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2013 Fungal Genetics Conference (Asilomar, USA, March 12-17, 2013)

2013 Fungal Genetics Conference (Asilomar, USA, March 12-17, 2013) | Mycorrhizal fungal genomes | Scoop.it

The Fungal Genetics Policy Committee invites you to attend the 27th Fungal Genetics Conference, sponsored by the Genetics Society of America. The meeting is held every two years at the Asilomar Conference Grounds, Pacific Grove, California (near Monterey, California). The conference will open on Tuesday evening, March 12 with an Opening Mixer from 7:30 pm – 10:30 pm and end on Sunday, March 17. Regine Kahmann will present the Perkins/Metzenberg Lecture on Saturday, March 16 at 6:30 pm, followed by the banquet and closing party.

 

Chairs of the Scientific Program:
Katherine Borkovich, University of California, Riverside
Francis Martin, INRA, Nancy, France

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Mycorrhizal fungal genomes
Genomes and Transcriptomes of Mycorrhizal fungi - by S. Ghignone & R. Balestrini
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Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota

Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota | Mycorrhizal fungal genomes | Scoop.it
Arbuscular mycorrhizal fungi (AMF, Glomeromycota) colonize roots of the majority of terrestrial plants. They provide essential minerals to their plant hosts and receive photosynthates in return. All major lineages of AMF harbor endobacteria classified as Mollicutes, and known as mycoplasma-related endobacteria (MRE). Except for their substantial intrahost genetic diversity and ability to transmit vertically, virtually nothing is known about the life history of these endobacteria. To understand MRE biology, we sequenced metagenomes of three MRE populations, each associated with divergent AMF hosts. We found that each AMF species harbored a genetically distinct group of MRE. Despite vertical transmission, all MRE populations showed extensive chromosomal rearrangements, which we attributed to genetic recombination, activity of mobile elements, and a history of plectroviral invasion. The MRE genomes are characterized by a highly reduced gene content, indicating metabolic dependence on the fungal host, with the mechanism of energy production remaining unclear. Several MRE genes encode proteins with domains involved in protein–protein interactions with eukaryotic hosts. In addition, the MRE genomes harbor genes horizontally acquired from AMF. Some of these genes encode small ubiquitin-like modifier (SUMO) proteases specific to the SUMOylation systems of eukaryotes, which MRE likely use to manipulate their fungal host. The extent of MRE genome plasticity and reduction, along with the large number of horizontally acquired host genes, suggests a high degree of adaptation to the fungal host. These features, together with the ubiquity of the MRE–Glomeromycota associations, emphasize the significance of MRE in the biology of Glomeromycota.

 

Mizue Naito, Joseph B. Morton, and Teresa E. Pawlowska

PNAS, doi: 10.1073/pnas.1501676112

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Frontiers | Expanding genomics of mycorrhizal symbiosis | Microbial Symbioses

Frontiers | Expanding genomics of mycorrhizal symbiosis | Microbial Symbioses | Mycorrhizal fungal genomes | Scoop.it
The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.
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Plant and fungal gene expression in mycorrhizal protocorms of the orchid Serapias vomeracea colonized by Tulasnella calospora

Plant and fungal gene expression in mycorrhizal protocorms of the orchid Serapias vomeracea colonized by Tulasnella calospora | Mycorrhizal fungal genomes | Scoop.it
Little is known on the molecular bases of plant–fungal interactions in orchid mycorrhiza. We developed a model system to investigate gene expression in mycorrhizal protocorms of Serapias vomeracea colonised by Tulasnella calospora. Our recent results with a small panel of genes as indicators of plant response to mycorrhizal colonization indicate that genes related with plant defense were not significantly up-regulated in mycorrhizal tissues. Here, we used laser microdissection to investigate whether expression of some orchid genes was restricted to specific cell types. Results showed that SvNod1, a S. vomeracea nodulin-like protein containing a plastocyanin-like domain, is expressed only in protocorm cells containing intracellular fungal hyphae. In addition, we investigated a family of fungal zinc metallopeptidases (M36). This gene family has expanded in the T. calospora genome and RNA-Seq experiments indicate that some members of the M36 metallopeptidases family are differentially regulated in orchid mycorrhizal protocorms.
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Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists | Mycorrhizal fungal genomes | Scoop.it
To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall–degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7–38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.
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JGI Mycorrhizal Genomics Initiative (MGI) project

JGI Mycorrhizal Genomics Initiative (MGI) project | Mycorrhizal fungal genomes | Scoop.it

JGI Mycorrhizal Genomics Initiative (MGI) project: list of available genomes

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Broad compatibility in fungal root symbioses

Broad compatibility in fungal root symbioses | Mycorrhizal fungal genomes | Scoop.it

Plants associate with a wide range of beneficial fungi in their roots which facilitate plant mineral nutrient uptake in exchange for carbohydrates and other organic metabolites. These associations play a key role in shaping terrestrial ecosystems and are widely believed to have promoted the evolution of land plants. To establish compatibility with their host, root-associated fungi have evolved diverse colonization strategies with distinct morphological, functional and genomic specializations as well as different degrees of interdependence. They include obligate biotrophic arbuscular mycorrhizal (AM), and facultative biotrophic ectomycorrhizal (ECM) interactions but are not restricted to these well-characterized symbioses. There is growing evidence that root endophytic associations, which due to their inconspicuous nature have been often overlooked, can be of mutualistic nature and represent important players in natural and managed environments. Recent research into the biology and genomics of root associations revealed fascinating insight into the phenotypic and trophic plasticity of these fungi and underlined genomic traits associated with biotrophy and saprotrophy. In this review we will consider the commonalities and differences of AM and ECM associations and contrast them with root endophytes.


Alga Zuccaro, Urs Lahrmann, Gregor Langen

Current Opinion in Plant Biology
Volume 20, August 2014, Pages 135–145

http://dx.doi.org/10.1016/j.pbi.2014.05.013

 


 

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Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus

Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus | Mycorrhizal fungal genomes | Scoop.it

Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregulariswith other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.

 

Lin K, Limpens E, Zhang Z, Ivanov S, Saunders DGO, et al. (2014) Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus. PLoS Genet 10(1): e1004078.

 

http://dx.doi.org/10.1371/journal.pgen.1004078

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Rhizophagus irregularis DAOM 181602 v1.0 - Home

Rhizophagus irregularis DAOM 181602 v1.0 - Home | Mycorrhizal fungal genomes | Scoop.it

The JGI R. irregularis genome Portal is now public.

Now no password is required for access. However, existing login is still necessary for manual curation of the genes on the Portal.

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[Gem from past] Arbuscular Mycorrhiza: The Challenge to Understand the Genetics of the Fungal Partner

[Gem from past] Arbuscular Mycorrhiza: The Challenge to Understand the Genetics of the Fungal Partner | Mycorrhizal fungal genomes | Scoop.it

Arbuscular mycorrhizal symbioses occur between fungi and the majority of plant species. They are important for plant nutrition, plant growth, protection from pathogens, plant diversity, nutrient cycling, and ecosystem processes. A key goal in research is to understand the molecular basis of the establishment, regulation, and functioning of the symbiosis. However, lack of knowledge on the genetics of the fungal side of this association has hindered progress. Here, we show how several key, recently discovered processes concerning the genetics of arbuscular mycorrhizal fungi could be essential for ultimately understanding the molecular genetics of this important symbiosis with plants.

 

Ian R. Sanders and Daniel Croll

Annual Review of Genetics, Vol. 44: 271-292 (Volume publication date December 2010) DOI: 10.1146/annurev-genet-102108-134239

 

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Tuber melanosporum from Genoscope - Home

Tuber melanosporum from Genoscope - Home | Mycorrhizal fungal genomes | Scoop.it

Tuber melanosporum was the second ectomycorrhizal fungus whose genome has been sequenced.

 

This copy of the genome was obtained from the Tuber Genome Browser at Genoscope. In order to allow comparative analyses with other fungal genomes sequenced by the Joint Genome Institute, a copy of this genome is incorporated into MycoCosm.

 

Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B, Percudani R, Porcel B, Rubini A, Amicucci A, Amselem J, Anthouard V, Arcioni S, Artiguenave F, Aury JM, Ballario P, Bolchi A, Brenna A, Brun A, Buée M, Cantarel B, Chevalier G, Couloux A, Da Silva C, Denoeud F, Duplessis S, Ghignone S, Hilselberger B, Iotti M, Marçais B, Mello A, Miranda M, Pacioni G, Quesneville H, Riccioni C, Ruotolo R, Splivallo R, Stocchi V, Tisserant E, Viscomi AR, Zambonelli A, Zampieri E, Henrissat B, Lebrun MH, Paolocci F, Bonfante P, Ottonello S, Wincker P. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature. 2010 Apr 15;464(7291):1033-8. Epub 2010 Mar 28.

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Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor

Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor | Mycorrhizal fungal genomes | Scoop.it

Background

 

The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome.

Methodology/Principal Findings

 

TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intact copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea.

Conclusions

 

This analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus.

 

Labbé J, Murat C, Morin E, Tuskan GA, Le Tacon F, et al. (2012) Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor. PLoS ONE 7(8): e40197.

 

http://dx.doi.org/10.1371/journal.pone.0040197

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JGI Mycorrhizal Genomics Initiative - Info

JGI Mycorrhizal Genomics Initiative - Info | Mycorrhizal fungal genomes | Scoop.it

List of fungi within the JGI Mycorrhizal Genomics Initiative whose genome has been released.

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Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association

Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association | Mycorrhizal fungal genomes | Scoop.it
For more than 450 million years, arbuscular mycorrhizal fungi (AMF) have formed intimate, mutualistic symbioses with the vast majority of land plants and are major drivers in almost all terrestrial ecosystems. The obligate plant-symbiotic AMF host additional symbionts, so-called Mollicutes-related endobacteria (MRE). To uncover putative functional roles of these widespread but yet enigmatic MRE, we sequenced the genome of DhMRE living in the AMF Dentiscutata heterogama. Multilocus phylogenetic analyses showed that MRE form a previously unidentified lineage sister to the hominis group of Mycoplasma species. DhMRE possesses a strongly reduced metabolic capacity with 55% of the proteins having unknown function, which reflects unique adaptations to an intracellular lifestyle. We found evidence for transkingdom gene transfer between MRE and their AMF host. At least 27 annotated DhMRE proteins show similarities to nuclear-encoded proteins of the AMF Rhizophagus irregularis, which itself lacks MRE. Nuclear-encoded homologs could moreover be identified for another AMF, Gigaspora margarita, and surprisingly, also the non-AMF Mortierella verticillata. Our data indicate a possible origin of the MRE-fungus association in ancestors of the Glomeromycota and Mucoromycotina. The DhMRE genome encodes an arsenal of putative regulatory proteins with eukaryotic-like domains, some of them encoded in putative genomic islands. MRE are highly interesting candidates to study the evolution and interactions between an ancient, obligate endosymbiotic prokaryote with its obligate plant-symbiotic fungal host. Our data moreover may be used for further targeted searches for ancient effector-like proteins that may be key components in the regulation of the arbuscular mycorrhiza symbiosis.

 

Gloria Torres-Cortés, Stefano Ghignone, Paola Bonfante, and Arthur Schüßler

PNAS, doi: 10.1073/pnas.1501540112

 

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Studying Genome Heterogeneity within the Arbuscular Mycorrhizal Fungal Cytoplasm

Studying Genome Heterogeneity within the Arbuscular Mycorrhizal Fungal Cytoplasm | Mycorrhizal fungal genomes | Scoop.it
Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustainable agricultural practices. However, measuring genetic diversity for these coenocytes is a major challenge: Within the same cytoplasm, AMF contain thousands of nuclei and show extremely high levels of genetic variation for some loci. The extent and physical location of polymorphism within and between AMF genomes is unclear. We used two complementary strategies to estimate genetic diversity in AMF, investigating polymorphism both on a genome scale and in putative single copy loci. First, we used data from whole-genome pyrosequencing of four AMF isolates to describe genetic diversity, based on a conservative network-based clustering approach. AMF isolates showed marked differences in genome-wide diversity patterns in comparison to a panel of control fungal genomes. This clustering approach further allowed us to provide conservative estimates of Rhizophagus spp. genomes sizes. Second, we designed new putative single copy genomic markers, which we investigated by massive parallel amplicon sequencing for two Rhizophagus irregularis and one Rhizophagus sp. isolates. Most loci showed high polymorphism, with up to 103 alleles per marker. This polymorphism could be distributed within or between nuclei. However, we argue that the Rhizophagus isolates under study might be heterokaryotic, at least for the putative single copy markers we studied. Considering that genetic information is the main resource for identification of AMF, we suggest that special attention is warranted for the study of these ecologically important organisms
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Symbiotic plant-fungi interactions stripped down to the root

Symbiotic plant-fungi interactions stripped down to the root | Mycorrhizal fungal genomes | Scoop.it
Mycorrhizal fungi live in the roots of host plants and are crucial components of all forest ecosystems. A large-scale study of fungal genomics provides new insights into the evolution of mycorrhizae and a deep exploration of mycorrhizal diversity that helps to uncover the molecular and genetic details of fungal symbiotic relationships with plants.
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The Mitochondrial Genome of the Glomeromycete Rhizophagus sp. DAOM 213198 Reveals an Unusual Organization Consisting of Two Circular Chromosomes

The Mitochondrial Genome of the Glomeromycete Rhizophagus sp. DAOM 213198 Reveals an Unusual Organization Consisting of Two Circular Chromosomes | Mycorrhizal fungal genomes | Scoop.it

Mitochondrial (mt) genomes are intensively studied in Ascomycota and Basidiomycota, but they are poorly documented in basal fungal lineages. In this study, we sequenced the complete mtDNA of Rhizophagus sp. DAOM 213198, a close relative to Rhizophagus irregularis, a widespread, ecologically and economical relevant species belonging to Glomeromycota. Unlike all other known taxonomically close relatives harboring a full-length circular chromosome, mtDNA of Rhizophagus sp. reveals an unusual organization with two circular chromosomes of 61,964 and 29,078 bp. The large chromosome contained nine protein-coding genes (atp9, nad5, cob, nad4, nad1, nad4L, cox1, cox2, and atp8), small subunit rRNA gene (rns), and harbored 20 tRNA-coding genes and 10 orfs, while the small chromosome contained five protein-coding genes (atp6, nad2, nad3, nad6, and cox3), large subunit rRNA gene (rnl) in addition to 5 tRNA-coding genes, and 8 plasmid-related DNA polymerases (dpo). Although structural variation of plant mt genomes is well documented, this study is the first report of the presence of two circular mt genomes in arbuscular mycorrhizal fungi. Interestingly, the presence of dpo at the breakage point in intergenes cox1-cox2 and rnl-atp6 for large and small mtDNAs, respectively, could be responsible for the conversion of Rhizophagus sp. mtDNA into two chromosomes. Using quantitative real-time polymerase chain reaction, we found that both mtDNAs have an equal abundance. This study reports a novel mtDNA organization in Glomeromycota and highlights the importance of studying early divergent fungal lineages to describe novel evolutionary pathways in the fungal kingdom.

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A field guide to whole-genome sequencing, assembly and annotation

A field guide to whole-genome sequencing, assembly and annotation | Mycorrhizal fungal genomes | Scoop.it

Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.


Via Francis Martin
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Frontiers | Cell wall remodeling in mycorrhizal symbiosis: a way towards biotrophism | Plant-Microbe Interaction

Frontiers | Cell wall remodeling in mycorrhizal symbiosis: a way towards biotrophism | Plant-Microbe Interaction | Mycorrhizal fungal genomes | Scoop.it
Cell walls are deeply involved in the molecular talk between partners during plant and microbe interactions, and their role in mycorrhizae, i.e., the widespread symbiotic associations established between plant roots and soil fungi, has been investigated extensively. All mycorrhizal interactions achieve full symbiotic functionality through the development of an extensive contact surface between the plant and fungal cells, where signals and nutrients are exchanged. The exchange of molecules between the fungal and the plant cytoplasm takes place both through their plasma membranes and their cell walls; a functional compartment, known as the symbiotic interface, is thus defined. Among all the symbiotic interfaces, the complex intracellular interface of arbuscular mycorrhizal (AM) symbiosis has received a great deal of attention since its first description. Here, in fact, the host plasmamembrane invaginates and proliferates around all the developing intracellular fungal structures, and cell wall material is laid down between this membrane and the fungal cell surface. By contrast, in ectomycorrhizae (ECM), where the fungus grows outside and between the root cells, plant and fungal cell walls are always in direct contact and form the interface between the two partners. The organization and composition of cell walls within the interface compartment is a topic that has attracted widespread attention, both in ecto- and endomycorrhizae. The aim of this review is to provide a general overview of the current knowledge on this topic by integrating morphological observations, which have illustrated cell wall features during mycorrhizal interactions, with the current data produced by genomic and transcriptomic approaches.

 

 

Balestrini R and Bonfante P (2014) Cell wall remodeling in mycorrhizal symbiosis: a way towards biotrophism. Front. Plant Sci. 5:237.

http://dx.doi.org/10.3389/fpls.2014.00237

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Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis | Mycorrhizal fungal genomes | Scoop.it

The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.


Tisserant et al.

Proceedings of the National Academy of Sciences of the United States of America

Volume 110, Issue 50, December 10, 2013, pages 20117–20122

 

http://dx.doi.org/10.1073/pnas.1313452110


 

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[Gem from past] Genomics of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi are soilborne microorganisms that form a mutualistic symbiotic association with most land plants. As obligate biotrophs these fungi are unable to complete their life cycle in the absence of the host plant. This symbiosis is increasingly being recognised as an integral and important part of natural ecosystems throughout the word. Because of the incalcitrance of arbuscular mycorrhizal fungi to grow in pure culture and consequently the difficulties in obtaining sufficiently large quantities of fungal material, the analysis of gene products has remained an extremely challenging but unexplored area. Until recently, little was known about the genomics of these fungi and it is only with the advent of powerful molecular techniques that it has been possible to venture research into their genetic makeup. This review surveys the most recent molecular genetics of arbuscular mycorrhizal fungi and their contributions to basic knowledge of the biology of this group of organisms.


Nuria Ferrol, Bert Bago, Philipp Franken, Armelle Gollotte, Manuel González-Guerrero, Lucy Alexandra Harrier, Luisa Lanfranco, Diederik van Tuinen, Vivienne Gianinazzi-Pearson

Applied Mycology and Biotechnology

Volume 4, 2004, Pages 379–403

 

http://dx.doi.org/10.1016/S1874-5334(04)80019-4

 

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Genetic and genomic glimpses of the elusive arbuscular mycorrhizal fungi

Genetic and genomic glimpses of the elusive arbuscular mycorrhizal fungi | Mycorrhizal fungal genomes | Scoop.it

Arbuscular mycorrhizal fungi (AMF), which form an ancient and widespread mutualistic symbiosis with plants, are a crucial but still enigmatic component of the plant microbiome. Nowadays, their obligate biotrophy is no longer an obstacle to deciphering the role played by AMF in this fascinating symbiosis. The first genome-wide transcriptomic analysis of an AMF showed a metabolic complexity with no sign of massive gene loss, and the presence of genes for meiotic recombination suggests that AMF are not simple clonal organisms, as originally thought. New findings on suppression of host defenses and nutrient exchange processes have shed light on the mechanisms that contribute to such an intimate and long-lasting integration between living plant and fungal cells.

 

Luisa Lanfranco, J Peter W Young

Current Opinion in Plant Biology

Volume 15, Issue 4, August 2012, Pages 454–461

 

http://dx.doi.org/10.1016/j.pbi.2012.04.003

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Laccaria bicolor v2.0 - Home

Laccaria bicolor v2.0 - Home | Mycorrhizal fungal genomes | Scoop.it

L. bicolor was the first ectomycorrhizal fungus to have its genome sequenced. 

The second version of the assembly is now available at the JGI portal.

 

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature. 2008 Mar 6;452(7183):88-92.

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Searching for clues of sexual reproduction in the genomes of arbuscular mycorrhizal fungi

Searching for clues of sexual reproduction in the genomes of arbuscular mycorrhizal fungi | Mycorrhizal fungal genomes | Scoop.it

Arbuscular mycorrhizal fungi (AMF) represent an ecologically relevant and evolutionarily intriguing group of land plant symbionts, which produce multinucleated spores and hyphae that are currently thought to have propagated clonally for over 500 million years. This long-term absence of sex in AMF is a puzzling evolutionary feature that has sparked scientific interest for some time, but a provoking explanation for their successful evolutionary history in the absence of an obvious sexual cycle is that these organisms may have cryptic sex, or a parasexual life cycle, allowing them to recombine alleles and compensate for deleterious mutations. Interestingly, the recent acquisition of large sequence data from many AMF species can finally allow this hypothesis to be tested more extensively. In this perspective, we highlight emerging evidence based on sequence data for the potential of AMF to have sexual reproduction, and propose a number of routes that could be taken to further explore the presence (or absence thereof) of sex in this poorly studied, yet highly relevant, fungal group.


Rohan Riley, Nicolas Corradi

Fungal Ecology

Volume 6, Issue 1, February 2013, Pages 44–49


http://dx.doi.org/10.1016/j.funeco.2012.01.010

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