Rhizoctonia solani is a major fungal pathogen of rice (Oryza sativa L.) that causes great yield losses in all rice-growing regions of the world. Here we report the draft genome sequence of the rice sheath blight disease pathogen, R. solani AG1 IA, assembled using next-generation Illumina Genome Analyser sequencing technologies. The genome encodes a large and diverse set of secreted proteins, enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, which probably reflect an exclusive necrotrophic lifestyle. We find few repetitive elements, a closer relationship to Agaricomycotina among Basidiomycetes, and expand protein domains and families. Among the 25 candidate pathogen effectors identified according to their functionality and evolution, we validate 3 that trigger crop defence responses; hence we reveal the exclusive expression patterns of the pathogenic determinants during host infection.
Via Kamoun Lab @ TSL
The work establishes an experimental framework for examining how plants interact with a microbial community that can influence their growth and development, productivity, and impact on the environment.
By the year 2050, the world's population will reach nine billion. The demand on the world's resources - energy, first and foremost - will be severe. But the road from now to then doesn't need be bleak.
A journal on Molecular Plant-Microbe Interactions granted by the Iowa Soybean Association (ISA) and the ISU Plant Sciences Institute reveals that Aphids cause malfunctions in the hormonal defense mechanism of the ...
o Plant Breeding for Agricultural Production. o Understanding Biological Mechanisms for Plant Production. o Understanding Plan-Associated Microorganisms and Plant-Microbe Interactions. o Controlling Weedy and Invasive ...
Legumes overcome nitrogen shortage by developing root nodules in which symbiotic bacteria fix atmospheric nitrogen in exchange for host-derived carbohydrates and mineral nutrients. Nodule development involves the distinct processes of nodule organogenesis, bacterial infection and the onset of nitrogen fixation. These entail profound, dynamic gene expression changes, notably contributed to by micro (mi)RNAs. Here, we used deep-sequencing, candidate-based expression studies and a selection of Lotus japonicus mutants uncoupling different symbiosis stages to identify miRNAs involved in symbiotic nitrogen fixation. Induction of a non-canonical miR171 isoform, which targets the key nodulation transcription factor NSP2, correlates with bacterial infection in nodules. A second candidate, miR397, is systemically induced in the presence of active, nitrogen-fixing nodules, but not in non-infected or inactive nodule organs. It is involved in nitrogen-fixation-related copper homeostasis and targets a member of the laccase copper protein family. These findings thus identify two miRNAs specifically responding to symbiotic infection and nodule function in legumes. De Luis A, Markmann K, Cognat V, Holt DB, Charpentier M, Parniske M, Stougaard J, Voinnet O. (2012). Plant Physiol. 2012 Oct 15. [Epub ahead of print]
Genome sequencing has been carried out on a small selection of major fungal ascomycete pathogens. These studies show that simple models whereby pathogens evolved from phylogenetically related saprobes by the acquisition or modification of a small number of key genes cannot be sustained.The genomes show that pathogens cannot be divided into three clearly delineated classes (biotrophs, hemibiotrophs and necrotrophs) but rather into a complex matrix of categories each with subtly different properties. It is clear that the evolution of pathogenicity is ancient, rapid and ongoing. Fungal pathogens have undergone substantial genomic rearrangements that can be appropriately described as ‘genomic tillage’. Genomic tillage underpins the evolution and expression of large families of genes – known as effectors – that manipulate and exploit metabolic and defence processes of plants so as to allow the proliferation of pathogens.
Keystone Symposia is pleased to announce its conference on “Plant Immunity: Pathways and Translation,” taking place April 7-12, 2013 at Big Sky Resort in Big Sky, Montana, USA.
Organized by Sophien Kamoun of Sainsbury Laboratory and Ken Shirasu of RIKEN, the four-day conference will:
• Convene with a keynote address by Paul M. Schulze-Lefert of Max Planck Institute for Plant Breeding Research, followed by four days of stimulating plenary sessions, workshops and poster sessions;
• Highlight the latest developments in understanding plant immune pathways, how these pathways are perturbed by pathogens, and how plants and their parasites co-evolve;
• Address how basic knowledge on plant immunity can be translated into applications of relevance to agriculture and the profile of translational plant pathology research in an era of looming food crisis.
Scholarships are available to students and postdocs and require submission of a brief application and abstract. Short talks will also be selected from submitted abstracts. Discounted student registrations are available. Note that registering by the early registration deadline saves US$150 on later fees.
Multilocus sequence analysis (MLSA) and type III effector (T3E) repertoire mining were performed to gain new insights into the genetic relatedness of Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), two major bacterial pathogens of rice. Based on a collection of 45 African and Asian strains, we first sequenced and analysed three housekeeping genes by MLSA, Bayesian clustering and a median-joining network approach. Second, we investigated the distribution of 32 T3E genes, which are known to be major virulence factors of plant pathogenic bacteria, in all selected strains, by polymerase chain reaction and dot-blot hybridization methods. The diversity observed within housekeeping genes, as well as within T3E repertoires, clearly showed that both pathogens belong to closely related, but distinct, phylogenetic groups. Interestingly, these evolutionary groups are differentiated according to the geographical origin of the strains, suggesting that populations of Xoo and Xoc might be endemic in Africa and Asia, and thus have evolved separately. We further revealed that T3E gene repertoires of both pathogens comprise core and variable gene suites that probably have distinct roles in pathogenicity and different evolutionary histories. In this study, we carried out a functional analysis of xopO, a differential T3E gene between Xoo and Xoc, to determine the involvement of this gene in tissue specificity. Altogether, our data contribute to a better understanding of the evolutionary history of Xoo and Xoc in Africa and Asia, and provide clues for functional studies aiming to understand the virulence, host and tissue specificity of both rice pathogens.
Bradyrhizobium strains sampled from 14 legume genera native to eastern North America showed substantial host-related phylogenetic clustering at three loci in the symbiotic island (SI) region (nodC, nifD, nifH), indicating selection of distinct suites of SI lineages by different legumes. Bacteria assorted consistently with particular legumes across two regions separated by 800 km, implying recurrent assembly of the same symbiotic combinations. High genetic polymorphism of all three SI loci relative to four nonsymbiotic loci supported the inference that a form of multiple-niche balancing selection has acted on the SI region, arising from differential symbiont utilization by different legume taxa. Extensive discordance between the tree for SI variants and a phylogenetic tree inferred for four housekeeping loci implied that lateral transfer of the symbiosis island region has been common (at least 26 transfer events among 85 Bradyrhizobium strains analysed). Patterns of linkage disequilibrium also supported the conclusion that recombination has impacted symbiotic and nonsymbiotic regions unequally. The high prevalence of lateral transfer suggests that acquisition of a novel SI variant may often confer a strong selective advantage for recipient cells.
Microevolution and origins of Bradyrhizobium populations associated with soybeans at two field sites (A and B, 280 km apart in Canada) with contrasting histories of inoculation was investigated using probabilistic analyses of six core (housekeeping) gene sequences. These analyses supported division of 220 isolates in five lineages corresponding either to B. japonicum groups 1 and 1a or to one of three novel lineages within the genus Bradyrhizobium. None of the isolates from site A and about 20% from site B (the only site with a recent inoculation history) were attributed to inoculation sources. The data suggest that most isolates were of indigenous origin based on sequence analysis of 148 isolates of soybean-nodulating bacteria from native legumes (Amphicarpaea bracteata and Desmodium canadense). Isolates from D. canadense clustered with B. japonicum group 1, whereas those from A. bracteata were placed in two novel lineages encountered at soybean field sites. One of these novel lineages predominated at soybean sites and exhibited a significant clonal expansion likely reflecting selection by the plant host. Homologous recombination events detected in the 35 sequence types from soybean sites had an effect on genetic diversification that was approximately equal to mutation. Interlineage transfer of core genes was infrequent and mostly attributable to gyrB that had a history of frequent recombination. Symbiotic gene sequences (nodC and nifH) of isolates from soybean sites and native legumes clustered in two lineages corresponding to B. japonicum and B. elkani with the inheritance of these genes appearing predominantly by vertical transmission. The data suggest that soybean-nodulating bacteria associated with native legumes represent a novel source of ecologically adapted bacteria for soybean inoculation.
Tang J, Bromfield ES, Rodrigue N, Cloutier S, Tambong JT. (2012). Ecol Evol. Dec;2(12):2943-61. doi: 10.1002/ece3.404. Epub 2012 Oct 22.
DOE JGI Science Highlights: Prototypical genomic study of Plant-Microbe Interaction. Instead of using dangerous and toxic pesticides or expensive fertilizers, farmers may one day use microbes to fully manage diseases in soil ...
Aphid attacks weaken genetic defenses in soybeans, may open door for other ...Phys.OrgThe study, published recently in the journal Molecular Plant-Microbe Interactions and made possible through grants from the Iowa Soybean Association and the ISU ...
JGI to Provide Sequencing and Analysis for New Microbial, Plant, Fungal ...GenomeWebThe projects receiving the 2013 Community Sequencing Program (CSP) awards will involve metagenomics analyses of microbes, will study niche microbial communities,...
Uredinia formed by the rust fungus Melampsora larici-populina 7 days after inoculation on susceptible poplar leaves (severe and weak infection are pictured above and below the midrib, respectively). The panels below show immunofluorescence localization of small secreted proteins at the periphery of distinct infection structures in poplar leaves.
Image by Benjamin Petre and Stephane Hacquard on the cover of the March 2012 issue of Molecular Plant Microbe Interactions.
Cytokinin regulates many aspects of plant development, and in legume crops, this phytohormone is necessary and sufficient for symbiotic nodule organogenesis, allowing them to fix atmospheric nitrogen. To identify direct links between cytokinins and nodule organogenesis, we determined a consensus sequence bound in vitro by a transcription factor (TF) acting in cytokinin signaling, the nodule-enhanced Medicago truncatula Mt RR1 response regulator (RR). Among genes rapidly regulated by cytokinins and containing this so-called RR binding site (RRBS) in their promoters, we found the nodulation-related Type-A RR Mt RR4 and the Nodulation Signaling Pathway 2 (NSP2) TF. Site-directed mutagenesis revealed that RRBS cis-elements in the RR4 and NSP2 promoters are essential for expression during nodule development and for cytokinin induction. Furthermore, a microRNA targeting NSP2 (miR171 h) is also rapidly induced by cytokinins and then shows an expression pattern anticorrelated with NSP2. Other primary targets regulated by cytokinins depending on the Cytokinin Response1 (CRE1) receptor were a cytokinin oxidase/dehydrogenase (CKX1) and a basic Helix-Loop-Helix TF (bHLH476). RNA interference constructs as well as insertion of a Tnt1 retrotransposon in the bHLH gene led to reduced nodulation. Hence, we identified two TFs, NSP2 and bHLH476, as direct cytokinin targets acting at the convergence of phytohormonal and symbiotic cues. Ariel F, Brault-Hernandez M, Laffont C, Huault E, Brault M, Plet J, Moison M, Blanchet S, Ichanté JL, Chabaud M, Carrere S, Crespi M, Chan RL, Frugier F. (2012). Plant Cell Sep 28. [Epub ahead of print]
Plants and pathogens evolve in response to each other. This co-evolutionary arms race is fueled by genetic variation underlying the recognition of pathogen proteins by the host and the defeat of host defenses by the pathogen. Together with new mutations, genetic diversity in populations of both the host and pathogen represent a pool of possible variants to maintain adaptation via natural selection.Drastic changes in genetic diversity in crop species have occurred as a consequence of domestication. Whether changes in the genetic composition of these host populations also have affected genetic diversity in pathogen species is, so far, poorly understood. Advances in comparative genomics and population genomic approaches open new avenues to study adaptive processes in plant pathogens and to infer the impact of agro-ecosystems on the evolution of pathogen populations. Here we summarize new insights gained from comparative genome studies and population genomics in host-pathogen systems.
The 10th European Nitrogen Fixation Meeting was held in Munich at the beginning of this month and attended by about 300 participants. The program (while it is still available) can be found at following this link...
Publication year: 2012Source:Current Opinion in Plant BiologyMaryam Rafiqi, Jeffrey G Ellis, Victoria A Ludowici, Adrienne R Hardham, Peter N Dodds Both mutualistic and biotrophic pathogenic fungi rely on living host plants for growth and...