Microbes, plant immunity, and crop science
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Nature: A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens (2012)

Nature: A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens (2012) | Microbes, plant immunity, and crop science | Scoop.it
Soybean (Glycine max (L.) Merr.) is an important crop that provides a sustainable source of protein and oil worldwide. Soybean cyst nematode (Heterodera glycines Ichinohe) is a microscopic roundworm that feeds on the roots of soybean and is a major constraint to soybean production. This nematode causes more than US$1 billion in yield losses annually in the United States alone1, making it the most economically important pathogen on soybean. Although planting of resistant cultivars forms the core management strategy for this pathogen, nothing is known about the nature of resistance. Moreover, the increase in virulent populations of this parasite on most known resistance sources necessitates the development of novel approaches for control. Here we report the map-based cloning of a gene at the Rhg4 (for resistance to Heterodera glycines 4) locus, a major quantitative trait locus contributing to resistance to this pathogen. Mutation analysis, gene silencing and transgenic complementation confirm that the gene confers resistance. The gene encodes a serine hydroxymethyltransferase, an enzyme that is ubiquitous in nature and structurally conserved across kingdoms. The enzyme is responsible for interconversion of serine and glycine and is essential for cellular one-carbon metabolism. Alleles of Rhg4 conferring resistance or susceptibility differ by two genetic polymorphisms that alter a key regulatory property of the enzyme. Our discovery reveals an unprecedented plant resistance mechanism against a pathogen. The mechanistic knowledge of the resistance gene can be readily exploited to improve nematode resistance of soybean, an increasingly important global crop.

Shiming Liu, Pramod K. Kandoth, Samantha D. Warren, Greg Yeckel, Robert Heinz, John Alden, Chunling Yang, Aziz Jamai, Tarik El-Mellouki, Parijat S. Juvale, John Hill, Thomas J. Baum, Silvia Cianzio, Steven A. Whitham, Dmitry Korkin, Melissa G. Mitchum & Khalid Meksem
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Bioconductor project: A test drive of a DNA-analysis toolkit in the cloud

Bioconductor project: A test drive of a DNA-analysis toolkit in the cloud | Microbes, plant immunity, and crop science | Scoop.it
Cloud-computing services offered by companies such as Amazon, Microsoft and Google have put high-performance computing in the hands of everyday researchers. And in the past decade, a project called Bioconductor has done something similar for the often complex field of bioinformatics. Launched in 2001 by a group of bioinformaticians led by Robert Gentleman, then at Harvard University in Cambridge, Massachusetts, the Bioconductor project offers a collection of software that makes it easy for researchers and engineers to analyse, visualize and share genomic data. The project has assembled thousands of tools for computational molecular biology, all of which work together in the R statistical-programming language in conjunction with the RStudio programming environment.
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daTALbase: a database for genomic and transcriptomic data related to TAL effectors. - http://bioinfo-web.mpl.ird.fr/cgi-bin2/datalbase/home.cgi

Perez Quintero et al, 2017

Transcription activator-like effectors (TALEs) are proteins found in the genus Xanthomonas of phytopathogenic bacteria. These proteins enter the nucleus of cells in the host plant and can induce the expression of susceptibility S genes, triggering disease. TALEs bind the promoter region of S genes following a specific code, which allows the prediction of binding sites based on TALEs’ amino acid sequence. New candidate susceptibility genes can then be discovered by finding the intersection between genes induced in the presence of TALEs and genes containing predicted effector binding elements (EBEs). By contrasting differential expression data and binding sites predictions across different datasets, patterns of TALE diversification and/or convergence may be unveiled, but this requires the seamless integration of different genomic and transcriptomic data. With this in mind we present daTALbase, a curated relational database that integrates TALE-related data including: bacterial TALE sequences, plant promoter sequences, predicted TALE binding sites, transcriptomic data of host plants in response to TALE-harboring bacteria, and other associated data. The database can be explored to uncover candidate new susceptibility genes, as well as to study variation in TALE repertories and their corresponding targets. The first version of the database here presented includes data for Oryza sp. - Xanthomonas pv. oryzae interactions. Future versions of the database will incorporate information for other pathosystems involving TALEs. daTALbase is accessible at http://bioinfo-web.mpl.ird.fr/cgi-bin2/datalbase/home.cgi


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PNAS: Genome of wild olive and the evolution of oil biosynthesis (2017)

Here we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae lineage-specific paleopolyploidy events, dated at ∼28 and ∼59 Mya. These events contributed to the expansion and neofunctionalization of genes and gene families that play important roles in oil biosynthesis. The functional divergence of oil biosynthesis pathway genes, such as FAD2, SACPD, EAR, and ACPTE, following duplication, has been responsible for the differential accumulation of oleic and linoleic acids produced in olive compared with sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by an siRNA derived from a transposable element-rich region, leading to suppressed levels of FAD2 gene expression. Additionally, neofunctionalization of members of the SACPD gene family has led to increased expression of SACPD2, 3, 5, and 7, consequently resulting in an increased desaturation of steric acid. Taken together, decreased FAD2 expression and increased SACPD expression likely explain the accumulation of exceptionally high levels of oleic acid in olive. The oleaster genome thus provides important insights into the evolution of oil biosynthesis and will be a valuable resource for oil crop genomics.
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Nature: Genome sequence of the progenitor of the wheat D genome Aegilops tauschii (2017)

Nature: Genome sequence of the progenitor of the wheat D genome Aegilops tauschii (2017) | Microbes, plant immunity, and crop science | Scoop.it

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat1 (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat2,3,4. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence5. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.

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Evidence for Two Distinct Stages in Secondary Cell Wall Formation of Xylem

Evidence for Two Distinct Stages in Secondary Cell Wall Formation of Xylem | Microbes, plant immunity, and crop science | Scoop.it
A hallmark of xylem development is the deposition of secondary cell wall material in specific patterns (reviewed in [Turner et al., 2007][1]). These cell wall deposits structurally reinforce the xylem to withstand negative pressure during water transport and differ in different xylem cell types.
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(JIA-2017-0457) Action modes of transcription activator-like effectors (TALEs) of Xanthomonas in plants - JIA

Xu et al, 2017

Plant-pathogenic Xanthomonas infects a wide variety of host plants and causes many devastating diseases on crops.  Transcription activator-like effectors (TALEs) are delivered by a type III secretion system (T3SS) of Xanthomonas into plant nuclei to directly bind specific DNA sequences (TAL effector-binding elements, EBEs) on either strand of host target genes with an unique modular DNA-binding domain and to bidirectionally drive host gene transcription.  The target genes in plants consist of host susceptibility (S) genes promoting disease (ETS) and resistance (R) gene triggering defense (ETI).  Here we generally summarized the discovery of TALEs in Xanthomonas species, their functions in bacterial pathogenicity in plants and their target genes in different host plants, and then focused on the newly revealed modes of protein action in triggering or suppressing plant defense.
 
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New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

Background Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. Results We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. Conclusions Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.


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Rescooped by Nicolas Denancé from Pathogens, speciation, domestication, genomics, fungi, biotic interactions
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Population genomics in wild tomatoes - the interplay of divergence and admixture

Population genomics in wild tomatoes - the interplay of divergence and admixture | Microbes, plant immunity, and crop science | Scoop.it

Hybridization between closely related plant species is widespread, but the outcomes of hybridization are not fully understood. This study investigates phylogenetic relationships and the history of hybridization in the wild tomato clade (Solanum sect. Lycopersicon). We sequenced RNA from individuals of 38 different populations and, by combining this with published data, build a comprehensive genomic dataset for the entire clade. The data indicate that many taxa are not monophyletic and many individuals are admixed due to repeated hybridization. The most polymorphic species, S. peruvianum, has two genetic and geographical subpopulations, while its sister species, S. chilense, has distinct coastal populations and reduced heterozygosity indicating a recent expansion south following speciation from S. peruvianum c. 1.25 million years ago. Discontinuous populations west of 72° are currently described as S. chilense, but are genetically intermediate between S. chilense and S. peruvianum. Based upon molecular, morphological, and crossing data, we test the hypothesis that these discontinuous ′S. chilense′ populations are an example of recombinational speciation. Recombinational speciation is rarely reported, and we discuss the difficulties in identifying it and differentiating between alternative demographic scenarios. This discovery presents a new opportunity to understand the genomic outcomes of hybridization in plants.


Via Pierre Gladieux
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Trends Plant Sci.: Challenges towards Revitalizing Hemp: A Multifaceted Crop (2017)

Trends Plant Sci.: Challenges towards Revitalizing Hemp: A Multifaceted Crop (2017) | Microbes, plant immunity, and crop science | Scoop.it
Hemp has been an important crop throughout human history for food, fiber, and medicine. Despite significant progress made by the international research community, the basic biology of hemp plants remains insufficiently understood. Clear objectives are needed to guide future research. As a semi-domesticated plant, hemp has many desirable traits that require improvement, including eliminating seed shattering, enhancing the quantity and quality of stem fiber, and increasing the accumulation of phytocannabinoids. Methods to manipulate the sex of hemp plants will also be important for optimizing yields of seed, fiber, and cannabinoids. Currently, research into trait improvement is hindered by the lack of molecular techniques adapted to hemp. Here we review how addressing these limitations will help advance our knowledge of plant biology and enable us to fully domesticate and maximize the agronomic potential of this promising crop.
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NAR: MetaCyc database of metabolic pathways and enzymes (2017)

NAR: MetaCyc database of metabolic pathways and enzymes (2017) | Microbes, plant immunity, and crop science | Scoop.it
MetaCyc (https://MetaCyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life. It contains more than 2570 pathways derived from >54 000 publications, making it the largest curated collection of metabolic pathways. The data in MetaCyc is strictly evidence-based and richly curated, resulting in an encyclopedic reference tool for metabolism. MetaCyc is also used as a knowledge base for generating thousands of organism-specific Pathway/Genome Databases (PGDBs), which are available in the BioCyc (https://BioCyc.org) and other PGDB collections. This article provides an update on the developments in MetaCyc during the past two years, including the expansion of data and addition of new features.
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A Beacon for Applied Plant Pathology: The Origins of Plant Disease

A Beacon for Applied Plant Pathology: The Origins of Plant Disease | Microbes, plant immunity, and crop science | Scoop.it
This year marks a full century since the founding of the journal Plant Disease. The story of how the journal developed, from its origins as a service publication of the USDA in 1917 to the leading applied journal in the field today, reflects on major historical themes in plant pathology. Central to this narrative is the delicate balancing act in plant pathology between fundamental and applied science. During the 1960s and 1970s, substantial numbers of plant pathologists in the U.S. expressed concerns through the American Phytopathological Society (APS) over what they viewed as an alarming and increasing scarcity of applied papers in the flagship journal, Phytopathology. These concerns led increasingly to calls for a second APS journal devoted to applied research. After a period of uncertainty and indecision, the dissolution of the USDA Plant Disease Reporter (PDR) in 1979 offered APS leadership an unusual opportunity to assume publication of a journal with a 63-year legacy of publishing practical plant pathology. In a bold move, APS Council, with the decision in 1979 to take on the publication of PDR under the new title, Plant Disease, provided plant pathologists and the larger agricultural science community with an innovative vehicle to communicate applied plant pathology.
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Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome | Microbes, plant immunity, and crop science | Scoop.it
The genome of the liverwort Marchantia polymorpha sheds light on the evolution of
land plants.
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Phytopathol.: Epidemiology: Past, Present, and Future Impacts on Understanding Disease Dynamics and Improving Plant Disease Management—A Summary of Focus Issue Articles (2017)

Epidemiology has made significant contributions to plant pathology by elucidating the general principles underlying the development of disease epidemics. This has resulted in a greatly improved theoretical and empirical understanding of the dynamics of disease epidemics in time and space, predictions of disease outbreaks or the need for disease control in real-time basis, and tactical and strategic solutions to disease problems. Availability of high-resolution experimental data at multiple temporal and spatial scales has now provided a platform to test and validate theories on the spread of diseases at a wide range of spatial scales ranging from the local to the landscape level. Relatively new approaches in plant disease epidemiology, ranging from network to information theory, coupled with the availability of large-scale datasets and the rapid development of computer technology, are leading to revolutionary thinking about epidemics that can result in considerable improvement of strategic and tactical decision making in the control and management of plant diseases. Methods that were previously restricted to topics such as population biology or evolution are now being employed in epidemiology to enable a better understanding of the forces that drive the development of plant disease epidemics in space and time. This Focus Issue of Phytopathology features research articles that address broad themes in epidemiology including social and political consequences of disease epidemics, decision theory and support, pathogen dispersal and disease spread, disease assessment and pathogen biology and disease resistance. It is important to emphasize that these articles are just a sample of the types of research projects that are relevant to epidemiology. Below, we provide a succinct summary of the articles that are published in this Focus Issue.
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New Phytol.: Sustaining global agriculture through rapid detection and deployment of genetic resistance to deadly crop diseases

New Phytol.: Sustaining global agriculture through rapid detection and deployment of genetic resistance to deadly crop diseases | Microbes, plant immunity, and crop science | Scoop.it
Genetically encoded resistance is a major component of crop disease management. Historically, gene loci conferring resistance to pathogens have been identified through classical genetic methods. In recent years, accelerated gene cloning strategies have become available through advances in sequencing, gene capture and strategies for reducing genome complexity. Here, I describe these approaches with key emphasis on the isolation of resistance genes to the cereal crop diseases that are an ongoing threat to global food security. Rapid gene isolation enables their efficient deployment through marker-assisted selection and transgenic technology. Together with innovations in genome editing and progress in pathogen virulence studies, this creates further opportunities to engineer long-lasting resistance. These approaches will speed progress towards a future of farming using fewer pesticides.
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New Phytologist: Effectors involved in fungal–fungal interaction lead to a rare phenomenon of hyperbiotrophy in the tritrophic system biocontrol agent–powdery mildew–plant (2017)

New Phytologist: Effectors involved in fungal–fungal interaction lead to a rare phenomenon of hyperbiotrophy in the tritrophic system biocontrol agent–powdery mildew–plant (2017) | Microbes, plant immunity, and crop science | Scoop.it
Tritrophic interactions involving a biocontrol agent, a pathogen and a plant have been analyzed predominantly from the perspective of the biocontrol agent. We have conducted the first comprehensive transcriptomic analysis of all three organisms in an effort to understand the elusive properties of Pseudozyma flocculosa in the context of its biocontrol activity against Blumeria graminis f.sp. hordei as it parasitizes Hordeum vulgare.After inoculation of P. flocculosa, the tripartite interaction was monitored over time and samples collected for scanning electron microscopy and RNA sequencing.Based on our observations, P. flocculosa indirectly parasitizes barley, albeit transiently, by diverting nutrients extracted by B. graminis from barley leaves through a process involving unique effectors. This brings novel evidence that such molecules can also influence fungal–fungal interactions. Their release is synchronized with a higher expression of powdery mildew haustorial effectors, a sharp decline in the photosynthetic machinery of barley and a developmental peak in P. flocculosa. The interaction culminates with a collapse of B. graminis haustoria, thereby stopping P. flocculosa growth, as barley plants show higher metabolic activity.To conclude, our study has uncovered a complex and intricate phenomenon, described here as hyperbiotrophy, only achievable through the conjugated action of the three protagonists.
Via Kamoun Lab @ TSL
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Genome sequence of the olive tree, Olea europaea

Genome sequence of the olive tree, Olea europaea | Microbes, plant immunity, and crop science | Scoop.it
The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.
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Multiple strategies for pathogen perception by plant immune receptors

Multiple strategies for pathogen perception by plant immune receptors | Microbes, plant immunity, and crop science | Scoop.it
Plants have evolved a complex immune system to protect themselves against phytopathogens. A major class of plant immune receptors called nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) is ubiquitous in plants and is widely used for crop disease protection, making these proteins critical contributors to global food security. Until recently, NLRs were thought to be conserved in their modular architecture and functional features. Investigation of their biochemical, functional and structural properties has revealed fascinating mechanisms that enable these proteins to perceive a wide range of pathogens. Here, I review recent insights demonstrating that NLRs are more mechanistically and structurally diverse than previously thought. I also discuss how these findings provide exciting future prospects to improve plant disease resistance.
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Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors - BMC Genomics

(via T. Lahaye, thx)

Ruh et al, 2017

Common bacterial blight is a devastating bacterial disease of common bean (Phaseolus vulgaris) caused by Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli. These phylogenetically distant strains are able to cause similar symptoms on common bean, suggesting that they have acquired common genetic determinants of adaptation to common bean. Transcription Activator-Like (TAL) effectors are bacterial type III effectors that are able to induce the expression of host genes to promote infection or resistance. Their capacity to bind to a specific host DNA sequence suggests that they are potential candidates for host adaption.

To study the diversity of tal genes from Xanthomonas strains responsible for common bacterial blight of bean, whole genome sequences of 17 strains representing the diversity of X. citri pv. fuscans and X. phaseoli pv. phaseoli were obtained by single molecule real time sequencing. Analysis of these genomes revealed the existence of four tal genes named tal23A, tal20F, tal18G and tal18H, respectively. While tal20F and tal18G were chromosomic, tal23A and tal18H were carried on plasmids and shared between phylogenetically distant strains, therefore suggesting recent horizontal transfers of these genes between X. citri pv. fuscans and X. phaseoli pv. phaseoli strains. Strikingly, tal23A was present in all strains studied, suggesting that it played an important role in adaptation to common bean. In silico predictions of TAL effectors targets in the common bean genome suggested that TAL effectors shared by X. citri pv. fuscans and X. phaseoli pv. phaseoli strains target the promoters of genes of similar functions. This could be a trace of convergent evolution among TAL effectors from different phylogenetic groups, and comforts the hypothesis that TAL effectors have been implied in the adaptation to common bean.

Altogether, our results favour a model where plasmidic TAL effectors are able to contribute to host adaptation by being horizontally transferred between distant lineages.


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Advances in Genetics: Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens (2017)

Advances in Genetics: Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens (2017) | Microbes, plant immunity, and crop science | Scoop.it

An unprecedented number of pathogenic fungi are emerging and causing disease in animals and plants, putting the resilience of wild and managed ecosystems in jeopardy. While the past decades have seen an increase in the number of pathogenic fungi, they have also seen the birth of new big data technologies and analytical approaches to tackle these emerging pathogens. We review how the linked fields of genomics and epigenomics are transforming our ability to address the challenge of emerging fungal pathogens. We explore the methodologies and bioinformatic toolkits that currently exist to rapidly analyze the genomes of unknown fungi, then discuss how these data can be used to address key questions that shed light on their epidemiology. We show how genomic approaches are leading a revolution into our understanding of emerging fungal diseases and speculate on future approaches that will transform our ability to tackle this increasingly important class of emerging pathogens.


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Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution

Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution | Microbes, plant immunity, and crop science | Scoop.it
Extensive research efforts have been dedicated to describing degradation of wood, which is a complex process; hence, microorganisms have evolved different enzymatic and non-enzymatic strategies to utilize this plentiful plant material. This review describes a number of fungal and bacterial organisms which have developed both competitive and mutualistic strategies for the decomposition of wood and to thrive in different ecological niches. Through the analysis of the enzymatic machinery engaged in wood degradation, it was possible to elucidate different strategies of wood decomposition which often depend on ecological niches inhabited by given organism. Moreover, a detailed description of low molecular weight compounds is presented, which gives these organisms not only an advantage in wood degradation processes, but seems rather to be a new evolutionatory alternative to enzymatic combustion. Through analysis of genomics and secretomic data, it was possible to underline the probable importance of certain wood-degrading enzymes produced by different fungal organisms, potentially giving them advantage in their ecological niches. The paper highlights different fungal strategies of wood degradation, which possibly correlates to the number of genes coding for secretory enzymes. Furthermore, investigation of the evolution of wood-degrading organisms has been described.

Via Francis Martin
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The ISME Journal - Ralstonia solanacearum lipopeptide induces chlamydospore development in fungi and facilitates bacterial entry into fungal tissues

The ISME Journal - Ralstonia solanacearum lipopeptide induces chlamydospore development in fungi and facilitates bacterial entry into fungal tissues | Microbes, plant immunity, and crop science | Scoop.it
Ralstonia solanacearum is a globally distributed soil-borne plant pathogenic bacterium, which shares a broad ecological range with many plant- and soil-associated fungi. We sought to determine if R. solanacearum chemical communication directs symbiotic development of polymicrobial consortia. R. solanacearum produced a diffusible metabolite that induced conserved morphological differentiation in 34 species of fungi across three diverse taxa (Ascomycetes, Basidiomycetes and Zygomycetes). Fungi exposed to this metabolite formed chlamydospores, survival structures with thickened cell walls. Some chlamydospores internally harbored R. solanacearum, indicating a newly described endofungal lifestyle for this important plant pathogen. Using imaging mass spectrometry and peptidogenomics, we identified an undescribed lipopeptide, ralsolamycin, produced by an R. solanacearum non-ribosomal peptide synthetase-polyketide synthase hybrid. Inactivation of the hybrid non-ribosomal peptide synthetase-polyketide synthase gene, rmyA, abolished ralsolamycin synthesis. R. solanacearum mutants lacking ralsolamycin no longer induced chlamydospore development in fungal coculture and invaded fungal hyphae less well than wild-type. We propose that ralsolamycin contributes to the invasion of fungal hyphae and that the formation of chlamydospores may provide not only a specific niche for bacterial colonization but also enhanced survival for the partnering fungus.

Via Ryohei Thomas Nakano, Stéphane Hacquard
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BMC Biology: Plant hormone transporters: what we know and what we would like to know (2017)

BMC Biology: Plant hormone transporters: what we know and what we would like to know (2017) | Microbes, plant immunity, and crop science | Scoop.it
Hormone transporters are crucial for plant hormone action, which is underlined by severe developmental and physiological impacts caused by their loss-of-function mutations. Here, we summarize recent knowledge on the individual roles of plant hormone transporters in local and long-distance transport. Our inventory reveals that many hormones are transported by members of distinct transporter classes, with an apparent dominance of the ATP-binding cassette (ABC) family and of the Nitrate transport1/Peptide transporter family (NPF). The current need to explore further hormone transporter regulation, their functional interaction, transport directionalities, and substrate specificities is briefly reviewed.
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NAR: AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog (2017)

NAR: AraGWAS Catalog: a curated and standardized  Arabidopsis thaliana  GWAS catalog (2017) | Microbes, plant immunity, and crop science | Scoop.it
The abundance of high-quality genotype and phenotype data for the model organism Arabidopsis thaliana enables scientists to study the genetic architecture of many complex traits at an unprecedented level of detail using genome-wide association studies (GWAS). GWAS have been a great success in A. thaliana and many SNP-trait associations have been published. With the AraGWAS Catalog (https://aragwas.1001genomes.org) we provide a publicly available, manually curated and standardized GWAS catalog for all publicly available phenotypes from the central A. thaliana phenotype repository, AraPheno. All GWAS have been recomputed on the latest imputed genotype release of the 1001 Genomes Consortium using a standardized GWAS pipeline to ensure comparability between results. The catalog includes currently 167 phenotypes and more than 222 000 SNP-trait associations with P < 10−4, of which 3887 are significantly associated using permutation-based thresholds. The AraGWAS Catalog can be accessed via a modern web-interface and provides various features to easily access, download and visualize the results and summary statistics across GWAS.
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Promoter variants of Xa23 alleles affect bacterial blight resistance and evolutionary pattern

Promoter variants of Xa23 alleles affect bacterial blight resistance and evolutionary pattern | Microbes, plant immunity, and crop science | Scoop.it

(via T. Schreiber & T. Lahaye, thx)

Cui et al, 2017

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most important bacterial disease in rice (Oryza sativa L.). Our previous studies have revealed that the bacterial blight resistance gene Xa23 from wild rice O. rufipogon Griff. confers the broadest-spectrum resistance against all the naturally occurring Xoo races. As a novel executor R gene, Xa23 is transcriptionally activated by the bacterial avirulence (Avr) protein AvrXa23 via binding to a 28-bp DNA element (EBEAvrXa23) in the promoter region. So far, the evolutionary mechanism of Xa23 remains to be illustrated. Here, a rice germplasm collection of 97 accessions, including 29 rice cultivars (indica and japonica) and 68 wild relatives, was used to analyze the evolution, phylogeographic relationship and association of Xa23 alleles with bacterial blight resistance. All the ~ 473 bp DNA fragments consisting of promoter and coding regions of Xa23 alleles in the germplasm accessions were PCR-amplified and sequenced, and nine single nucleotide polymorphisms (SNPs) were detected in the promoter regions (~131 bp sequence upstream from the start codon ATG) of Xa23/xa23 alleles while only two SNPs were found in the coding regions. The SNPs in the promoter regions formed 5 haplotypes (Pro-A, B, C, D, E) which showed no significant difference in geographic distribution among these 97 rice accessions. However, haplotype association analysis indicated that Pro-A is the most favored haplotype for bacterial blight resistance. Moreover, SNP changes among the 5 haplotypes mostly located in the EBE/ebe regions (EBEAvrXa23 and corresponding ebes located in promoters of xa23 alleles), confirming that the EBE region is the key factor to confer bacterial blight resistance by altering gene expression. Polymorphism analysis and neutral test implied that Xa23 had undergone a bottleneck effect, and selection process of Xa23 was not detected in cultivated rice. In addition, the Xa23 coding region was found highly conserved in the Oryza genus but absent in other plant species by searching the plant database, suggesting that Xa23 originated along with the diversification of the Oryza genus from the grass family during evolution. This research offers a potential for flexible use of novel Xa23 alleles in rice breeding programs and provide a model for evolution analysis of other executor R genes.


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NAt. Ecol. Evol.: Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time (2017)

Rapid phenotypic evolution of quantitative traits can occur within years, but its underlying genetic architecture remains uncharacterized. Here we test the theoretical prediction that genes with intermediate pleiotropy drive adaptive evolution in nature. Through a resurrection experiment, we grew Arabidopsis thaliana accessions collected across an 8-year period in six micro-habitats representative of that local population. We then used genome-wide association mapping to identify the single-nucleotide polymorphisms (SNPs) associated with evolved and unevolved traits in each micro-habitat. Finally, we performed a selection scan by testing for temporal differentiation in these SNPs. Phenotypic evolution was consistent across micro-habitats, but its associated genetic bases were largely distinct. Adaptive evolutionary change was most strongly driven by a small number of quantitative trait loci (QTLs) with intermediate degrees of pleiotropy; this pleiotropy was synergistic with the per-trait effect size of the SNPs, increasing with the degree of pleiotropy. In addition, weak selection was detected for frequent micro-habitat-specific QTLs that shape single traits. In this population, A. thaliana probably responded to local warming and increased competition, in part mediated by central regulators of flowering time. This genetic architecture, which includes both synergistic pleiotropic QTLs and distinct QTLs within particular micro-habitats, enables rapid phenotypic evolution while still maintaining genetic variation in wild populations.
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