Microbes, plant immunity, and crop science
50.6K views | +3 today
Follow
 
Scooped by Nicolas Denancé
onto Microbes, plant immunity, and crop science
Scoop.it!

PLOS Genetics: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry (...

PLOS Genetics: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry (... | Microbes, plant immunity, and crop science | Scoop.it

We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an α-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.

 

Pierre J. G. M. de Wit, Ate van der Burgt, Bilal Ökmen, Ioannis Stergiopoulos, Kamel A. Abd-Elsalam, Andrea L. Aerts, Ali H. Bahkali, Henriek G. Beenen, Pranav Chettri, Murray P. Cox, Erwin Datema, Ronald P. de Vries, Braham Dhillon, Austen R. Ganley, Scott A. Griffiths, Yanan Guo, Richard C. Hamelin, Bernard Henrissat, M. Shahjahan Kabir, Mansoor Karimi Jashni, Gert Kema, Sylvia Klaubauf, Alla Lapidus, Anthony Levasseur, Erika Lindquist, Rahim Mehrabi, Robin A. Ohm, Timothy J. Owen, Asaf Salamov, Arne Schwelm, Elio Schijlen, Hui Sun, Harrold A. van den Burg, Roeland C. H. J. van Ham, Shuguang Zhang, Stephen B. Goodwin, Igor V. Grigoriev, Jérôme Collemare, Rosie E. Bradshaw

 

 

more...
No comment yet.
Microbes, plant immunity, and crop science
Your new post is loading...
Your new post is loading...
Scooped by Nicolas Denancé
Scoop.it!

Plant Cell: Defended to the Nines: 25 years of Resistance Gene Cloning Identifies Nine Mechanisms for R Protein Function (2018)

Plant Cell: Defended to the Nines: 25 years of Resistance Gene Cloning Identifies Nine Mechanisms for R Protein Function (2018) | Microbes, plant immunity, and crop science | Scoop.it
Plants display extensive genetic variation at resistance (R) gene loci for resistance to a variety of pathogens. The first R gene, Hm1, was cloned over 25 years ago, and many different R genes have since been identified and isolated. The encoded proteins have provided clues to diverse molecular mechanisms underlying immunity. The majority encode either cell-surface or intracellular receptors, and we present here a meta- analysis of 314 cloned R genes. We distinguish nine molecular mechanisms by which R proteins can elevate or trigger disease resistance. These mechanisms include direct (1) and indirect (2) perception of pathogen-derived molecules on the cell surface by receptor-like proteins and -kinases; intracellular detection of pathogen-derived molecules by nucleotide-binding, leucine-rich repeat receptors (NLRs), either directly (3), indirectly (4) or through integrated domains (5); perception of Transcription Activator-like (TAL) effectors through activation of Executor genes (6); and loss-of-susceptibility, either active (7), passive (8), or by host reprogramming (9). Although the molecular mechanisms underlying the function of R genes are only understood for a small proportion of these, a clearer understanding of mechanisms is emerging and will be crucial for rational engineering and deployment of novel R genes.
more...
No comment yet.
Rescooped by Nicolas Denancé from Transport in plants and fungi
Scoop.it!

Vacuolar transporters - Companions on a longtime journey

Vacuolar transporters - Companions on a longtime journey | Microbes, plant immunity, and crop science | Scoop.it
Biochemical and electrophysiological studies on plant vacuolar transporters became feasible in the late 1970th and early 1980th when methods to isolate large quantities of intact vacuoles and purified vacuolar membrane vesicles were established. However, with the exception of the H+-ATPase and H+-PPase that could be followed due to their hydrolytic activities attempts to purify tonoplast transporters were for a long time not successful. Heterologous complementation, T-DNA insertion mutants and later proteomic studies allowed the next steps starting from the 1990s. Nowadays our knowledge about vacuolar transporters has greatly increased. Nevertheless, there are several transporters of central importance that have still to be identified at the molecular level or have even not been characterized at the biochemically. Furthermore our knowledge about regulation of the vacuolar transporters is very limited and much work is needed to get a holistic view about the interplay of the vacuolar transportome. The huge amount of information generated during the last 35 years does not allow to be summarized in such a review. Therefore I decided to concentrate on some aspects where we were involved during my research on vacuolar transporters, for some our laboratory contributed more, for others less.

Via Kevin Garcia
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

IJSEM: Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes (2018)

IJSEM: Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes (2018) | Microbes, plant immunity, and crop science | Scoop.it
Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

NAt. Genet.: Bacterial genomics of plant adaptation

What allows bacteria, both pathogens and mutualists alike, to survive in close association with a eukaryotic host? A new study performed a large-scale comparative genomics analysis to identify novel genetic and genomic traits that are enriched in plant-associated bacterial taxa.
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

Plant J.: Pattern recognition receptors and signaling in plant‐microbe interactions (2017)

Plant J.: Pattern recognition receptors and signaling in plant‐microbe interactions (2017) | Microbes, plant immunity, and crop science | Scoop.it
Plants solely rely on innate immunity of each individual cell to deal with a diversity of microbes in the environment. Extracellular recognition of microbe- and host damage-associated molecular patterns (MAMPs and DAMPs, respectively) leads to the first layer of inducible defenses, termed pattern-triggered immunity (PTI). In plants, pattern recognition receptors (PRRs) described to date are all membrane-associated receptor-like kinases (RLKs) or receptor-like proteins (RLPs), reflecting the prevalence of apoplastic colonization of plant-infecting microbes. An increasing inventory of elicitor-active patterns and PRRs indicates that a large number of them are limited to a certain range of plant groups/species, pointing to dynamic and convergent evolution of pattern recognition specificities. In addition to common molecular principles of PRR signaling, recent studies have revealed substantial diversification between PRRs in their functions and regulatory mechanisms. This serves to confer robustness and plasticity to the whole PTI system in natural infections, wherein different PRRs are simultaneously engaged and faced with microbial assaults. We review the functional significance and molecular basis of PRR-mediated pathogen recognition and disease resistance, and also an emerging role for PRRs in homeostatic association with beneficial or commensal microbes.
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

Is it ordered correctly? Validating genome assemblies by optical mapping

Is it ordered correctly? Validating genome assemblies by optical mapping | Microbes, plant immunity, and crop science | Scoop.it
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

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.
more...
No comment yet.
Rescooped by Nicolas Denancé from TAL effector science
Scoop.it!

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


Via dromius
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

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.
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

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.

more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

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.
more...
No comment yet.
Rescooped by Nicolas Denancé from TAL effector science
Scoop.it!

(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.
 
Full PDF:

 

 


Via dromius
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

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.

more...
No comment yet.
Rescooped by Nicolas Denancé from TAL effector science
Scoop.it!

Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effecto...

Gochez et al, 2018

Xanthomonas citri, a causal agent of citrus canker, has been a well-studied model system due to recent availability of whole genome sequences of multiple strains from different geographical regions. Major limitations in our understanding of the evolution of pathogenicity factors in X. citri strains sequenced by short-read sequencing methods have been tracking plasmid reshuffling among strains due to inability to accurately assign reads to plasmids, and analyzing repeat regions among strains. X. citri harbors major pathogenicity determinants, including variable DNA-binding repeat region containing Transcription Activator-like Effectors (TALEs) on plasmids. The long-read sequencing method, PacBio, has allowed the ability to obtain complete and accurate sequences of TALEs in xanthomonads. We recently sequenced Xanthomonas citri str. Xc-03-1638-1-1, a copper tolerant A group strain isolated from grapefruit in 2003 from Argentina using PacBio RS II chemistry. We analyzed plasmid profiles, copy number and location of TALEs in complete genome sequences of X. citri strains. We utilized the power of long reads obtained by PacBio sequencing to enable assembly of a complete genome sequence of strain Xc-03-1638-1-1, including sequences of two plasmids, 249 kb (plasmid harboring copper resistance genes) and 99 kb (pathogenicity plasmid containing TALEs). The pathogenicity plasmid in this strain is a hybrid plasmid containing four TALEs. Due to the intriguing nature of this pathogenicity plasmid with Tn3-like transposon association, repetitive elements and multiple putative sites for origins of replication, we might expect alternative structures of this plasmid in nature, illustrating the strong adaptive potential of X. citri strains. Analysis of the pathogenicity plasmid among completely sequenced X. citri strains, coupled with Southern hybridization of the pathogenicity plasmids, revealed clues to rearrangements of plasmids and resulting reshuffling of TALEs among strains. We demonstrate in this study the importance of long-read sequencing for obtaining intact sequences of TALEs and plasmids, as well as for identifying rearrangement events including plasmid reshuffling. Rearrangement events, such as the hybrid plasmid in this case, could be a frequent phenomenon in the evolution of X. citri strains, although so far it is undetected due to the inability to obtain complete plasmid sequences with short-read sequencing methods.


Via dromius
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

A Practical Guide to Visualization and Statistical Analysis of R. solanacearum Infection Data Using R

A Practical Guide to Visualization and Statistical Analysis of R. solanacearum Infection Data Using R | Microbes, plant immunity, and crop science | Scoop.it
This paper describes and summarizes approaches for visualization and statistical analysis using data from Ralstonia solanacearum infection experiments based on methods and concepts that are broadly applicable. Members of the R. solanacearum species complex cause bacterial wilt disease. Bacterial wilt is a lethal plant disease and has been studied for over 100 years. During this time various methods to quantify disease and different ways to analyze the generated data have been employed. Here, I aim to provide a general background on three distinct and commonly used measures of disease: the area under the disease progression curve, longitudinal recordings of disease severity and host survival. I will discuss how one can proceed with visualization, statistical analysis and interpretation using different datasets while revisiting the general concepts of statistical analysis. Datasets and R code to perform all analyses discussed here are included in the supplement.
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

Cooperative interactions between seed-borne bacterial and air-borne fungal pathogens on rice

Cooperative interactions between seed-borne bacterial and air-borne fungal pathogens on rice | Microbes, plant immunity, and crop science | Scoop.it
Bacterial-fungal interactions are widely found in distinct environments and contribute to ecosystem processes. Previous studies of these interactions have mostly been performed in soil, and only limited studies of aerial plant tissues have been conducted. Here we show that a seed-borne plant pathogenic bacterium, Burkholderia glumae (Bg), and an air-borne plant pathogenic fungus, Fusarium graminearum (Fg), interact to promote bacterial survival, bacterial and fungal dispersal, and disease progression on rice plants, despite the production of antifungal toxoflavin by Bg. We perform assays of toxoflavin sensitivity, RNA-seq analyses, lipid staining and measures of triacylglyceride content to show that triacylglycerides containing linolenic acid mediate resistance to reactive oxygen species that are generated in response to toxoflavin in Fg. As a result, Bg is able to physically attach to Fg to achieve rapid and expansive dispersal to enhance disease severity.
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

Plant J.: Plant cell wall‐mediated immunity: Cell wall changes trigger disease resistance responses (2017)

Plant J.: Plant cell wall‐mediated immunity: Cell wall changes trigger disease resistance responses (2017) | Microbes, plant immunity, and crop science | Scoop.it

Plants have evolutionary developed a repertoire of monitoring systems to sense plant morphogenesis and to face environmental changes and threats caused by different attackers. These systems integrate different signals into overreaching triggering pathways, which coordinate developmental and defensive-associated responses. The plant cell wall, a dynamic and complex structure surrounding every plant cell, has emerged recently as an essential component of plant monitoring systems, thus expanding its function as a passive defensive barrier. Plants have a dedicated cell wall integrity (CWI) maintenance mechanism which comprises a diverse set of plasma membrane-resident sensors and Pattern Recognition Receptors (PRRs). PRRs perceive plant-derived ligands, such as peptides or wall glycans, known as Damage-Associated Molecular Patterns (DAMPs). DAMPs function as “danger” alert signals activating DAMP-Triggered Immunity (DTI), which shares signalling components and responses with the immune pathways triggered by non-self Microbe-Associated Molecular Patterns that mediate disease resistance. Alteration of CWI by impairing the expression or activity of proteins involved in cell wall biosynthesis and/or remodelling, as it occurs in some plant cell wall mutants, or by wall damages caused by pathogens/pests colonization, activate specific defensive and growth responses. Our current understanding of how these alterations of CWI are perceived by the wall monitoring systems is scarce and few plant sensors/PRRs and DAMPs have been characterised. The identification of these CWI sensors and PRRs-DAMPs pairs will contribute to understand the immune functions of the wall monitoring system, and might allow to breed crop varieties and to design agricultural strategies that would enhance crops disease resistance.Plants have evolutionary developed a repertoire of monitoring systems to sense plant morphogenesis and to face environmental changes and threats caused by different attackers. These systems integrat

more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

J. Exp. Bot.: roles of auxin during interactions between bacterial plant pathogens and their hosts

J. Exp. Bot.: roles of auxin during interactions between bacterial plant pathogens and their hosts | Microbes, plant immunity, and crop science | Scoop.it
Plant pathogens have evolved several strategies to manipulate the biology of their hosts to facilitate colonization, growth to high levels in plant tissue, and production of disease. One of the less well known of these strategies is the synthesis of plant hormones and hormone analogs, and there is growing evidence that modulation of host hormone signaling is important during pathogenesis. Several plant pathogens produce the auxin indole-3-acetic acid (IAA) and/or virulence factors that modulate host auxin signaling. Auxin is well known for being involved in many aspects of plant growth and development, but recent findings have revealed that elevated IAA levels or enhanced auxin signaling can also promote disease development in some plant–pathogen interactions. In addition to stimulating plant cell growth during infection by gall-forming bacteria, auxin and auxin signaling can antagonize plant defense responses. Auxin can also act as a microbial signaling molecule to impact the biology of some pathogens directly. In this review, we summarize recent progress towards elucidating the roles that auxin production, modification of host auxin signaling, and direct effects of auxin on pathogens play during pathogenesis, with emphasis on the impacts of auxin on interactions with bacterial pathogens.
more...
No comment yet.
Rescooped by Nicolas Denancé from MycorWeb Plant-Microbe Interactions
Scoop.it!

Genomic features of bacterial adaptation to plants

Genomic features of bacterial adaptation to plants | Microbes, plant immunity, and crop science | Scoop.it
Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe–microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant–microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.

Via Francis Martin
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

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.
more...
No comment yet.
Rescooped by Nicolas Denancé from Plants and Microbes
Scoop.it!

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
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

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.
more...
No comment yet.
Scooped by Nicolas Denancé
Scoop.it!

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.
more...
No comment yet.
Rescooped by Nicolas Denancé from TAL effector science
Scoop.it!

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.


Via dromius
more...
No comment yet.
Rescooped by Nicolas Denancé from Plant Pathogenomics
Scoop.it!

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.


Via Kamoun Lab @ TSL
more...
No comment yet.