Annegret Kohler

Annegret Kohler
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Interactions Arbres/Micro-organismes (IAM)

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267
Publications
68,336
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17,521
Citations
Additional affiliations
January 2007 - December 2012
January 2003 - December 2004
Université Henri Poincaré Nancy 1
January 2002 - present

Publications

Publications (267)
Preprint
Full-text available
The jasmonic acid (JA) signaling pathway plays an important role in the establishment of the ectomycorrhizal symbiosis (ECM) between Laccaria bicolor and poplar. We previously showed that the L. bicolor effector MiSSP7 induces the stabilization of the poplar JAZ6, a JA co-repressor protein that binds to Populus MYC2.1 and MYC2.2, orthologs of the A...
Article
Full-text available
High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis rev...
Article
Fungivory of mycorrhizal hyphae has a significant impact on fungal fitness and, by extension, on nutrient transfer between fungi and host plants in natural ecosystems. Mycorrhizal fungi have therefore evolved an arsenal of chemical compounds that are hypothesized to protect the hyphal tissues from being eaten, such as the protease inhibitors mycocy...
Article
Full-text available
Orchid seed germination in nature is an extremely complex physiological and ecological process involving seed development and mutualistic interactions with a restricted range of compatible mycorrhizal fungi. The impact of the fungal species' partner on the orchids' transcriptomic and metabolic response is still unknown. In this study, we performed...
Article
Full-text available
Highlight Comparative transcriptomic analysis from the cambium of two Populus genotypes with contrasting adventitious rooting phenotype revealed a higher transcriptional activity in the easy-to-root genotype compared to the difficult-to-root one. Abstract Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially...
Article
Full-text available
Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotyp...
Article
Full-text available
The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seve...
Article
Full-text available
In ectomycorrhiza, root penetration and colonization of the intercellular space by symbiotic hyphae is thought to rely on the mechanical force that results from hyphal tip growth, enhanced by the activity of secreted cell-wall-degrading enzymes. Here, we characterize the biochemical properties of the symbiosis-induced polygalacturonase LbGH28A from...
Article
Full-text available
Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and the extramatricular mycelium explores soil for nutrients. Ev...
Article
Full-text available
The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate that root mycobiota members evolved from ancestors wi...
Article
The ectomycorrhizal (ECM) symbiosis has independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic signatures of the transition to the ECM habit within the hyper-diverse Russulaceae. We present comparative analyses of the genomic architecture and the total and secreted gene repertoires of 18 speci...
Article
In this review, we highlight the main insights that have been gathered from recent developments using large-scale genomics of fungal saprotrophs and symbiotrophs (including ectomycorrhizal and orchid and ericoid mycorrhizal fungi) inhabiting forest ecosystems. After assessing the goals and motivations underlying our approach, we explore our current...
Article
We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales, by comparing the genomes of 21 symbiotrophic species to their saprotrophic brown‐rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharpl...
Preprint
Full-text available
In ectomycorrhiza, root penetration and colonization of the intercellular space by symbiotic hyphae is thought to rely on the mechanical force that results from hyphal tip growth, enhanced by the activity of secreted cell-wall-degrading enzymes. Here, we characterize the biochemical properties of the symbiosis-induced polygalacturonase LbGH28A from...
Preprint
Full-text available
Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotyp...
Preprint
Full-text available
In this study, we aim to identify genomic traits of the transitions to the ectomycorrhizal ecology within the Boletales, one of the most diverse lineages of symbiotrophic fungi. We sequenced the genomes and compared the gene repertoires of symbiotrophic Boletales species to their saprotrophic brown-rot relatives. We also reconstructed gene duplicat...
Article
Full-text available
Ectomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho‐species and cryptic lineages, with weak morphological...
Preprint
Full-text available
Ectomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho-species and cryptic lineages, with weak morphological...
Article
Full-text available
Globalization and international trade have impacted organisms around the world leading to a considerable number of species establishing in new geographic areas. Many organisms have taken advantage of human‐made environments, including buildings. One such species is the dry rot fungus Serpula lacrymans, which is the most aggressive wood‐decay fungus...
Preprint
Full-text available
Roots of Arabidopsis thaliana do not engage in symbiotic associations with mycorrhizal fungi but host taxonomically diverse fungal communities that influence health and disease states. We sequenced the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with 79 other plant-associated fungi. We rep...
Preprint
Full-text available
The ectomycorrhizal symbiosis is an essential guild of many forested ecosystems and has a dynamic evolutionary history across kingdom Fungi, having independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic features of the transition to the ectomycorrhizal habit within the Russulaceae, one of the...
Preprint
Full-text available
Globalization and international trade have impacted organisms around the world leading to a considerable number of species establishing in new geographic areas. Many organisms have taken advantage of human-made environments, including buildings. One such species is the dry rot fungus Serpula lacrymans , which is the most aggressive wood-decay fungu...
Article
Full-text available
Tuber brumale and Tuber indicum (Pezizomycetes) are two edible black truffles establishing ectomycorrhizal symbiosis with trees and shrubs. T. brumale is ubiquitous in Europe, and T. indicum is mainly found in China. Here, we present the draft genome sequences of T. brumale and T. indicum .
Article
The Omega class of glutathione transferases (GSTs) forms a distinct class within the cytosolic GST superfamily because most of them possess a catalytic cysteine residue. The human GST Omega 1 isoform was first characterized twenty years ago, but it took years of work to clarify the roles of the human isoforms. Concerning the kingdom of fungi, littl...
Preprint
Full-text available
Background When identifying transcript abundance in response to treatment, accurate quantification is critical, especially when examining subtle differences in expression. In particular, data normalization is necessary to account for differences among samples including those associated with RNA quantity and quality. Due to the capacity of droplet d...
Article
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Despite the pivotal role of jasmonic acid in the outcome of plant-microorganism interactions, JA-signaling components in roots of perennial trees like western balsam poplar (Populus trichocarpa) are poorly characterized. Here we decipher the poplar-root JA-perception complex centered on PtJAZ6, a co-repressor of JA-signaling targeted by the effecto...
Article
Ectomycorrhizal (ECM) fungi are integral to boreal and temperate forest ecosystem functioning and nutrient cycling. ECM fungi, however, originate from diverse saprotrophic lineages and the impacts of genetic variation across species, and especially within a given ECM species, on function and interactions with the environment is not well understood....
Article
Full-text available
Desert truffles are edible hypogeous fungi forming ectendomycorrhizal symbiosis with plants of Cistaceae family. Knowledge about the reproductive modes of these fungi and the molecular mechanisms driving the ectendomycorrhizal interaction is lacking.  Genomes of the highly appreciated edible desert truffles, Terfezia claveryi Chatin and Tirmania n...
Article
Full-text available
Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucor-omycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present...
Article
Full-text available
This study investigates the impact of the alteration of the monolignol biosynthesis pathway on the establishment of the in vitro interaction of poplar roots either with a mutualistic ectomycorrhizal fungus or with a pathogenic root-knot nematode. Overall, the five studied transgenic lines downregulated for caffeoyl-CoA O-methyltransferase (CCoAOMT)...
Article
Pathogenic microbes are known to manipulate the defences of their hosts through the production of secreted effector proteins. More recently, mutualistic mycorrhizal fungi have also been described as using these secreted effectors to promote host colonization. Here we characterise a mycorrhiza‐induced small secreted effector protein of 10 kDa produc...
Article
Full-text available
The success of Ericaceae in stressful habitats enriched in heavy metals has been ascribed to the distinctive abilities of their mycorrhizal fungal partners to withstand heavy metal stress and to enhance metal tolerance in the host plant. Whereas heavy metal tolerance has been extensively investigated in some ericoid mycorrhizal (ERM) fungi, the mol...
Article
Full-text available
To establish and maintain a symbiotic relationship, the ectomycorrhizal fungus Laccaria bicolor releases mycorrhiza‐induced small secreted proteins (MiSSPs) into host roots. Here, we have functionally characterized the MYCORRHIZA‐iNDUCED SMALL SECRETED PROTEIN OF 7.6 kDa (MiSSP7.6) from L. bicolor by assessing its induced expression in ectomycorrhi...
Article
Full-text available
The Target Of Rapamycin (TOR) signaling pathway is known to regulate growth in response to nutrient availability and stress in eukaryotic cells. In the present study, we have investigated the TOR pathway in the white-rot fungus Phanerochaete chrysosporium. Inhibition of TOR activity by rapamycin affects conidia germination and hyphal growth highlig...
Poster
Full-text available
Fungi produce a wide variety of biologically active secondary metabolites, a large proportion of them being polyketides, a group of compounds characterized by a great complexity and structural diversity. Fungal polyketides are produced by polyketide synthases (PKSs), very large multifunctional iterative enzymes. Several functions have been attribut...
Article
Full-text available
One of the most striking features occurring in the root-knot nematode Meloidogyne incognita induced galls is the reorganization of the vascular tissues. During the interaction of the model tree species Populus and M. incognita, a pronounced xylem proliferation was previously described in mature galls. To better characterise changes in expression of...
Article
The phytohormones jasmonate, gibberellin, salicylate, and ethylene regulate an interconnected reprogramming network integrating root development with plant responses against microbes. The establishment of mutualistic ectomycorrhizal symbiosis requires the suppression of plant defense responses against fungi as well as the modification of root archi...
Article
Microbial communities interplay with their environment through their functional traits that can be as a response or an effect to the environment. Here we explore how a functional trait – the decomposition of organic matter, can be addressed based on genetic markers and how the expression of these markers reflect ecological strategies of two fungal...
Preprint
Full-text available
The Target Of Rapamycin (TOR) signaling pathway is known to regulate growth in response to nutrient availability and stress in eukaryotic cells. In the present study, we have investigated the TOR pathway in the white-rot fungus Phanerochaete chrysosporium . Inhibition of TOR activity by rapamycin affects conidia germination and hyphal growth highli...
Article
Full-text available
Ectomycorrhizal (ECM) fungi are important root symbionts of trees, as they can have significant effects on the nutrient status of plants. In polluted environments, particular ECM fungi can protect their host tree from Zn toxicity by restricting the transfer of Zn while securing supply of essential nutrients. However, mechanisms and regulation of ce...
Poster
Full-text available
Fungi produce a wide variety of biologically acIve secondary metabolites, a large proportion of them being polyketides, a group of compounds characterized by a great complexity and structural diversity. Polyketides are produced by polyketide synthases (PKSs), very large multi-functional iterative enzymes. Several functions have been attributed to f...
Article
Full-text available
Plant‐tissue‐colonising fungi fine‐tune the deconstruction of plant‐cell walls (PCW) using different sets of enzymes according to their lifestyle. However, some of these enzymes are conserved among fungi with dissimilar lifestyles. We identified genes from Glycoside Hydrolase family GH131 as commonly expressed during plant‐tissue colonisation by sa...
Article
Full-text available
Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Périgord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) an...
Poster
Full-text available
Ectomycorrhizal (ECM) fungi play key roles in the biogeochemical cycles in forest ecosystems. In the history of fungal evolution, various lineages of mycorrhizal fungi have appeared in the phyla Ascomycota and Basidiomycota leading to ectomycorrhizae (ECM), ericoid mycorrhizae (ERM), and orchid mycorrhizae (ORM). Little is known on the mechanisms d...
Article
Extensive evidence showed that the efficiency of fungal wood degradation is closely dependent on their ability to cope with the myriad of putative toxic compounds called extractives released during this process. By analyzing global gene expression of Phanerochaete chrysosporium after short oak extractive treatment (1, 3 and 6h), we show that the ea...
Article
Full-text available
The deconstruction of recalcitrant woody substrates is a central component of carbon cycling and forest health. Laboratory investigations have contributed substantially toward understanding the mechanisms employed by model wood decay fungi, but few studies have examined the physiological processes in natural environments. Herein, we identify the fu...
Article
Full-text available
Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes 1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times 2 . With 450 species spread throughout Asia, Europe and America 3 , oaks constitute a critical global...
Article
Full-text available
The ascomycete Tuber borchii (Pezizomycetes) is a whitish edible truffle that establishes ectomycorrhizal symbiosis with trees and shrubs. This fungus is ubiquitous in Europe and is also cultivated outside Europe. Here, we present the draft genome sequence of T. borchii strain Tbo3840 (97.18 Mb in 969 scaffolds, with 12,346 predicted protein-coding...
Chapter
Sequencing of a high number of fungal genomes has become possible due to the development of next generation sequencing techniques (NGS). The most recent developments aim to sequence single-molecule long-reads in order to improve genome assemblies, but consequently needs higher quality (minimum >20 kbp) DNA as starting material. However, environment...
Article
Full-text available
Mutualistic and pathogenic plant-colonizing fungi use effector molecules to manipulate the host cell metabolism to allow plant tissue invasion. Some small secreted proteins (SSPs) have been identified as fungal effectors in both ectomycorrhizal and arbuscular mycorrhizal fungi, but it is currently unknown whether SSPs also play a role as effectors...
Poster
Full-text available
Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum