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Microbiology Open: Live-cell imaging of rice cytological changes reveals the importance of host vacuole maintenance for biotrophic invasion by blast fungus, Magnaporthe oryzae (2015)

Microbiology Open: Live-cell imaging of rice cytological changes reveals the importance of host vacuole maintenance for biotrophic invasion by blast fungus, Magnaporthe oryzae (2015) | Agriculture | Scoop.it

The rice blast fungus Magnaporthe oryzae grows inside living host cells. Cytological analyses by live-cell imaging have revealed characteristics of the biotrophic invasion, particularly the extrainvasive hyphal membrane (EIHM) originating from the host plasma membrane and a host membrane-rich structure, biotrophic interfacial complex (BIC). Here, we observed rice subcellular changes associated with invasive hyphal growth using various transformants expressing specifically localized fluorescent proteins. The invasive hyphae did not penetrate across but were surrounded by the host vacuolar membrane together with EIHM even after branching. High-resolution imaging of BICs revealed that the host cytosol was accumulated at BIC with aggregated EIHM and a symplastic effector, Pwl2, in a punctate form. The vacuolar membrane did not aggregate in but closely surrounded the BIC. A good correlation was observed between the early collapse of vacuoles and damage of invasive hyphae in the first-invaded cell. Furthermore, a newly developed, long-term imaging method has revealed that the central vacuole gradually shrank until collapse, which was caused by the hyphal invasion occurring earlier in the neighboring cells than in the first-invaded cells. These data suggest that M. oryzae may suppress host vacuole collapse during early infection stages for successful infection.


Via Yogesh Gupta, Elsa Ballini, Kamoun Lab @ TSL
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Scientific Reports: Function and evolution of Magnaporthe oryzae avirulence gene AvrPib responding to the rice blast resistance gene Pib (2015)

Scientific Reports: Function and evolution of Magnaporthe oryzae avirulence gene AvrPib responding to the rice blast resistance gene Pib (2015) | Agriculture | Scoop.it

Magnaporthe oryzae (Mo) is the causative pathogen of the damaging disease rice blast. The effector gene AvrPib, which confers avirulence to host carrying resistance gene Pib, was isolated via map-based cloning. The gene encodes a 75-residue protein, which includes a signal peptide. Phenotyping and genotyping of 60 isolates from each of five geographically distinct Mo populations revealed that the frequency of virulent isolates, as well as the sequence diversity within the AvrPib gene increased from a low level in the far northeastern region of China to a much higher one in the southern region, indicating a process of host-driven selection. Resequencing of the AvrPiballele harbored by a set of 108 diverse isolates revealed that there were four pathoways, transposable element (TE) insertion (frequency 81.7%), segmental deletion (11.1%), complete absence (6.7%), and point mutation (0.6%), leading to loss of the avirulence function. The lack of any TE insertion in a sample of non-rice infecting Moisolates suggested that it occurred after the host specialization of Mo. Both the deletions and the functional point mutation were confined to the signal peptide. The reconstruction of 16 alleles confirmed seven functional nucleotide polymorphisms for the AvrPiballeles, which generated three distinct expression profiles.


Via Kamoun Lab @ TSL
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Rescooped by Shaikhul Islam from Rhizobium Research
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An online database for plant image analysis software tools

An online database for plant image analysis software tools | Agriculture | Scoop.it

Background Recent years have seen an increase in methods for plant phenotyping using image analyses. These methods require new software solutions for data extraction and treatment. These solutions are instrumental in supporting various research pipelines, ranging from the localisation of cellular compounds to the quantification of tree canopies. However, due to the variety of existing tools and the lack of central repository, it is challenging for researchers to identify the software that is best suited for their research.Results We present an online, manually curated, database referencing more than 90 plant image analysis software solutions. The website, plant-image-analysis.org, presents each software in a uniform and concise manner enabling users to identify the available solutions for their experimental needs. The website also enables user feedback, evaluations and new software submissions.Conclusions The plant-image-analysis.org database provides an overview of existing plant image analysis software. The aim of such a toolbox is to help users to find solutions, and to provide developers a way to exchange and communicate about their work.


Via Jean-Michel Ané, IvanOresnik
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Jean-Michel Ané's curator insight, November 2, 2013 12:08 AM

A bit off-topic... but lots of great tools to analyze root systems in particular.

Rescooped by Shaikhul Islam from Plant Pathogenomics
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Nature Communications: High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus (2013)

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

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


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Annual Review Microbiology: A Paradigm for Endosymbiotic Life: Cell Differentiation of Rhizobium Bacteria Provoked by Host Plant Factors (2013)

Annual Review Microbiology: A Paradigm for Endosymbiotic Life: Cell Differentiation of Rhizobium Bacteria Provoked by Host Plant Factors (2013) | Agriculture | Scoop.it

Symbiosis between Rhizobium bacteria and legumes leads to the formation of the root nodule. The endosymbiotic bacteria reside in polyploid host cells as membrane-surrounded vesicles where they reduce atmospheric nitrogen to support plant growth by supplying ammonia in exchange for carbon sources and energy. The morphology and physiology of endosymbionts, despite their common function, are highly divergent in different hosts. In galegoid plants, the endosymbionts are terminally differentiated, uncultivable polyploid cells, with remarkably elongated and even branched Y-shaped cells. Bacteroid differentiation is controlled by host peptides, many of which have antibacterial activity and require the bacterial function of BacA. Although the precise and combined action of several hundred host peptides and BacA has yet to be discovered, similarities, especially to certain insect-bacterium symbioses involving likewise host peptides for manipulation of endosymbionts, suggest convergent evolution. Rhizobium-legume symbiosis provides a rich source of information for understanding host-controlled endosymbiotic life in eukaryotic cells.


Via IvanOresnik, Jean-Michel Ané, Kamoun Lab @ TSL
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Annual Review of Microbiology: Fusarium Pathogenomics (2013)

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

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


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

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

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


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Jie Wang's comment, September 18, 2013 11:43 PM
Good paper
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News: 'Wheat blast' threatens yield in Bangladesh (2016)

News: 'Wheat blast' threatens yield in Bangladesh (2016) | Agriculture | Scoop.it

Wheat blast disease has become a serious threat to grain quality and yield, incurring losses to the farmers in six southwestern districts.

 

Scientists and specialists after laboratory tests claimed that this is the first time in Bangladesh in which the seasonal crop got infected with this disease.

 

Officials at the Department of Agricultural Extension (DAE) and Wheat Research Centre (WRC) of the Bangladesh Agricultural Research Institute said they have examined samples from the fields and confirmed that the disease is a blast infection.

 

They identified the fungus that might have grown due to unexpected temperature fluctuation and several days of continuous rain in the first week of February.

 

Experts also have tested the seeds used to be sure of the infection, the officials said.

 

The affected districts include Kushtia, Meherpur, Chuadanga, Jhenidah, Jessore, and Magura.

 

DAE officials, who visited the affected fields, said Meherpur was the badly hit. Around 2,000 hectares of wheat fields had been damaged by the fungus.

 

According to farmers, they have marked yellow and black spots on the leaves and sheaves of wheat. After a few days, the spots got larger and spread over the entire plant.

 

At one stage, both the sheaves and flowers turned yellow and white, and finally the plant dried up without producing any grain.

 

Mustafizur Rahman, deputy director of Meherpur DAE, said farmers started informing them about the matter from mid-February.

 

“We told the higher authorities about the problem after visiting the fields,” he said.

 

A team, led by Paritosh Kumar Malaker, chief scientific officer of Wheat Research Centre in Dinajpur, visited the affected fields in Meherpur, Chuadanga, and Jhenidah on Wednesday.

 

“We have made pathogen tests using the diagnostic technique, called 'field pathogenomics', and confirmed the symptoms of the disease,” he said.

 

He said, "As it [disease] is the first infection in Bangladesh, we need to be more careful.”

 

Farmers and DAE officials said the areas experienced rain in the first week of February. After five to seven days, farmers observed spots on wheat leaves and sheaves.

 

This correspondent visited Garadoba, Saharbati, Dhankhola, Bamundi of Gangni upazila, and Khoksa, Chandbeel, Madandanga in Meherpur Sadar upazila and found a large number of affected fields.

 

Farmers Ripon and Mawla Boksh of Madandanga told this correspondent that they jointly cultivated wheat on five bigahs of land. About half of the crop was damaged. They have to incur a huge loss, they said.

 

Sources at the DAE divisional office in Jessore said farmers in the six southwestern districts cultivated wheat on around 58,135 hectares. Some 16,710 hectares are in Kushtia, 10,320 hectares in Jhenidah, 7,020 hectares in Magura, 5,810 hectares in Chuadanga, 4,400 hectares in Jessore and 13,875 hectares in Meherpur.

 

Mustafizur Rahman, deputy director of Meherpur DAE, said they were holding meetings with the farmers and distributing leaflets to create awareness among the farmers.

 

The DAE office also advised the farmers to spray Nativo and Folico on the affected fields.

 

He primarily estimated that 5 percent of the total production might be affected.

 

However, Chief Scientific Officer of WRC Paritosh Kumar said wheat production would decrease by around 10-40 percent.


Via Kamoun Lab @ TSL
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PLOS ONE: Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs (2013)

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

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


Via Kamoun Lab @ TSL
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Rescooped by Shaikhul Islam from Rhizobium Research
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Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in the semi-arid of Brazil

Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in the semi-arid of Brazil | Agriculture | Scoop.it

Analysis of 16S rRNA gene of eight strains (BR 3299T, BR 3296, BR 10192, BR 10193, BR 10194, BR 10195, BR 10196 and BR 10197) isolated from nodules of cowpea collected at a semi-arid region of Brazil showed 97% of similarity to sequences of recently described rhizobial species of Microvirga. Phylogenetic analyses of four housekeeping genes (gyrB, recA, dnaK and rpoB), DNA-DNA relatedness and AFLP further indicated that these strains belong to a new species within the genus Microvirga. Our data support the hypothesis that genes related to nitrogen fixation were obtained via horizontal gene transfer, as sequences of nifH genes were very similar to Rhizobium and Mesorhizobium, which are not next relative of Microvirga as shown by the 16S rRNA analysis. Phenotypic traits, such as host range and carbon utilization, emphasizes their differentiation from its most related species, M. lotononidis, M. zambiensis and M. lupini. Therefore, a novel species is proposed for these symbiotic nitrogen-fixing bacteria, for which the name Microvirga vignae sp. nov. is suggested. The type strain is BR3299T (= HAMBI 3457).

 

Radl V, Simões-Araújo JL, Leite J, Passos SR, Martins LM, Xavier GR, Rumjanek NG, Baldani JI, Zilli JE.(2013). Int J Syst Evol Microbiol. Oct 31. [Epub ahead of print]


Via IvanOresnik
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An online database for plant image analysis software tools

An online database for plant image analysis software tools | Agriculture | Scoop.it

Background Recent years have seen an increase in methods for plant phenotyping using image analyses. These methods require new software solutions for data extraction and treatment. These solutions are instrumental in supporting various research pipelines, ranging from the localisation of cellular compounds to the quantification of tree canopies. However, due to the variety of existing tools and the lack of central repository, it is challenging for researchers to identify the software that is best suited for their research.Results We present an online, manually curated, database referencing more than 90 plant image analysis software solutions. The website, plant-image-analysis.org, presents each software in a uniform and concise manner enabling users to identify the available solutions for their experimental needs. The website also enables user feedback, evaluations and new software submissions.Conclusions The plant-image-analysis.org database provides an overview of existing plant image analysis software. The aim of such a toolbox is to help users to find solutions, and to provide developers a way to exchange and communicate about their work.


Via Jean-Michel Ané, IvanOresnik
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Jean-Michel Ané's curator insight, November 2, 2013 12:08 AM

A bit off-topic... but lots of great tools to analyze root systems in particular.

Rescooped by Shaikhul Islam from Agriculture
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Nature Reviews Microbiology: Horizontal gene transfer in osmotrophs: playing with public goods (2013)

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

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


Via Kamoun Lab @ TSL, Shaikhul Islam
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Jie Wang's comment, September 18, 2013 11:43 PM
Good paper
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PLOS Pathogens: Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease (2013)

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

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


Via Kamoun Lab @ TSL
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