Genome-wide survey of repetitive DNA elements in the button mushroom Agaricus bisporus
M Foulongne-Oriol, C Murat, R Castanera, L Ramírez, ASM Sonnenberg
Fungal Genetics and Biology

Abstract

Repetitive DNA elements are ubiquitous constituents of eukaryotic genomes. The biological roles of these repetitive elements, supposed to impact genome organization and evolution, are not completely elucidated yet. The availability of whole genome sequence offers the opportunity to draw a picture of the genome-wide distribution of these elements and provide insights into potential mechanisms of genome plasticity. The present study uses in silico approaches to describe tandem repeats and transposable elements distribution in the genome of the button mushroom, Agaricus bisporus. Transposable elements comprised 12.43% of the assembled genome, and 66% of them were found clustered in the centromeric or telomeric regions. Methylation of retrotransposon has been demonstrated. A total of 1996 mini-, 4062 micro-, and 37 satellites motifs were identified. The microsatellites appeared widely and evenly spread over the whole genome sequence, whereas the minisatellites were not randomly distributed. Indeed, minisatellites were found to be associated with transposable elements clusters. Telomeres exhibited a specific sequence with a T_nAG_nsignature. A comparison between the two available genome sequences of A. bisporus was also performed and sheds light on the genetic divergence between the two varieties. Beyond their role in genome structure, repeats provide a virtually endless source of molecular markers useful for genetic studies in this cultivated species.

Optimization of a real-time PCR assay for the detection of the quarantine pathogen< i> Melampsora medusae</i> f. sp.< i> deltoidae</i>
AL Boutigny, C Guinet, A Vialle, R Hamelin, A Andrieux, P Frey, C Husson, R Ioos
Fungal Biology

Melampsora medusae, one of the causal agents of poplar rust, is classified as an A2 quarantine pest for EPPO and its presence in Europe is strictly controlled. Two formae speciales have been described within M. medusae, M. medusae f. sp. deltoidae and M. medusae f. sp. tremuloidae on the basis of their pathogenicity on Populus species from the section Aigeiros (e.g. Populus deltoides) or Populus (e.g. Populus tremuloides), respectively. In this study, a real-time PCR assay was developed allowing the detection of M. medusae f. sp.deltoidae, the forma specialis that is economically harmful. A set of primers and hydrolysis probe was designed based on sequence polymorphisms in the large ribosomal RNA subunit (28S). The real-time PCR assay was optimized and performance criteria of the detection method, i.e. sensitivity, specificity, repeatability, reproducibility and robustness, were assessed. The real-time PCR method was highly specific and sensitive and allowed the detection of one single urediniospore of M. medusae f. sp. deltoidae in a mixture of 2 mg of urediniospores of other Melampsora species. This test offers improved specificity over currently existing conventional PCR tests and can be used for specific surveys in European nurseries and phytosanitary controls, in order to avoid introduction and spread of this pathogen in Europe.

Keywords

• Melampsora;
• poplar rust;
• real-time PCR;
• quarantine pathogen

An improved method compatible with metagenomic analyses to extract genomic DNA from soils in Tuber melanosporum orchards
S Antony‐Babu, C Murat, A Deveau, F Tacon, P Frey‐Klett, S Uroz
Journal of Applied Microbiology

Keywords:

DNA extraction; Soil; Tuber melanosporum ; Calcareous soil

Biotrophic transportome in mutualistic plant–fungal interactions
L Casieri, NA Lahmidi, J Doidy, C Veneault-Fourrey, A Migeon, L Bonneau, PE …
Mycorrhiza, 1-29

Abstract

Fine‐scale spatial genetic structure of the black truffle (Tuber melanosporum) investigated with neutral microsatellites and functional mating type genes
C Murat, A Rubini, C Riccioni, H la Varga, E Akroume, B Belfiori, M Guaragno …
New Phytologist

Keywords:

Cysteine-based redox regulation and signalling in plants J. Couturier, K. Chibani, JP Jacquot Jacquot and N. Rouhier. Frontiers in Plant Proteomics

Living organisms are subjected to oxidative stress conditions which are characterized by the production of reactive oxygen (ROS), nitrogen (RNS) and sulfur (RSS) species. In plants as in other organisms, many of these compounds have a dual function as they damage different types of macromolecules but they also likely fulfil an important role as secondary messengers. Owing to the reactivity of their thiol groups, some protein cysteine residues are particularly prone to oxidation by these molecules. In the past years, besides their recognized catalytic and regulatory functions, the modification of cysteine thiol group was increasingly viewed as either protective or redox signalling mechanisms. The most physiologically relevant reversible redox post-translational modifications (PTMs) are disulfide bonds, sulfenic acids, S-glutathionylated adducts, S-nitrosothiols and to a lesser extent S-sulfenylamides, thiosulfinates and S-persulfides. These redox PTMs are mostly controlled by two oxidoreductase families, thioredoxins and glutaredoxins. This review focuses on recent advances highlighting the variety and physiological roles of these PTMs and the proteomic strategies used for their detection.

Microbe-independent entry of oomycete RxLR effectors and fungal RxLR-like effectors into plant and animal cells is specific and reproducible
BM Tyler, SD Kale, Q Wang, K Tao, HR Clark, K Drews, V Antignani, A Rumore …
Molecular Plant-Microbe Interactions

Abstract:

A wide diversity of pathogens and mutualists of plant and animal hosts, including oomycetes and fungi, produce effector proteins that enter the cytoplasm of host cells. A major question has been whether or not entry by these effectors can occur independently of the microbe or requires machinery provided by the microbe. Numerous publications have documented that oomycete RxLR effectors and fungal RxLR-like effectors can enter plant and animal cells independent of the microbe. A recent re-examination of whether the RxLR domain of oomycete RxLR effectors is sufficient for microbe-independent entry into host cells, concluded that the RxLR domains of P. infestans Avr3a and of P. sojae Avr1b alone are NOT sufficient to enable microbe-independent entry of proteins into host and non-host plant and animal cells. Here we present new, more detailed data that unambiguously demonstrate that the RxLR domain of Avr1b does show efficient and specific entry into soybean root cells, and also into wheat leaf cells, at levels well above background non-specific entry. We also summarize host cell entry experiments with a wide diversity of oomycete and fungal effectors with RxLR or RxLR-like motifs that have been independently carried out by the six different labs that co-authored this letter. Finally we discuss possible technical reasons why specific cell entry may have been not detected.

Who is Controlling whom within the Ectomycorrhizal Symbiosis: Insights from Genomic and Functional Analyses
C Veneault‐Fourrey, JM Plett, F Martin
Molecular Microbial Ecology of the Rhizosphere: Volume 1 & 2, 501-512

Keywords: