Microbes, plant immunity, and crop science
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Plant J.: The Magnaporthe oryzae effector AVR1-C039 is translocated into rice cells independently of a fungal-derived machinery (2012)

Plant J.: The Magnaporthe oryzae effector AVR1-C039 is translocated into rice cells independently of a fungal-derived machinery  (2012) | Microbes, plant immunity, and crop science | Scoop.it

Effector proteins are key elements in plant fungal interactions. The rice blast fungus Magnaporthe oryzae secretes numerous effectors suspected to be translocated inside plant cells. However, their cellular targets and the mechanisms of translocation are still unknown. Here, we have identified the open reading frame (ORF3) corresponding to the M. oryzae avirulence gene AVR1-C039 interacting with the rice resistance gene Pi-CO39 and encoding a small secreted protein without homologies to other proteins. We demonstrate that AVR1-C039 is specifically expressed and secreted at the plant fungal interface during the biotrophic phase of infection. Live cell imaging with M. oryzae transformants expressing a translational fusion between AVR1-C039 and the monomeric red fluorescent protein (mRFP), indicates that AVR1-C039 is translocated into the cytoplasm of infected rice cells. Transient expression of an AVR1-C039 isoform without signal peptide in rice protoplasts triggers a Pi-C039 specific HR suggesting that the recognition of AVR1-C039 by the Pi-C039 gene product occurs in the cytoplasm of rice cells. The native AVR1-C039 enters into the secretory pathway of rice protoplasts as demonstrated by the ER localization of AVR1-CO39:mRFP:HDEL translational fusions and is correctly processed as shown by Western blotting. However, this secreted AVR1-C039 isoform triggers Pi-CO39 specific HR and accumulates inside rice protoplasts as shown by western blotting and localisation of AVR1-C039:mRFP translational fusions. This indicates that AVR1-C039 is secreted by rice protoplasts and re-enters into the cytoplasm by unknown mechanisms suggesting that translocation of AVR1-C039 into rice cells occurs independently of fungal factors.

 

Cécile Ribot, Stella Césari, Imène Abidi, Véronique Chalvon, Caroline Bournaud, Julie Vallet, Marc-Henri Lebrun, Jean-Benoit Morel and Thomas Kroj

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Nature Biotech.: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

Nature Biotech.: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | Microbes, plant immunity, and crop science | Scoop.it
We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
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Nature Plants: MicroRNAs in crop improvement: fine-tuners for complex traits

Nature Plants: MicroRNAs in crop improvement: fine-tuners for  complex traits | Microbes, plant immunity, and crop science | Scoop.it
One of the most common challenges for both conventional and modern crop improvement is that the appearance of one desir- able trait in a new crop variety is always balanced by the impairment of one or more other beneficial characteristics. The best way to overcome this problem is the flexible utilization of regulatory genes, especially genes that provide more efficient and precise regulation in a targeted manner. MicroRNAs (miRNAs), a type of short non-coding RNA, are promising candidates in this area due to their role as master modulators of gene expression at the post-transcriptional level, targeting messenger RNAs for cleavage or directing translational inhibition in eukaryotes. We herein highlight the current understanding of the biological role of miRNAs in orchestrating distinct agriculturally important traits by summarizing recent functional analyses of 65 miRNAs in 9 major crops worldwide. The integration of current miRNA knowledge with conventional and modern crop improvement strategies is also discussed.
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A bacterial acetyltransferase triggers immunity in Arabidopsis thaliana independent of hypersensitive response

A bacterial acetyltransferase triggers immunity in Arabidopsis thaliana independent of hypersensitive response | Microbes, plant immunity, and crop science | Scoop.it

Type-III secreted effectors (T3Es) play critical roles during bacterial pathogenesis in plants. Plant recognition of certain T3Es can trigger defence, often accompanied by macroscopic cell death, termed the hypersensitive response (HR). Economically important species of kiwifruit are susceptible to Pseudomonas syringae pv. actinidiae (Psa), the causal agent of kiwifruit bacterial canker. Although Psa is non-pathogenic in Arabidopsis thaliana, we observed that a T3E, HopZ5 that is unique to a global outbreak clade of Psa, triggers HR and defence in Arabidopsis accession Ct-1. Ws-2 and Col-0 accessions are unable to produce an HR in response to Pseudomonas-delivered HopZ5. While Ws-2 is susceptible to virulent bacterial strain Pseudomonas syringae pv. tomato DC3000 carrying HopZ5, Col-0 is resistant despite the lack of an HR. We show that HopZ5, like other members of the YopJ superfamily of acetyltransferases that it belongs to, autoacetylates lysine residues. Through comparisons to other family members, we identified an acetyltransferase catalytic activity and demonstrate its requirement for triggering defence in Arabidopsis and Nicotiana species. Collectively, data herein indicate that HopZ5 is a plasma membrane-localized acetyltransferase with autoacetylation activity required for avirulence.

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Nature: Improved maize reference genome with single-molecule technologies

Nature: Improved maize reference genome with single-molecule technologies | Microbes, plant immunity, and crop science | Scoop.it
Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.
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Plant Cell: Direct and Indirect Visualization of Bacterial Effector Delivery into Diverse Plant Cell Types During Infection (2017)

Plant Cell: Direct and Indirect Visualization of Bacterial Effector Delivery into Diverse Plant Cell Types During Infection (2017) | Microbes, plant immunity, and crop science | Scoop.it
To cause disease, diverse pathogens deliver effector proteins into host cells. Pathogen effectors can inhibit defense responses, alter host physiology, and represent important cellular probes to investigate plant biology. However, effector function and localization have primarily been investigated after overexpression in planta. Visualizing effector delivery during infection is challenging due to the plant cell wall, autofluorescence, and low effector abundance. Here, we utilized a GFP strand system to directly visualize bacterial effectors delivered into plant cells through the Type III secretion system. GFP is a beta barrel that can be divided into 11 strands. We generated transgenic Arabidopsis thaliana plants expressing GFP1-10 (strands 1 to 10). Multiple bacterial effectors tagged with the complementary strand 11 epitope retained their biological function in Arabidopsis and tomato (Solanum lycopersicum). Infection of plants expressing GFP1-10 with bacteria delivering GFP11-tagged effectors enabled direct effector detection in planta. We investigated the temporal and spatial delivery of GFP11-tagged effectors during infection with the foliar pathogen Pseudomonas syringae and the vascular pathogen Ralstonia solanacearum. Thus, the GFP strand system can be broadly used to investigate effector biology in planta.
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Nature Genetics: High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.
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Laboratoire d'Innovation Territorial (LIT) Ouest Territoires d'Elevage

LIT Ouest Territoires d’Elevage, L’élevage à vivre ensemble.
Un consortium d’acteurs des 3 régions Bretagne, Normandie et Pays de la Loire, et des filières agricoles et agroalimentaires du Grand Ouest (GO) de la France se sont saisis de cette opportunité pour travailler à la construction du Laboratoire d’Innovation Territorial « Ouest Territoires d’Élevage ». Il comporte: 3 coopératives polyvalentes et multi-espèces animales de l’Ouest : Agrial, Terrena et Triskalia, le pôle de compétitivité Valorial, les 3 Chambres Régionales d’Agriculture de Bretagne, de Normandie et des Pays de la Loire, les 3 instituts techniques agricoles (ITAs) du domaine animal :Ifip pour le porc, Itavi pour la volaille, Idele pour les ruminants, et des acteurs de la recherche et de l’enseignement supérieur agronomique et vétérinaire implantés dans l’Ouest :Inra, Irstea , Agrocampus Ouest, Oniris. Le LIT Ouest Territoires d’Elevage porte sur le développement d’élevages répondant mieux aux attentes des consommateurs, des citoyens et des politiques en matière de conditions d’élevage, plus spécifiquement en matière d’amélioration du bien-être des animaux d’élevage et de moindre recours aux médicaments en élevage.
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NAture: The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution (2017)

NAture: The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution (2017) | Microbes, plant immunity, and crop science | Scoop.it
The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.
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Nat. Commun.: Sequencing and de novo assembly of a near complete indica rice genome (2017)

Nat. Commun.: Sequencing and de novo assembly of a near complete indica rice genome (2017) | Microbes, plant immunity, and crop science | Scoop.it
A high-quality reference genome is critical for understanding genome structure, genetic variation and evolution of an organism. Here we report the de novo assembly of an indica rice genome Shuhui498 (R498) through the integration of single-molecule sequencing and mapping data, genetic map and fosmid sequence tags. The 390.3 Mb assembly is estimated to cover more than 99% of the R498 genome and is more continuous than the current reference genomes of japonica rice Nipponbare (MSU7) and Arabidopsis thaliana (TAIR10). We annotate high-quality protein-coding genes in R498 and identify genetic variations between R498 and Nipponbare and presence/absence variations by comparing them to 17 draft genomes in cultivated rice and its closest wild relatives. Our results demonstrate how to de novo assemble a highly contiguous and near-complete plant genome through an integrative strategy. The R498 genome will serve as a reference for the discovery of genes and structural variations in rice.
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Front. Plant Sci.: A transcriptomics and comparative genomics analysis reveals gene families with a role in body plan complexity (2017)

We analyzed tissue-specific transcriptomes of Arabidopsis thaliana and identified 66 gene families with a high frequency of “gradient genes” - genes showing a significant expression gradient between tissues. Gradient gene families include many with roles in hormone and peptide signaling, cell wall synthesis and remodeling, secondary metabolism, transcriptional regulation, and transport between cells. We compared the size of the gradient gene families among the genomes of four plant species with radically different body plans – a single-celled algae, a moss, a eudicot, and a monocot – and found that most of the gradient gene families (58/66) expanded in parallel with the evolution of morphological complexity. A novel measure of tissue diversity was used to show that members of any one gradient gene family tend not to be clustered in a single tissue, but are rather apportioned evenly across the tissues studied. Considered together, our results suggest that the diversification of these gene families supported the diversification of tissue types and the evolution of body plan complexity in plants.
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BMC Genomics: Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host rang...

BMC Genomics: Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host rang... | Microbes, plant immunity, and crop science | Scoop.it
Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuticular space without penetrating plant cells, it is assumed that effectors that contribute to virulence and determination of host range will be secreted into this plant-pathogen interface. Thus the predicted secretomes of a range of isolates of Venturia with distinct host-ranges were interrogated to reveal putative proteins involved in virulence and pathogenicity. Genomes of Venturia pirina (one European pear scab isolate) and Venturia inaequalis (three apple scab, and one loquat scab, isolates) were sequenced and the predicted secretomes of each isolate identified. RNA-Seq was conducted on the apple-specific V. inaequalis isolate Vi1 (in vitro and infected apple leaves) to highlight virulence and pathogenicity components of the secretome. Genes encoding over 600 small secreted proteins (candidate effectors) were identified, most of which are novel to Venturia, with expansion of putative effector families a feature of the genus. Numerous genes with similarity to Leptosphaeria maculans AvrLm6 and the Verticillium spp. Ave1 were identified. Candidates for avirulence effectors with cognate resistance genes involved in race-cultivar specificity were identified, as were putative proteins involved in host-species determination. Candidate effectors were found, on average, to be in regions of relatively low gene-density and in closer proximity to repeats (e.g. transposable elements), compared with core eukaryotic genes. Comparative secretomics has revealed candidate effectors from Venturia fungal plant pathogens that attack pome fruit. Effectors that are putative determinants of host range were identified; both those that may be involved in race-cultivar and host-species specificity. Since many of the effector candidates are in close proximity to repetitive sequences this may point to a possible mechanism for the effector gene family expansion observed and a route to diversification via transposition and repeat-induced point mutation.
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Plant Methods: A novel hairpin library-based approach to identify NBS–LRR genes required for effector-triggered hypersensitive response in Nicotiana benthamiana (2017)

Plant Methods: A novel hairpin library-based approach to identify NBS–LRR genes required for effector-triggered hypersensitive response in Nicotiana benthamiana (2017) | Microbes, plant immunity, and crop science | Scoop.it
PTI and ETI are the two major defence mechanisms in plants. ETI is triggered by the detection of pathogen effectors, or their activity, in the plant cell and most of the time involves internal receptors known as resistance (R) genes. An increasing number of R genes responsible for recognition of specific effectors have been characterised over the years; however, methods to identify R genes are often challenging and cannot always be translated to crop plants. We present a novel method to identify R genes responsible for the recognition of specific effectors that trigger a hypersensitive response (HR) in Nicotiana benthamiana. This method is based on the genome-wide identification of most of the potential R genes of N. benthamiana and a systematic silencing of these potential R genes in a simple transient expression assay. A hairpin-RNAi library was constructed covering 345 R gene candidates of N. benthamiana. This library was then validated using several previously described R genes. Our approach indeed confirmed that Prf, NRC2a/b and NRC3 are required for the HR that is mediated in N. benthamiana by Pto/avrPto (prf, NRC2a/b and NRC3) and by Cf4/avr4 (NRC2a/b and NRC3). We also confirmed that NRG1, in association with N, is required for the Tobacco Mosaic Virus (TMV)-mediated HR in N. benthamiana. We present a novel approach combining bioinformatics, multiple-gene silencing and transient expression assay screening to rapidly identify one-to-one relationships between pathogen effectors and host R genes in N. benthamiana. This approach allowed the identification of previously described R genes responsible for detection of avirulence determinants from Pseudomonas, Cladosporium and TMV, demonstrating that the method could be applied to any effectors/proteins originating from a broad range of plant pathogens that trigger an HR in N. benthamiana. Moreover, with the increasing availability of genome sequences from model and crop plants and pathogens, this approach could be implemented in other plants, accelerating the process of identification and characterization of novel resistance genes.
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Mol. Plant.: Emerging Jasmonate Transporters (2017)

Mol. Plant.: Emerging Jasmonate Transporters (2017) | Microbes, plant immunity, and crop science | Scoop.it
Empty descriJasmonic acid (JA) and methyl jasmonate (MeJA) are highly mobile and, when applied to intact plants, these compounds powerfully modulate gene expression. Moreover, activation of jasmonate-responsive genes usually occurs in tissues distal to the treatments. It therefore comes as no surprise that there are jasmonate transporters; these proteins are only now emerging and their discovery is important for a number of reasons. Firstly, biologically active jasmonates such as jasmonoyl-isoleucine (JA-Ile) are potent regulators that are made in small quantities and that need to be delivered to the correct cellular and subcellular sites. Secondly, jasmonates act to redirect resources from growth to defense. For example, when shoots are wounded, jasmonates help to coordinate the appropriate growth of roots so that organ growth rates are balanced even when a distal part of the plant is damaged. Moreover, some plants (Arabidopsis is an example) produce large quantities of the JA-Ile precursor JA upon wounding. JA and/or its immediate precursor can be transported from cell to cell and even from shoot to root (Gasperini et al., 2015; Figure 1A–1C ). The mechanisms underlying this transport need to be identified. However, a difficulty for the jasmonate field is that many studies of JA/JA-Ile transport have used exogenous jasmonates applied at sometimes non-physiological levels to plant tissues. These studies can be difficult to interpret, so the discovery of jasmonate transporter mutants represents a welcome breakthrough. Among these is the newly reported jasmonate transporter (JAT1) from Arabidopsis (Li et al., 2017).ption
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Science: Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

Science: Wild emmer genome architecture and diversity elucidate wheat evolution and domestication | Microbes, plant immunity, and crop science | Scoop.it
Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat’s domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 (TtBtr1) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.
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UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties - Bioinformatics

UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties - Bioinformatics | Microbes, plant immunity, and crop science | Scoop.it
Motivation: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed.
Results: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties.
Availability: UpSetR is available at
https://github.com/hms-dbmi/UpSetR/
and released under the MIT License. A Shiny app is available at
https://gehlenborglab.shinyapps.io/upsetr/

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Plant Methods: A multiplex PCR for rapid identification of Brassica species in the triangle of U

Plant Methods: A multiplex PCR for rapid identification of Brassica species in the triangle of U | Microbes, plant immunity, and crop science | Scoop.it
Within the Brassicaceae, six species from the genus Brassica are widely cultivated throughout the world as oilseed, condiment, fodder or vegetable crops. The genetic relationships among the six Brassica species are described by U’s triangle model. Extensive shared traits and diverse morphotypes among Brassica species make identification and classification based on phenotypic data alone challenging and unreliable, especially when dealing with large germplasm collections. Consequently, a major issue for genebank collections is ensuring the correct identification of species. Molecular genotyping based on simple sequence repeat (SSR) marker sequencing or the Illumina Infinium Brassica napus 60K single nucleotide polymorphism (SNP) array has been used to identify species and assess genetic diversity of Brassica collections. However, these methods are technically challenging, expensive and time-consuming, making them unsuitable for routine or rapid screening of Brassica accessions for germplasm management. A cheaper, faster and simpler method for Brassica species identification is described here. A multiplex polymerase chain reaction (MPCR) consisting of new and existing primers specific to the Brassica A, B and C genomes was able to reliably distinguish all six Brassica species in the triangle of U with 16 control samples of known species identity. Further validation against 120 Brassica accessions previously genotyped showed that the MPCR is highly accurate and comparable to more advanced techniques such as SSR marker sequencing or the Illumina Infinium B. napus 60K SNP array. In addition, the MPCR was sensitive enough to detect seed contaminations in pooled seed samples of Brassica accessions. A cheap and fast multiplex PCR assay for identification of Brassica species in the triangle of U was developed and validated in this study. The MPCR assay can be readily implemented in any basic molecular laboratory and should prove useful for the management of Brassica germplasm collections in genebanks.
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Trends Ecol. Evol.: Integrating Biogeography with Contemporary Niche Theory (2017)

There is no consensus on when biotic interactions impact the range limits of species. Starting from MacArthur’s use of invasibility to understand how biotic interactions influence coexistence, here we examine how biotic interactions shape species distributions. Range limits emerge from how birth, death, and movement rates vary with the environment. We clarify some basic issues revolving around niche definitions, illustrated with simple resource–consumer theory. We then highlight two different avenues for linking community theory and range theory; the first based on calculating the effects of biotic interactions on range limits across scales and landscape configurations, and the second based on aggregate measures of diffuse interactions and network strength. We conclude with suggestions for a future research agenda.
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Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus

Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus | Microbes, plant immunity, and crop science | Scoop.it
Divergence of breeding system plays an important role in fungal speciation. Ectomycorrhizal fungi, however, pose a challenge for the study of reproductive biology because most cannot be mated under laboratory conditions. To overcome this barrier, we sequenced the draft genomes of the ectomycorrhizal sister species Rhizopogon vinicolor Smith and Zeller and R. vesiculosus Smith and Zeller (Basidiomycota, Boletales)—the first genomes available for Basidiomycota truffles—and characterized gene content and organization surrounding their mating type loci. Both species possess a pair of homeodomain transcription factor homologs at the mating type A -locus as well as pheromone receptor and pheromone precursor homologs at the mating type B -locus. Comparison of Rhizopogon genomes with genomes from Boletales, Agaricales, and Polyporales revealed synteny of the A -locus region within Boletales, but several genomic rearrangements across orders. Our findings suggest correlation between gene content at the B -locus region and breeding system in Boletales with tetrapolar species possessing more diverse gene content than bipolar species. Rhizopogon vinicolor possesses a greater number of B -locus pheromone receptor and precursor genes than R. vesiculosus , as well as a pair of isoprenyl cysteine methyltransferase genes flanking the B -locus compared to a single copy in R. vesiculosus . Examination of dikaryotic single nucleotide polymorphisms within genomes revealed greater heterozygosity in R. vinicolor , consistent with increased rates of outcrossing. Both species possess the components of a heterothallic breeding system with R. vinicolor possessing a B -locus region structure consistent with tetrapolar Boletales and R. vesiculosus possessing a B -locus region structure intermediate between bipolar and tetrapolar Boletales.

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Plant Cell: The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies (2017)

Plant Cell: The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies (2017) | Microbes, plant immunity, and crop science | Scoop.it
The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa L. ssp. japonica), which completes its life cycle in 9 weeks. We sequenced 1,504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.
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fast moving genomics tools for rice!
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Recontres plantes-bactéries, 29/01-02/02/2018, Aussois

Recontres plantes-bactéries, 29/01-02/02/2018, Aussois | Microbes, plant immunity, and crop science | Scoop.it
- Huit thématiques sont proposées à l’appel à communication : *Structure et fonction du microbiome au sein du phytobiome *Programmes symbiotiques : composantes, contrôle, origine évolutive
*Réponses moléculaires et résistance des plantes
*Evolution, phylogénie et génomique comparative des bactéries *Métabolisme et métabolites des interactions
*Régulation et signalisation
*Gestion de la santé des plantes : diagnostic, biocontrôle et autres méthodes de lutte
*Emergence, épidémiologie, écologie et biologie des populations bactériennes associées aux plantes
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Mining microbes: Creating genomic tools to fight disease

Mining microbes: Creating genomic tools to fight disease | Microbes, plant immunity, and crop science | Scoop.it
In 2015, several patients in the intensive care unit of the Royal Brompton Hospital in London came down with an unexplained illness. Doctors suspected a fungal infection—but those can be difficult to diagnose, and culturing fungi from patient blood samples takes time.
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La Bibliothèque du Vivant : une référence génomique pour les espèces

La Bibliothèque du Vivant : une référence génomique pour les espèces | Microbes, plant immunity, and crop science | Scoop.it
Bibliothèque du Vivant (BdV) est un appel à projets financé par le CNRS, l'INRA et le MNHN de 2011 et 2013 et qui a bénéficié du support technique du Génoscope pour le séquençage massif de l’ADN. BdV avait pour objectif de soutenir et d’accompagner cent équipes françaises portant des projets d’étude de la biodiversité. Il voulait accélérer le séquençage massif de gènes, ou partie de gènes d’organismes pluricellulaires appartenant à différents groupes taxinomiques (plantes, champignons, vertébrés, insectes etc.) pour compléter une bibliothèque de codes-barres ADN de référence pour le vivant et ainsi accéder à phylogénie moléculaires de ces organismes. Des travaux issus de ce programme font l’objet d’un volume spécial "DNA library of life" (2017) publié dans la revue European Journal of Taxonomy.

 

CNRS - Institut écologie et environnement - Actualités de l'institut, 05.05.2017


Via Bernadette Cassel
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A noter : 4ème Colloque de Génomique Environnementale 13615/09 à Marseille  http://gdr3692.wixsite.com/gdrge/4e-colloque-genomique-environnement
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Is There an Upper Limit to Genome Size?

Is There an Upper Limit to Genome Size? | Microbes, plant immunity, and crop science | Scoop.it

At 50-fold the size of the human genome (3 Gb), the staggeringly huge genome of 147.3 Gb recently discovered in the fern Tmesipteris obliqua is comparable in size to those of the other plant and animal record-holders (i.e., Paris japonica, a flowering plant with a genome size of 148.8 Gb, and Protopterus aethiopicus, a lungfish with a genome of 130 Gb). The synthesis of available information on giant genomes suggests that the biological limit to genome size expansion in eukaryotes may have been reached. We propose several explanations for why the genomes of ferns, flowering plants, and lungfish, all of which have independently undergone dramatic increases in genome size through a variety of mechanisms, do not exceed 150 Gb.


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Curr. Biol.: Phylogenetic comparative methods (2017)

Curr. Biol.: Phylogenetic comparative methods (2017) | Microbes, plant immunity, and crop science | Scoop.it
Phylogenetic comparative methods (PCMs) enable us to study the history of organismal evolution and diversification. PCMs comprise a collection of statistical methods for inferring history from piecemeal information, primarily combining two types of data: first, an estimate of species relatedness, usually based on their genes, and second, contemporary trait values of extant organisms. Some PCMs also incorporate information from geological records, especially fossils, but also other gradual and episodic events in the Earth’s history (for example, trait data from fossils or the global oxygen concentration as an independent variable). It is important to note at the outset that PCMs are not concerned with reconstructing the evolutionary relationships among species; this has to do with estimating the phylogeny from genetic, fossil and other data, and a separate set of methods for this process makes up the field of phylogenetics. PCMs as a set of methods are distinct from, but are not completely independent of, phylogenetics. PCMs are used to address the questions: how did the characteristics of organisms evolve through time and what factors influenced speciation and extinction?
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Plant J.: Advances on plant–pathogen interactions from molecular toward systems biology perspectives (2017)

Plant J.: Advances on plant–pathogen interactions from molecular toward systems biology perspectives (2017) | Microbes, plant immunity, and crop science | Scoop.it
In the past 2 decades, progress in molecular analyses of the plant immune system has revealed key elements of a complex response network. Current paradigms depict the interaction of pathogen-secreted molecules with host target molecules leading to the activation of multiple plant response pathways. Further research will be required to fully understand how these responses are integrated in space and time, and exploit this knowledge in agriculture. In this review, we highlight systems biology as a promising approach to reveal properties of molecular plant–pathogen interactions and predict the outcome of such interactions. We first illustrate a few key concepts in plant immunity with a network and systems biology perspective. Next, we present some basic principles of systems biology and show how they allow integrating multiomics data and predict cell phenotypes. We identify challenges for systems biology of plant–pathogen interactions, including the reconstruction of multiscale mechanistic models and the connection of host and pathogen models. Finally, we outline studies on resistance durability through the robustness of immune system networks, the identification of trade-offs between immunity and growth and in silico plant–pathogen co-evolution as exciting perspectives in the field. We conclude that the development of sophisticated models of plant diseases incorporating plant, pathogen and climate properties represent a major challenge for agriculture in the future.
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