Population genomics of symbiosis
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Rescooped by Silke Werth from Plant immunity and legume symbiosis
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Opening the black box: outcomes of interactions between arbuscular mycorrhizal (AM) and non-host genotypes of Medicago depend on fungal identity, interplay between P uptake pathways and external P ...

We investigated the physiology that underlies the influence of arbuscular mycorrhizal (AM) colonization on outcomes of interactions between plants. We grew Medicago truncatula A17 and its AM-defective mutant dmi1 in intragenotypic (two plants per pot of the same genotype, x2) or intergenotypic (one plant of each genotype, 1+1) combinations, inoculated or not with Rhizophagus irregularis (formerly Glomus intraradices) or Gigaspora margarita. We measured plant growth, colonization, contributions of AM and direct P uptake pathways using 32P, and expression of plant Pi transporter genes at two levels of P supply. A17 (x2) responded positively to inoculation only at Low P. The response was enhanced with 1+1 even at High P where colonization in A17 was reduced. With R. irregularis P uptake by the AM pathway was unaffected by P supply, whereas with G. margarita the AM pathway was lower at High P, and direct uptake higher. Gene expression varied and was unrelated to P uptake through the two pathways. There was no evidence of plant control of P uptake via R. irregularis at High P but there was via G. margarita. Importantly, growth responses of plant genotypes grown alone did not predict outcomes of intergenotypic interactions.


Via Christophe Jacquet
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Scooped by Silke Werth
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BMC Genomics: Characterization of a transcriptome from a non-model organism, Cladonia rangiferina, the grey reindeer lichen, using high-throughput next generation sequencing and EST se...

BMC Genomics: Characterization of a transcriptome from a non-model organism, Cladonia rangiferina, the grey reindeer lichen, using high-throughput next generation sequencing and EST se... | Population genomics of symbiosis | Scoop.it

Lichens are symbiotic organisms that have a remarkable ability to survive in some of the most extreme terrestrial climates on earth. Lichens can endure frequent desiccation and wetting cycles and are able to survive in a dehydrated molecular dormant state for decades at a time. Genetic resources have been established in lichen species for the study of molecular systematics and their taxonomic classification. No lichen species have been characterised yet using genomics and the molecular mechanisms underlying the lichen symbiosis and the fundamentals of desiccation tolerance remain undescribed. We report the characterisation of a transcriptome of the grey reindeer lichen, Cladonia rangiferina, using high-throughput next-generation transcriptome sequencing and traditional Sanger EST sequencing data.

 

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Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen

Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen | Population genomics of symbiosis | Scoop.it

In western North America, the current outbreak of the mountain pine beetle (MPB) and its microbial associates has destroyed wide areas of lodgepole pine forest, including more than 16 million hectares in British Columbia. Grosmannia clavigera (Gc), a critical component of the outbreak, is a symbiont of the MPB and a pathogen of pine trees. To better understand the interactions between Gc, MPB, and lodgepole pine hosts, we sequenced the ∼30-Mb Gc genome and assembled it into 18 supercontigs. We predict 8,314 protein-coding genes, and support the gene models with proteome, expressed sequence tag, and RNA-seq data. This work is a major step toward understanding the biological interactions between the tripartite MPB/fungus/forest system.

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Analysis of an EST library from the dinoflagellate (Symbiodinium sp.) symbiont of reef-building corals

Analysis of an EST library from the dinoflagellate (Symbiodinium sp.) symbiont of reef-building corals | Population genomics of symbiosis | Scoop.it

Dinoflagellates (Symbiodinium sp. Freud.) are an obligatory endosymbiont of the reef-building corals. Recent changes to the environment surrounding coral reefs (e.g., global warming) have demonstrated that this endosymbiotic relationship between corals and Symbiodinium is particularly sensitive to environmental changes. Therefore, understanding gene expression patterns of Symbiodinium is critical to understanding why coral reefs are susceptible to global climate change. This study identified 1456 unique expression sequence tags (ESTs) generated for Symbiodinium (clade C3) from the staghorn coral Acropora aspera following exposure to a variety of stresses. Of these, only 10% matched previously reported dinoflagellate ESTs, suggesting that the conditions used in the construction of the library resulted in a novel transcriptome. The function of 561 (44%) of these ESTs could be identified. The majority of these genes coded for proteins involved in posttranslational modification, protein turnover, and chaperones (12.3%); energy production and conversion (12%); or an unknown function (18.6%).

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Genome Biology: Transcriptome analysis of Sinorhizobium meliloti during symbiosis

Genome Biology: Transcriptome analysis of Sinorhizobium meliloti during symbiosis | Population genomics of symbiosis | Scoop.it

Rhizobia induce the formation on specific legumes of new organs, the root nodules, as a result of an elaborated developmental program involving the two partners. In order to contribute to a more global view of the genetics underlying this plant-microbe symbiosis, we have mined the recently determined Sinorhizobium meliloti genome sequence for genes potentially relevant to symbiosis. We describe here the construction and use of dedicated nylon macroarrays to study simultaneously the expression of 200 of these genes in a variety of environmental conditions, pertinent to symbiosis.

In addition to exploring conditions for a genome-wide transcriptome analysis of the model rhizobium S. meliloti, the present work has highlighted the differential expression of several classes of genes during symbiosis. These genes are related to invasion, oxidative stress protection, iron mobilization, and signaling, thus emphasizing possible common mechanisms between symbiosis and pathogenesis.

 

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Rescooped by Silke Werth from MycorWeb Plant-Microbe Interactions
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The Ecological Genomics of Fungi - Wiley Online Library

The Ecological Genomics of Fungi - Wiley Online Library | Population genomics of symbiosis | Scoop.it

This unique book covers a broad diversity of fungal systems and provides unique insight into the functions of those fungi in various ecosystems - from soil, to plant, to human. Bringing together fungal genomic information on a variety of lifestyles and traits, the book covers saprotrophism, pathogenesis (including biotrophs, hemibiotrophs, necrotrophs) and symbiosis. Advances in high-throughput sequencing now offer unprecedented opportunities for identification of novel key molecular mechanisms controlling plant-microbe interactions, evolution of fungi and developmentally- and ecologically-relevant traits,  this book explores how these massive streams of fungal sequences can be exploited to gain a deeper understanding of the evolution of fungi and their ecological role.

 

 


Via Francis Martin
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Francis Martin's curator insight, October 3, 2013 3:07 AM

This was cool editing this book. Thanks to the authors. They did a great job in bridging genomics and ecology. I hope you will enjoy reading these chapters as I did

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PLOS ONE: Heart of Endosymbioses: Transcriptomics Reveals a Conserved Genetic Program among Arbuscular Mycorrhizal, Actinorhizal and Legume-Rhizobial Symbioses

PLOS ONE: Heart of Endosymbioses: Transcriptomics Reveals a Conserved Genetic Program among Arbuscular Mycorrhizal, Actinorhizal and Legume-Rhizobial Symbioses | Population genomics of symbiosis | Scoop.it

To improve their nutrition, most plants associate with soil microorganisms, particularly fungi, to form mycorrhizae. A few lineages, including actinorhizal plants and legumes are also able to interact with nitrogen-fixing bacteria hosted intracellularly inside root nodules. 

We used a comparative transcriptomics approach to identify genes involved in establishing these 3 endosymbioses and their functioning.  A comparison with genes induced in AM in Medicago truncatula and Oryza sativa revealed a common set of genes induced in AM. A comparison with genes induced in nitrogen-fixing nodules of C. glauca and M. truncatula also made it possible to define a common set of genes induced in these three endosymbioses. The existence of this core set of genes is in accordance with the proposed recycling of ancient AM genes for new functions related to nodulation in legumes and actinorhizal plants.

 

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