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Updates from the group of Sophien Kamoun at The Sainsbury Lab
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Rescooped by Kamoun Lab @ TSL from Plant Pathogenomics
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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, 1:42 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, 11:30 AM

A long awaited genome! More rust genomes needed.

Rescooped by Kamoun Lab @ TSL from Plants and Microbes
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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, 5:59 AM

Beautiful work

Steve Marek's curator insight, January 12, 9:36 AM

Hypervariable rDNA explains high internuclear diversity

Comparative genomics returns prodigal glomeraleans to the zygomycetes 

Jennifer Mach's curator insight, January 12, 1:20 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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Rescooped by Kamoun Lab @ TSL from Plants and Microbes
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PLOS ONE: Major Transcriptome Reprogramming Underlies Floral Mimicry Induced by the Rust Fungus Puccinia monoica in Boechera stricta (2013)

PLOS ONE: Major Transcriptome Reprogramming Underlies Floral Mimicry Induced by the Rust Fungus Puccinia monoica in Boechera stricta (2013) | Publications | Scoop.it

Puccinia monoica is a spectacular plant parasitic rust fungus that triggers the formation of flower-like structures (pseudoflowers) in its Brassicaceae host plant Boechera stricta. Pseudoflowers mimic in shape, color, nectar and scent co-occurring and unrelated flowers such as buttercups. They act to attract insects thereby aiding spore dispersal and sexual reproduction of the rust fungus. Although much ecological research has been performed on P.monoica-induced pseudoflowers, this system has yet to be investigated at the molecular or genomic level. To date, the molecular alterations underlying the development of pseudoflowers and the genes involved have not been described. To address this, we performed gene expression profiling to reveal 256 plant biological processes that are significantly altered in pseudoflowers. Among these biological processes, plant genes involved in cell fate specification, regulation of transcription, reproduction, floral organ development, anthocyanin (major floral pigments) and terpenoid biosynthesis (major floral volatile compounds) were down-regulated in pseudoflowers. In contrast, plant genes involved in shoot, cotyledon and leaf development, carbohydrate transport, wax biosynthesis, cutin transport and L-phenylalanine metabolism (pathway that results in phenylethanol and phenylacetaldehyde volatile production) were up-regulated. These findings point to an extensive reprogramming of host genes by the rust pathogen to induce floral mimicry. We also highlight 31 differentially regulated plant genes that are enriched in the biological processes mentioned above, and are potentially involved in the formation of pseudoflowers. This work illustrates the complex perturbations induced by rust pathogens in their host plants, and provides a starting point for understanding the molecular mechanisms of pathogen-induced floral mimicry.

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Nanci J. Ross's curator insight, September 18, 2013 10:30 AM

ok, this is just so cool (even if it is a fungus!)

Steve Marek's curator insight, September 18, 2013 11:57 AM

So very cool...So what's wrong with insects attracted to purple flowers?

As a rust, why not just put your spores in the anthers like Microbotryum?

Rescooped by Kamoun Lab @ TSL from MutMap
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PLOS ONE: MutMap+: Genetic Mapping and Mutant Identification without Crossing in Rice (2013)

PLOS ONE: MutMap+: Genetic Mapping and Mutant Identification without Crossing in Rice (2013) | Publications | Scoop.it

Advances in genome sequencing technologies have enabled researchers and breeders to rapidly associate phenotypic variation to genome sequence differences. We recently took advantage of next-generation sequencing technology to develop MutMap, a method that allows rapid identification of causal nucleotide changes of rice mutants by whole genome resequencing of pooled DNA of mutant F2 progeny derived from crosses made between candidate mutants and the parental line. Here we describe MutMap+, a versatile extension of MutMap, that identifies causal mutations by comparing SNP frequencies of bulked DNA of mutant and wild-type progeny of M3 generation derived from selfing of an M2 heterozygous individual. Notably, MutMap+ does not necessitate artificial crossing between mutants and the wild-type parental line. This method is therefore suitable for identifying mutations that cause early development lethality, sterility, or generally hamper crossing. Furthermore, MutMap+ is potentially useful for gene isolation in crops that are recalcitrant to artificial crosses.

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Teresa M. Nash's comment, November 27, 2013 7:14 PM
nice
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New Phytologist: MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii (2013)

New Phytologist: MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii (2013) | Publications | Scoop.it

Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole-genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions missing from the reference (gaps) cannot be identified by simple alignment.Here we report on a method called ‘MutMap-Gap’, which involves delineating a candidate region harboring a mutation of interest using the recently reported MutMap method, followed by de novo assembly, alignment, and identification of the mutation within genome gaps.We applied MutMap-Gap to isolate the blast resistant gene Pii from the rice cv Hitomebore using mutant lines that have lost Pii function.MutMap-Gap should prove useful for cloning genes that exhibit significant structural variations such as disease resistance genes of the nucleotide-binding site-leucine rich repeat (NBS-LRR) class.

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Plant Phys: Regulation of transcription of NB-LRR-encoding genes SNC1 and RPP4 via H3K4 tri-methylation (2013)

Plant Phys: Regulation of transcription of NB-LRR-encoding genes SNC1 and RPP4 via H3K4 tri-methylation (2013) | Publications | Scoop.it

Plant nucleotide-binding leucine-rich repeat (NB-LRR) proteins serve as intracellular sensors to detect pathogen effectors and trigger immune responses. Transcription of the NB-LRR-encoding Resistance (R) genes needs to be tightly controlled to avoid inappropriate defense activation. How the expression of the NB-LRR R genes is regulated is poorly understood. The Arabidopsis snc1 mutant carries a gain-of-function mutation in a TIR-NB-LRR-encoding gene, resulting in the constitutive activation of plant defence responses. A snc1 suppressor screen identified modifier of snc1, 9 (mos9), which partially suppresses the autoimmune phenotypes of snc1. Positional cloning revealed that MOS9 encodes a plant-specific protein of unknown function. Expression analysis showed that MOS9 is required for the full expression of TIR-NB-LRR protein-encoding RPP4 and SNC1, both of which reside in the RPP4 cluster. Co-immunoprecipitation and mass spectrometry analyses revealed that MOS9 associates with the Set1 class H3K4 methyl transferase ATXR7. Like MOS9, ATXR7 is also required for the full expression of SNC1 and the autoimmune phenotypes in the snc1 mutant. In atxr7 mutant plants, the expression of RPP4 is similarly reduced and resistance against Hyaloperonospora arabidopsidis Emwa1 is compromised. Consistent with the attenuated expression of SNC1 and RPP4, H3K4me3 marks are reduced around the promoters of SNC1 and RPP4 in mos9 plants. Our data suggest that MOS9 functions together with ATXR7 to regulate the expression of SNC1 and RPP4 through H3K4 methylation, which plays an important role in fine-tuning their transcription levels and functions in plant defence.

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Rescooped by Kamoun Lab @ TSL from Plants and Microbes
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eLife: The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine (2013)

eLife: The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine (2013) | Publications | Scoop.it

Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the nineteenth century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the twentieth century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity.

 

eLife http://elife.elifesciences.org/content/2/e00731

 

arXiv preprint http://arxiv.org/abs/1305.4206

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Alejandro Rojas's curator insight, May 21, 2013 4:54 AM

I'm so excited to see a paper like this!, It is so great to have acces to papers like this through systems like ArXiv.  

Jennifer Mach's comment, May 21, 2013 6:34 AM
Nature News and Views article: http://www.nature.com/news/pathogen-genome-tracks-irish-potato-famine-back-to-its-roots-1.13021
Mary Williams's comment, May 21, 2013 8:45 AM
On the radio http://kamounlab.tumblr.com/post/50992192578/go-back-to-the-past-to-better-prepare-for-the
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BBC Radio 4: Diane Saunders speaking about ash fungus genomics and crowdsourcing (2013)

Listen to Diane Saunders speak about ash fungus genomics and crowdsourcing on BBC Radio 4. See also BBC News - Ash fungus genetic code unravelled http://bbc.in/ZkqY1N

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GigaScience: Crowdsourcing genomic analyses of ash and ash dieback -- power to the people (2013)

GigaScience: Crowdsourcing genomic analyses of ash and ash dieback -- power to the people (2013) | Publications | Scoop.it

Ash dieback is a devastating fungal disease of ash trees that has swept across Europe and recently reached the UK. This emergent pathogen has received little study in the past and its effect threatens to overwhelm the ash populations. In response to this we have produced some initial genomics datasets and taken the unusual step of releasing them to the scientific for analysis without first performing our own. In this manner we hope to 'crowdsource' analyses and bring the expertise of the community to bear on this problem as quickly as possible. Our data has been released through our website at oadb.tsl.ac.uk and a public GitHub repository.

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OpenAshDieBack » How useful is the AT1 assembly? (2012)

OpenAshDieBack » How useful is the AT1 assembly? (2012) | Publications | Scoop.it
Chalara ash dieback was first confirmed in the natural environment in the UK in late autumn based on samples from Ashwellthorpe Wood near Norwich. We decided early on in this project that speed would be a critical driver given the emergency nature of the problem. We decided that we should generate genetic sequences as rapidly as possible, release them to the community, and prompt the crowdsourcing exercise we have been publicizing since Friday.

The normal procedure would be to culture the pathogen and sequence the genome and transcriptome from cultured material and controlled laboratory infections. Here, we decided to take the unusual step of directly sequencing the “interaction transcriptome” of a lesion dissected from an infected ash twig. This was the most rapid way to proceed to generate useful information without proceeding through standard laboratory culturing. This is the shortest route from the wood to the sequencer to the computer. The question that many of you must be asking is how useful is this data? This post addresses this question and summarizes the preliminary analyses that the TSL team has produced.
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Freddy Monteiro's comment, December 17, 2012 5:06 AM
This is such a wonderful initiative. Definitively one more proof that science can be open to the public and to other scientists. One more prove that in situations like this, collaborative efforts are much worthwhile than competitive ones ! Thank's for sharing
Kamoun Lab @ TSL's comment, December 17, 2012 6:38 AM
Thanks much Freddy! OpenSource Biology Rules!
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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 29, 11:09 PM

I just really love the idea of synthetic immune receptors!

nosehound's comment, April 6, 10:21 PM
Its striking
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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, 12:52 PM

What a great week for effector biology!!

Freddy Monteiro's comment, March 14, 5:42 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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Nature Biotech: Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease (2013)

Nature Biotech: Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease (2013) | Publications | Scoop.it

Sustainable intensification of crop production is essential to ensure food demand is matched by supply as the human population continues to increase. This will require high-yielding crop varieties that can be grown sustainably with fewer inputs on less land. Both plant breeding and genetic modification (GM) methods make valuable contributions to varietal improvement, but targeted genome engineering promises to be critical to elevating future yields. Most such methods require targeting DNA breaks to defined locations followed by either nonhomologous end joining (NHEJ) or homologous recombination. Zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) can be engineered to create such breaks, but these systems require two different DNA binding proteins flanking a sequence of interest, each with a C-terminal FokI nuclease module. We report here that the bacterial clustered, regularly interspaced, short palindromic repeats (CRISPR) system, comprising a CRISPR-associated (Cas)9 protein and an engineered single guide RNA (sgRNA) that specifies a targeted nucleic acid sequence, is applicable to plants to induce mutations at defined loci.

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Elizabeth Jones's curator insight, October 2, 2013 1:25 PM

CRISPR-Cas9 is hot right now, and it's being used in several different ways: for genome-editing in cells of various species (here they're showing it works in plants),  or to create heritable changes (i.e. new transgenic animal lines), and also as a transcription factor to regulate gene expression without altering the nuclear DNA. 

 

Constructs that use Cas9 and synthetic guide RNA (sgRNA) can be customized to target any gene of interest, and can produce insertions, deletions, or incorportation of variant sequences into genomic DNA. Customized constructs can be ordered from gene synthesis suppliers such as GenScript, and delivered much more quickly and cheaply than they can be produced in a typical lab using traditional molecular cloning techniques. 

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Genome Biology: From pathogen genomes to host plant processes: the power of plant parasitic oomycetes (2013)

Genome Biology: From pathogen genomes to host plant processes: the power of plant parasitic oomycetes (2013) | Publications | Scoop.it

Recent pathogenomic research on plant parasitic oomycete effector function and plant host responses has resulted in major conceptual advances in plant pathology, which has been possible thanks to the availability of genome sequences.

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PLOS Genetics: Hooked and Cooked: A Fish Killer Genome Exposed (2013)

PLOS Genetics: Hooked and Cooked: A Fish Killer Genome Exposed (2013) | Publications | Scoop.it

Few microorganisms match the impact that the oomycetes have had on mankind. This distinct lineage of eukaryotes is well-known for its most notorious member, Phytophthora infestans, the agent of the nineteenth century Irish potato famine, and several other devastating pathogens of cultivated and wild plants [1]. Indeed, more than 60% of oomycete species infect plants [2]. Less known is the fact that many oomycetes are parasitic on animals, from freshwater fish and crustaceans to mammals, such as livestock, pets, and humans [3]. Animal parasitic oomycetes have received much less attention than their plant pathogenic kin, and our understanding of their virulence mechanisms is rudimentary. However, research momentum is poised to accelerate with the first report of the genome of an animal parasitic oomycete. In this issue of PLOS Genetics, Jiang et al. [4] describe the 63 Mbp genome sequence of the fish pathogen Saprolegnia parasitica and highlight a distinct repertoire of candidate virulence genes.

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NPR Weekend All Things Considered: Scientists Trace Source Of Famed Irish Potato Famine (2013)

NPR Weekend All Things Considered: Scientists Trace Source Of Famed Irish Potato Famine (2013) | Publications | Scoop.it

We now know what caused the Irish potato famine. Scientists have pinpointed the pathogen by using plant samples collected in the mid-19th century. Weekends on All Things Considered host Jacki Lyden talks about it with the study's co-author, Sophien Kamoun of the Sainsbury Lab in the United Kingdom.

 

Other interviews about the Yoshida et al. eLife paper:

 

The Naked Scientists “The bug behind the potato blight.” http://www.thenakedscientists.com/HTML/content/interviews/interview/1000238/

 

BBC World Service http://kamounlab.tumblr.com/post/50996438105/listen-to-the-interview-on-bbc-world-service

 

BBC Radio Ulster http://kamounlab.tumblr.com/post/50992192578/go-back-to-the-past-to-better-prepare-for-the

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zhouxia's curator insight, May 31, 2013 2:03 AM

npr

BLC3's curator insight, June 4, 2013 3:43 AM

Scientists can even help history out. 

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BMC Genomics: Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors (2013)

BMC Genomics: Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors (2013) | Publications | Scoop.it

Background - Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the molecular basis of PST pathogenicity. In particular, the characterisation of the structure, function and evolutionary dynamics of secreted effector proteins that are detected by host immune receptors can help guide and prioritize breeding efforts. However, to date, our knowledge of the effector repertoire of cereal rust pathogens is limited.

 

Results - We re-sequenced genomes of four PST isolates from the US and UK to identify effector candidates and relate them to their distinct virulence profiles. First, we assessed SNP frequencies between all isolates, with heterokaryotic SNPs being over tenfold more frequent (5.29 +/- 2.23 SNPs/kb) than homokaryotic SNPs (0.41 +/- 0.28 SNPs/kb). Next, we implemented a bioinformatics pipeline to integrate genomics, transcriptomics, and effector-focused annotations to identify and classify effector candidates in PST. RNAseq analysis highlighted transcripts encoding secreted proteins that were significantly enriched in haustoria compared to infected tissue. The expression of 22 candidate effector genes was characterised using qRT-PCR, revealing distinct temporal expression patterns during infection in wheat. Lastly, we identified proteins that displayed non-synonymous substitutions specifically between the two UK isolates PST-87/7 and PST-08/21, which differ in virulence to two wheat varieties. By focusing on polymorphic variants enriched in haustoria, we identified five polymorphic effector candidates between PST-87/7 and PST-08/21 among 2,999 secreted proteins. These allelic variants are now a priority for functional validation as virulence/avirulence effectors in the corresponding wheat varieties.

 

Conclusions - Integration of genomics, transcriptomics, and effector-directed annotation of PST isolates has enabled us to move beyond the single isolate-directed catalogues of effector proteins and develop a framework for mining effector proteins in closely related isolates and relate these back to their defined virulence profiles. This should ultimately lead to more comprehensive understanding of the PST pathogenesis system, an important first step towards developing more effective surveillance and management strategies for one of the most devastating pathogens of wheat.

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Plant J: Deployment of Burkholderia glumae type III secretion system as an efficient tool for translocating pathogen effectors to monocot cells (2013)

Plant J: Deployment of Burkholderia glumae type III secretion system as an efficient tool for translocating pathogen effectors to monocot cells (2013) | Publications | Scoop.it

Genome sequences of plant fungal pathogens have enabled the identification of effectors that cooperatively modulate the cellular environment for successful fungal growth and suppress host defense. Identification and characterization of novel effector proteins are crucial to understand pathogen virulence and host plant defense mechanisms. Previous reports indicate that the Pseudomonas syringae pv. tomato DC3000 type III secretion system (T3SS) can be used to study how non-bacterial effectors manipulate dicot plant cell function using the Effector Detector Vector (pEDV) system. Here we report a pEDV-based effector delivery system in which the T3SS of Burkholderia glumae, an emerging rice pathogen, is used to translocate the AVR-Pik and AVR-Pii effectors of fungal pathogen Magnaporthe oryzae to rice cytoplasm. The translocated AVR-Pik and AVR-Pii showed avirulence activity when tested in rice cultivars containing the cognate R genes. AVR-Pik reduced and delayed the hypersensitive response triggered by B. glumae in the non-host plant Nicotiana benthamiana indicative of an immunosuppressive virulence activity. AVR proteins fused with fluorescent protein and nuclear localization signal were delivered by B. glumae T3SS and observed in the nuclei of infected cells in rice, wheat, barley and N. benthamiana. Our bacterial T3SS-enabled eukaryotic effector delivery and subcellular localization assays provide a useful method to identify and study effector functions in monocot plants.


Via Nicolas Denancé, Freddy Monteiro, Kamoun Lab @ TSL
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Freddy Monteiro's comment, March 10, 2013 9:50 AM
Nico, this paper comes in time to feature in the general discussion of my dissertation, in a section where I explore if a temporal effector translocation hirarchy would exist in R. solanacearum. I wanted to cite a couple papers characterizing effector translocation in planta and this one is a perfect fit. It is amazing how the principle behind the use of NLS, so common nowadays for the characterization of oomycete effectors, could be successfully applied to bacteria pathogens. I hope this method could be useful in the future to the validation (re-validation) of pathogen effector proteins. Thank you for sharing.
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Plant J: QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations (2013)

Plant J: QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations (2013) | Publications | Scoop.it

The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci: QTL). QTL mapping and isolation is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. Since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been however time consuming and labor intensive. Here we report a rapid identification of plant QTL by whole genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines (RILs) and F2 populations and successfully identified QTL for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTL over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps.

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Teresa M. Nash's comment, November 27, 2013 10:23 PM
Nice.