Genomics for plant health
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Field trial of Xanthomonas wilt disease-resistant bananas in East Africa : Nature Biotechnology : Nature Publishing Group

Field trial of Xanthomonas wilt disease-resistant bananas in East Africa : Nature Biotechnology : Nature Publishing Group | Genomics for plant health | Scoop.it
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The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes

The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes | Genomics for plant health | Scoop.it
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Small homologous blocks in Phytophthora genomes do not point to an ancient whole-genome duplication

Small homologous blocks in Phytophthora genomes do not point to an ancient whole-genome duplication | Genomics for plant health | Scoop.it
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Genome Biol Evol: Small homologous blocks in Phytophthora genomes do not point to an ancient whole-genome duplication (2014)

Genome Biol Evol: Small homologous blocks in Phytophthora genomes do not point to an ancient whole-genome duplication (2014) | Genomics for plant health | Scoop.it

Genomes of the plant-pathogenic genus Phytophthora are characterized by small duplicated blocks consisting of two consecutive genes (2HOM blocks) as well as by an elevated abundance of similarly aged gene duplicates. Both properties, in particular the presences of 2HOM blocks, have been attributed to a whole-genome duplication (WGD) at the last common ancestor of Phytophthora. However large intra-species synteny – compelling evidence for a WGD – has not been detected. Here we revisited the WGD hypothesis by deducing the age of 2HOM blocks. Two independent timing methods reveal that the majority of 2HOM blocks arose after divergence of the Phytophthora lineages. In addition, a large proportion of the 2HOM block copies co-localize on the same scaffold. Therefore, the presence of 2HOM blocks does not support a WGD at the last common ancestor of Phytophthora. Thus, genome evolution ofPhytophthora is likely driven by alternative mechanisms, such as bursts of transposon activity.


Via Kamoun Lab @ TSL
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The genome sequence and effector complement of the flax rust pathogen Melampsora lini

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
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Francis Martin's curator insight, March 4, 2014 2:30 PM

A long awaited genome! More rust genomes needed.

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UK lacks experts to deal with tree and plant diseases, say MPs - Blue and Green Tomorrow

UK lacks experts to deal with tree and plant diseases, say MPs - Blue and Green Tomorrow | Genomics for plant health | Scoop.it

“The UK does not have enough expertise in the field of tree and plant diseases, according to a report by MPs on the environment, food and rural affairs comm (Government "must act with urgency" to address UK skills gap in plant and tree diseases”

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Insights into the Dekkera bruxellensis Genomic Landscape: Comparative Genomics Reveals Variations in Ploidy and Nutrient Utilisation Potential amongst Wine Isolates

Insights into the Dekkera bruxellensis Genomic Landscape: Comparative Genomics Reveals Variations in Ploidy and Nutrient Utilisation Potential amongst Wine Isolates | Genomics for plant health | Scoop.it
PLOS Genetics is an open-access
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European Journal of Plant Pathology: Phylogeny and evolution of plant pathogenic oomycetes - a global overview (2014)

European Journal of Plant Pathology: Phylogeny and evolution of plant pathogenic oomycetes - a global overview (2014) | Genomics for plant health | Scoop.it
Oomycetes have colonised all continents and oceans in a great variety of habitats and are arguably one of the most successful eukaryotic lineages. This is contrasted by the limited knowledge available for this group in various fields in comparison to other ubiquitous eukaryotes, such as unikont fungi, animals or plants. In this review an overview is given on the evolution and diversification of the oomycetes, with focus on the plant parasitic lineages and aspects of wild pathosystems.
Via Kamoun Lab @ TSL
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Jumping Hosts | The Scientist Magazine®

Jumping Hosts | The Scientist Magazine® | Genomics for plant health | Scoop.it
A single amino acid change helps a plant pathogen related to the causative agent of the Irish potato famine infect a new host.
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PLOS Pathogens: Origin, Migration Routes and Worldwide Population Genetic Structure of the Wheat Yellow Rust Pathogen Puccinia striiformis f.sp. tritici

PLOS Pathogens: Origin, Migration Routes and Worldwide Population Genetic Structure of the Wheat Yellow Rust Pathogen Puccinia striiformis f.sp. tritici | Genomics for plant health | Scoop.it
From molecules to physiology
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Agronomy | Free Full-Text | A Draft Genome Sequence for Ensete ventricosum, the Drought-Tolerant “Tree Against Hunger”

We present a draft genome sequence for enset (Ensete ventricosum) available via the Sequence Read Archive (accession number SRX202265) and GenBank (accession number AMZH01.
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PLOS Genetics: Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus (2013)

PLOS Genetics: Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus (2013) | Genomics for plant health | 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, 2014 8:59 AM

Beautiful work

Steve Marek's curator insight, January 12, 2014 12:36 PM

Hypervariable rDNA explains high internuclear diversity

Comparative genomics returns prodigal glomeraleans to the zygomycetes 

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Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding

Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding | Genomics for plant health | Scoop.it
PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.
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Budget boosts fight for kauri - Northern Advocate - Northern Advocate News

Budget boosts fight for kauri - Northern Advocate - Northern Advocate News | Genomics for plant health | Scoop.it
One of the quieter offerings of Budget 2014 is a multi-million-dollar weapon to help fight the disease that threatens Northern New Zealand's iconic kauri trees. - Northern Advocate
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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) | Genomics for plant health | 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.


Via Kamoun Lab @ TSL
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Mary Williams's curator insight, April 25, 2014 3:02 AM

Good overview for students - very accessible and interesting!

Freddy Monteiro's comment, April 25, 2014 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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Feeding 9 Billion - National Geographic

Feeding 9 Billion - National Geographic | Genomics for plant health | Scoop.it
When we think about threats to the environment, we tend to picture cars and smokestacks, not dinner. But the truth is, our need for food poses one of the biggest dangers to the planet.
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Automated alignment-based curation of gene models in filamentous fungi


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Strategies of attack and defence in woody plant–Phytophthora interactions

Strategies of attack and defence in woody plant–Phytophthora interactions | Genomics for plant health | Scoop.it

This review comprises both well-known and recently described Phytophthora species and concentrates on Phytophthora–woody plant interactions. First, comprehensive data on infection strategies are presented which were the basis for three models that explain invasion and spread of Phytophthora pathogens in different woody host plants. The first model describes infection of roots, the second concentrates on invasion of the trunk, and the last one summarizes infection and invasion of host plants via leaves. On the basis of morphological, physiological, biochemical and molecular data, scenarios are suggested which explain the sequences of reactions that occur in susceptible and tolerant plants following infections of roots or of stem bark. Particular emphasis is paid to the significance ofPhytophthora elicitins for such host–pathogen interactions. The overall goal is to shed light on the sequences of pathogenesis to better understand how Phytophthora pathogens harm their host plants.


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Transcriptome Analysis Reveals Pathogenicity and Evolutionary History of the Pathogenic Oomycete Pythium insidiosum

Transcriptome Analysis Reveals Pathogenicity and Evolutionary History of the Pathogenic Oomycete Pythium insidiosum | Genomics for plant health | Scoop.it
Oomycetes form a unique group of microorganisms that share hyphal morphology with fungi. Most of pathogenic oomycetes infect plants, while some species are capable of infecting animals. Pythium insidiosumis the only oomycete that can infect both humans and animals, and causes a life-threatening infectious disease, called “pythiosis”. Controlling an infection caused by P. insidiosum is problematic because effective antimicrobial drugs are not available. Information on the biology and pathogenesis of P. insidiosum is limited. We generated a P. insidiosum transcriptome of 26,735 unigenes, using the 454 sequencing platform. As adaptations to increased temperature inside human hosts are required for a successful pathogen, we generated P. insidiosum transcriptomes at 28°C and 37°C and identified 625 up-regulated and 449 down-regulated genes at 37°C. Comparing the proteomes of oomycetes, fungi, and parasites provided clues on the evolutionary history of P. insidiosum. Potential virulence factors of P. insidiosum, including putative effectors, were indentified. P. insidiosum harbored an extensive repertoire of ∼300 elicitin domain-containing proteins. The transcriptome, presented herein, provides an invaluable resource for exploring P. insidiosum’s biology, pathogenesis, and evolution.
Via Niklaus Grunwald
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European Journal of Plant Pathology: Phylogeny and evolution of plant pathogenic oomycetes - a global overview (2014)

European Journal of Plant Pathology: Phylogeny and evolution of plant pathogenic oomycetes - a global overview (2014) | Genomics for plant health | Scoop.it
Oomycetes have colonised all continents and oceans in a great variety of habitats and are arguably one of the most successful eukaryotic lineages. This is contrasted by the limited knowledge available for this group in various fields in comparison to other ubiquitous eukaryotes, such as unikont fungi, animals or plants. In this review an overview is given on the evolution and diversification of the oomycetes, with focus on the plant parasitic lineages and aspects of wild pathosystems.
Via Kamoun Lab @ TSL
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Effector Specialization in a Lineage of the Irish Potato Famine Pathogen

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How online gamers are solving science's biggest problems

How online gamers are solving science's biggest problems | Genomics for plant health | Scoop.it
A new generation of online games don't just provide entertainment – they help scientists solve their trickiest puzzles. Dara Mohammadi picks 10 of the best
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Big Data Revolution and Genomics Analysis

Big Data Revolution and Genomics Analysis | Genomics for plant health | Scoop.it
Curoverse and Tute Genomics secured $1.5 million each in seed funding in the past month aiming to bring gene sequencing to the masses.
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PLOS ONE: Population History and Pathways of Spread of the Plant Pathogen Phytophthora plurivora (2014)

PLOS ONE: Population History and Pathways of Spread of the Plant Pathogen Phytophthora plurivora (2014) | Genomics for plant health | Scoop.it
Human activity has been shown to considerably affect the spread of dangerous pests and pathogens worldwide. Therefore, strict regulations of international trade exist for particularly harmful pathogenic organisms. Phytophthora plurivora, which is not subject to regulations, is a plant pathogen frequently found on a broad range of host species, both in natural and artificial environments. It is supposed to be native to Europe while resident populations are also present in the US. We characterized a hierarchical sample of isolates from Europe and the US and conducted coalescent-, migration, and population genetic analysis of sequence and microsatellite data, to determine the pathways of spread and the demographic history of this pathogen. We found P. plurivora populations to be moderately diverse but not geographically structured. High levels of gene flow were observed within Europe and unidirectional from Europe to the US. Coalescent analyses revealed a signal of a recent expansion of the global P. plurivora population. Our study shows that P. plurivora has most likely been spread around the world by nursery trade of diseased plant material. In particular, P. plurivora was introduced into the US from Europe. International trade has allowed the pathogen to colonize new environments and/or hosts, resulting in population growth.
Via Niklaus Grunwald, Kamoun Lab @ TSL
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