants. Phytophthora, which stems from Greek words meaning plant-destroyer, is a diverse group of plant pathogens with over 100 species known to science . It includes the infamous Irish potato famine pathogen Phytophthora infestans. When this pathogen reached Ireland in the 1840s, it triggered famine and mayhem with one million people dead and another million forced to leave the island. Today, the late blight disease caused by P. infestans threatens not only tomatoes and potatoes in your gardens but also commercial and subsistence farming worldwide. Matt Fisher, Sarah Gurr and their colleagues recently estimated that losses due to late blight add up to enough calories to feed hundreds of millions of people.


So what are these oomycetes that are so feared by gardeners and farmers alike? Traditionally oomycetes were thought to be fungi (yeasts, molds and mushrooms). They are not. Modern methods of evolutionary analyses, known as phylogenetics, have cemented the view that oomycetes are only distant relatives of the fungi. In fact, fungi are more closely related to you and I than they are to the oomycetes. Oomycete biologists like to quip “bats are not birds, dolphins are not fish, and oomycetes are not fungi.” In fact, oomycetes turned out to have unexpected marine cousins in brown algae (kelp) and diatoms in a grouping known as the heterokonts. Oomycetes form a very deep branch in the tree of life and may have evolved from marine parasitic microorganisms. Just a few months ago, while I was visiting Christine Strullu-Derrien and Paul Kenrick at the Natural History Museum in London, I had the amazing opportunity to hold a fossil oomycete that is 300 million year old. Already in those ancient times, oomycetes were successful colonizers of plants and may even have been parasitic.


But evolution is a complicated process. More often than widely assumed, it proceeded as a reticulate network rather than a straight line. One example is the transfer of genes from one organism to another. This process, known as horizontal or lateral gene transfer, has occurred frequently in bacteria but is not as well documented in more complex organisms like oomycetes and fungi. Nonetheless, Tom Richard and colleagues at Exeter University reported that oomycetes have at some point in their evolution acquired genes from fungi. Whether this took place hundreds million years ago or more recently is not yet resolved. But as Tom likes to say “oomycetes are 99% not fungi”. How this phenomenon has contributed to the evolution of oomycetes into destructive plant pathogens is an interesting research topic.


But why all the misery? Why are oomycetes the scourge of farmers worldwide? The truth is, although Phytophthora are astonishing plant killers that can wipe out crops in days, the secret of their success is their ability to rapidly adapt to resistant plant varieties. Just like the constantly morphing flu virus, the potato blight pathogen and its relatives continuously spawn new races adapted to the resistant varieties released by plant breeders and even occasionally to new host plants. Like Lewis Carroll’s fictional Red Queen, plant breeders and biotechnologists only hope is to strenuously run to keep in the same place. If only we could produce resistant varieties more often then perhaps we’ll have a chance to outrace the ever-evolving blight pathogen.


So while you lament your blighted potatoes and your dying tomatoes, take a moment to ponder over the awesome parasite that’s making your vegetable garden look so gloomy. That microbe has already colonized plants way before humans emerged on earth. And for hundreds of millions of years it has kept on changing, evolving, and adapting ensuring its uninterrupted survival on an astonishing array of plant species and varieties. When humans domesticated plants, it could not resist the offering and adopted the crops as its new hosts. Ultimately, it moved to new continents and farmlands causing misery and despair. But we haven’t given up. Plant pathologists are hard at work learning more about these parasites and applying new knowledge and technologies to build disease-resistant crops.

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bioRxiv: Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community (2014)

bioRxiv: Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community (2014) | Publications | Scoop.it

Ash dieback is a fungal disease of ash trees caused by Hymenoscyphus pseudoalbidus that has swept across Europe in the last two decades and is a significant threat to the ash population. This emergent pathogen has been relatively poorly studied and little is known about its genetic make-up. In response to the arrival of this dangerous pathogen in the UK we took the unusual step of providing an open access database and initial sequence datasets to the scientific community for analysis prior to performing an analysis of our own. Our goal was to crowdsource genomic and other analyses and create a community analysing this pathogen. In this report on the evolution of the community and data and analysis obtained in the first year of this activity, we describe the nature and the volume of the contributions and reveal some preliminary insights into the genome and biology of H. pseudoalbidus that emerged. In particular our nascent community generated a first-pass genome assembly containing abundant collapsed AT-rich repeats indicating a typically complex genome structure. Our open science and crowdsourcing effort has brought a wealth of new knowledge about this emergent pathogen within a short time-frame. Our community endeavour highlights the positive impact that open, collaborative approaches can have on fast, responsive modern science.

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Niklaus Grunwald's curator insight, April 26, 12:46 PM

An example of crowdsourcing genomics ...

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Methods in Molecular Biology: Two-Dimensional Data Binning for the Analysis of Genome Architecture in Filamentous Plant Pathogens and Other Eukaryotes (2014)

Methods in Molecular Biology: Two-Dimensional Data Binning for the Analysis of Genome Architecture in Filamentous Plant Pathogens and Other Eukaryotes (2014) | Publications | Scoop.it

Genome architecture often reflects an organism’s lifestyle and can therefore provide insights into gene function, regulation, and adaptation. In several lineages of plant pathogenic fungi and oomycetes, characteristic repeat-rich and gene-sparse regions harbor pathogenicity-related genes such as effectors. In these pathogens, analysis of genome architecture has assisted the mining for novel candidate effector genes and investigations into patterns of gene regulation and evolution at the whole genome level. Here we describe a two-dimensional data binning method in R with a heatmap-style graphical output to facilitate analysis and visualization of whole genome architecture. The method is flexible, combining whole genome architecture heatmaps with scatter plots of the genomic environment of selected gene sets. This enables analysis of specific values associated with genes such as gene expression and sequence polymorphisms, according to genome architecture. This method enables the investigation of whole genome architecture and reveals local properties of genomic neighborhoods in a clear and concise manner.

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rougeforfire's curator insight, April 7, 4:42 AM

This seems pretty interesting.. That's a nice gift idea

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Frontiers Plant Science: The genome sequence and effector complement of the flax rust pathogen Melampsora lini (2014)

Frontiers Plant Science: The genome sequence and effector complement of the flax rust pathogen Melampsora lini (2014) | Publications | Scoop.it

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimise parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analysed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.


Via Francis Martin, Kamoun Lab @ TSL
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Francis Martin's curator insight, March 4, 2:30 PM

A long awaited genome! More rust genomes needed.

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PLOS Biology: Unsolved Mystery - How Do Filamentous Pathogens Deliver Effector Proteins into Plant Cells? (2014)

PLOS Biology: Unsolved Mystery - How Do Filamentous Pathogens Deliver Effector Proteins into Plant Cells? (2014) | Publications | Scoop.it

Fungal and oomycete plant parasites are among the most devastating pathogens of food crops. These microbes secrete effector proteins inside plant cells to manipulate host processes and facilitate colonization. How these effectors reach the host cytoplasm remains an unclear and debated area of plant research. In this article, we examine recent conflicting findings that have generated discussion in the field. We also highlight promising approaches based on studies of both parasite and host during infection. Ultimately, this knowledge may inform future broad spectrum strategies for protecting crops from such pathogens.

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PLOS Genetics: Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus (2014)

PLOS Genetics: Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus (2014) | Publications | Scoop.it

Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregulariswith other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.

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Jean-Michel Ané's curator insight, January 10, 8:59 AM

Beautiful work

Steve Marek's curator insight, January 12, 12:36 PM

Hypervariable rDNA explains high internuclear diversity

Comparative genomics returns prodigal glomeraleans to the zygomycetes 

Jennifer Mach's curator insight, January 12, 4:20 PM

Single nucleus sequencing!

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PLOS ONE: Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data (2013)

PLOS ONE: Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data (2013) | Publications | Scoop.it

Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/.

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