Archive for July, 2011

The Earth’s vast Symbiosphere

July 26th, 2011

The 7th International Symbiosis Congress will be held in Kraków from July 22-28.

 

Photo: Kraków castle © F Martin

Génomique des Populations des Champignons Ectomycorhiziens

July 24th, 2011

Un sujet de thèse de doctorat est à pourvoir au sein de l’Equipe « Ecogénomique des Interactions » de l’UMR « Interactions Arbres-Microorganismes » de l’INRA de Nancy

Titre : Mise en évidence des déterminants de l’évolution de la symbiose ectomycorhizienne chez les champignons symbiotiques ectomycorhiziens par une approche de génomique des populations.

Résumé : Les champignons jouent un rôle fondamental dans les écosystèmes forestiers en agissant sur les cycles biogéochimiques, la croissance et la santé des plantes. Les champignons ectomycorhiziens établissent une interaction symbiotique mutualiste avec leurs arbres-hôtes. Notre laboratoire étudie les mécanismes moléculaires régissant le développment et le fonctionnement de cette symbiose, ainsi que la structure des génomes de plusieurs espèces modèles (Laccaria bicolor, Tuber melanosporum). Nous développons également des approches de génétique des populations afin d’identifier les moteurs de la structuration des populations de ces champignons symbiotiques. Grâce au développement rapide des nouvelles technologies de séquençage (NTS), nous pouvons désormais étudier les mécanismes moléculaires impliqués dans l’adaptation de ces champignons ectomycorhiziens aux changements environnementaux via l’analyse de leurs génomes. Les objectifs scientifiques sont une meilleure compréhension des mécanismes d’évolution des populations soumises aux changement globaux pour à terme développer des outils facilitant leur gestion.

La génomique populationnelle est une discipline prolongeant la génétique des populations – définie comme l’étude des changements des fréquences génétiques dans les populations et de leurs causes (sélection, migration, hasard). La génomique des populations s’emploie ainsi à quantifier, à l’échelle de génomes entiers, l’importance de la sélection, de la recombinaison et des facteurs démographiques – la migration par exemple – dans les différences observées entre populations d’une même espèce. En scrutant les génomes complets de nombreux individus d’une même population ou de populations distinctes et en s’appuyant sur les NTS, il est désormais possible d’identifier des portions de génome fortement différenciées et possiblement impliquées dans des adaptations particulières aux changements environnementaux, biotiques et abiotiques.

Dans le cadre de ce projet, le doctorant étudiera les rôles respectifs de l’histoire démographique et des événements de sélection dans la distribution actuelle des variations quantitatives observées dans la capacité symbiotique. Dans ce contexte, à l’aide de marqueurs neutres nucléaires (SNP, microsatellites), ce projet établira la distribution géographique de la diversité génétique neutre dans les populations de Truffe noire du Périgord (T. melanosporum) et du Laccaire (L. bicolor). Il visera à une meilleure compréhension de la phylogéographie de ces espèces et des flux de gènes récents entre populations. Une approche de génomique des populations permettra ensuite d’identifier les régions génomiques soumises à sélection et potentiellement impliquées dans l’adaptation de ces espèces à leur environnement et à leur mode de vie symbiotique.

Formation et compétences requises :

– Une formation en génétique des populations ou en génétique évolutive avec des compétences en génomique et bioinformatique est recommandée. Le candidat sera amené à utiliser des méthodes statistiques et informatiques pour évaluer l’influence de la sélection naturelle, des migrations et de la structure spatiale sur la diversité génétique des populations naturelles de ces symbiontes.

– De bonnes connaissances des environnements UNIX, la maîtrise d’un langage de programmation (perl ou python) et une première expérience de traitement des données de séquençage à haut débit (ex. Illumina) seraient appréciées.

Contacts :

Francis Martin, fmartin[at]nancy.inra.fr

Claude Murat, claude.murat[at]nancy.inra.fr

 

Evolution of Obligate Biotrophy

July 22nd, 2011

Eukaryotic microbes are colonizing a wide range of environments, including living plants and animals. Parasites, endophytes and symbionts have evolved complex mechanisms to interact with their host. Plant pathologists have attempted to classify pathogens into groups called necrotrophs, biotrophs and, more recently, hemibiotrophs. Biotrophs derive energy from living cells. Necrotrophs derive energy from killed cells. Hemibiotrophs have an initial period of biotrophy followed by a necrotrophic phase. But this division into groups based on nutritional mode is poorly supported by recent genomics studies (see Oliver & Ipcho, 2004).

Evolution to obligate biotrophy occurred independently in fungal and in oomycetous pathogens (rusts, downy and powdery mildews) and molecular features driving this adaptation have been studied in a series of recent papers (e.g., Baxter et al., 2010Spanu et al., 2010; Duplessis et al., 2011).

In their recent PLoS Biology paper, Kemen et al. elegantly investigated the mechanisms leading to obligate biotrophy in the white rust pathogen Albugo laibachii (Oomycota). Their comparison of the Albugo genome to Hyaloperonospora arabidopsidis genome (Baxter et al., 2010) sheds light on the evolution of biotrophy in Oomycetes and they nicely summarized the current knowledge of gain and loss of genes and pathways in the figure below.

Figure. Gain and loss of genes and pathways for selected Chromalveolata in comparison to A. laibachii. © PLoS Biology.

Kemen et al. (2011) Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis thaliana. PLoS 9,  e1001094.

 

CDD Bioinfo

July 19th, 2011

Recherche … Ingénieur d’étude en Bioinformatique

Contrat: CDD 16 mois à partir du 1er septembre 2011

Localisation: INRA Unité Interactions Arbre-Microorganismes – Centre INRA de Nancy – Champenoux

Mots-clefs : Nouvelles technologies de séquençage, analyse de séquences, génomique comparative

Contexte : L’unité « Interactions Arbres-Microorganismes » (UMR1136) vient de se doter d’un séquenceur 454 GS Junior (http://www.gsjunior.com/). Ce séquenceur sera utilisé dans le cadre des projets 1) de génomique comparative chez les champignons forestiers et 2) de métagénomique et métataxonomie comparée des sols forestiers et agricoles. Pour plus d’informations voir le site web de l’unité : http://mycor.nancy.inra.fr.

Mission : Au sein du laboratoire, le candidat participera à la mise en place des outils liés à la gestion et à l’analyse des données générées par le séquenceur GS junior mais aussi par d’autres méthodes de séquençage (GS Titanium et Illumina/solexa). Les principales missions seront :

  • traitement des données brutes et évaluation de leur qualité
  • analyse des données : recherche de SNP, denoising, clustering …
  • outils de visualisation
  • intégration de ces différents outils pour la création de pipelines d’analyses

Profil recherché :

  • Master 2 en bioinformatique
  • Maîtriser le langage perl, le développement orienté objet, les bases de données (MySQL, PostgreSQL)
  • Bonnes connaissances des environnements UNIX
  • Maîtriser l’anglais technique
  • Bon sens relationnel, esprit d’équipe et autonomie.

Poste : Contrat à durée déterminée de 16 mois. Le poste est localisé à l’INRA de Champenoux.

Dossier : CV détaillé, Lettre de motivation

Contacts : Francis Martin, fmartin[at]nancy.inra.fr, 0383394080

Emmanuelle Morin, emmanuelle.morin[at]nancy.inra.fr, 0383394133

 

Date Palm Genome

July 17th, 2011

The Date palm, Phoenix dactylifera L., is a tree of the palm family (Arecaceae, or Palmae), native to desert regions of the Persian Gulf. Mentioned in the Qur’an and Bible, its fruits have been a staple food in the Middle East since the neolithic. Today, dates are amongst the most important crop of many countries in the Arabian Gulf and North Africa.

A draft version of the genome of the Khalas variety has been published by a team of the Weill Cornell Medical College in Qatar in the June 2011 issue of Nature Biotechnology.

The Khalas genome has been sequenced using the Illumina GA IIx and the WGS assembly only covered 380 Mbp of the total ~658 Mbp genome size. As expected, large repeated regions were not included in the assembly, but most of the gene space has been assembled. Although a detailed analysis of the metabolic and developmental pathways is missing from this paper, the draft genome has been used to generate very useful genetic tools. The genome sequences of eight additional cultivars were used for an in-depth SNP/CNV analysis. A set of 32 SNPs has been identified for discriminating varieties, a long awaited tool for breeders. A region linked to gender determination was also characterized.

This genome and genetic resources should be very useful for improving traits such a fruit quality.

Image: Palmier dattier by Martiros Sarian (1880-1972).

28th NPS

July 15th, 2011

La Mérule démasquée

July 15th, 2011

Après le Concombre Masquée, voici la Mérule Démasquée … notre Mission COM à de l’imagination.

JGI Summer 2011 Primer

July 15th, 2011

The summer edition of the U.S Department of Energy (DOE) Joint Genome Institute (JGI) newsletter The Primer is now available for download: http://1.usa.gov/orAs40

…featuring articles and images:

  • Report from the 2011 Sequencing, Finishing and Analysis in the Future (SFAF) Meeting held in Santa Fe, NM, June 1–3, 2011
  • DOE Funds Restored Wetlands Study
  • Countering Rust Fungal Outbreaks
  • Detailing Lignin’s Development
  • Notable Publications & more…

 

Breaking down cellulose without blasting lignin

July 14th, 2011

JGI Press release

Read more …

The Dry Rot Genome & Wood Decay Machinery in Forest Fungi

July 14th, 2011

The other good news of this Bastille Day: our paper on the Serpula lacrymans genome is reported online July 14 in Science Express.

The Domestic Dry Rot (Serpula lacrymans, Basidiomycete, Coniophoraceae) comprises two subgroups, S. lacrymans var shastensis, found in montane conifer forests in the Himalayan foothills, and S. lacrymans var lacrymans, cause of building dry rot, which diverged in historic time [Kauserud et al. (2007) Mol. Ecol. 16: 3350-3360]. This brown rot fungus is the most damaging destroyer of wood construction materials in temperate regions. It has a powerful capacity for cellulolysis and mycelial colonization of coarse solid materials. It has been suggested that Northern Europe buildings offer a substitute environment for the forest floor in the Himalayan foothills where wild isolates of S. lacrymans have been spotted.

As most brown rot fungi, S. lacrymans selectively depolymerises the lignin component of wood lignocellulose to assess and degrade cellulose. Brown rot wood decay involves an initial non-enzymic attack on the wood cell wall  generating hydroxyl radicals (∙OH) extracellularly via  the Fenton reaction. Residues from fungal brown rot of wood compose most of the carbon sequestered in boreal forest soil.

Serpula’ capacity to break down the cellulose in wood led to its selection for sequencing by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) in the Community Sequencing Program 2007, with the goal of identifying the enzymes involved in the wood decay process and using the information to improve cellulosic biofuels production. Within the framework of the MycoCosm project, we have also compared the genome of S. lacrymans to the available genomes of white-rotters and the ectomycorrhizal symbiont Laccaria bicolor to study the evolution of ecological lifestyles in forest fungi and how the plant cell wall decomposing machinery of fungi underlies their functional diversity in forests. This study is published online July 14 in Science Express by Dan Eastwood and the Serpula Genome Consortium.

The genome of S. lacrymans S7.9 was 42.8 Mbp, containing 12,917 gene predictions. Comparative and functional genomics of S. lacrymans showed that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, such as the enzymes degrading plant cell wall polysaccharides. Brown rot and ectomycorrhizal fungi have the fewest hydrolytic CAZy genes. Brown rot fungi have fewest oxidoreductases, due, not to gene losses, but to gene duplications in white rot species. This finding suggests that Serpula had cast off the energetically expensive apparatus of ligninolysis and acquired alternative mechanisms of initial attack of lignocellulose. It appears that S. lacrymans synthesized high level of variegatic acid, an iron-reducing phenolate, to enhance the Fenton’s reaction in contact with wood.

We are also suggesting that the loss of aggressive ligninolysis might have permitted brown rot transitions to biotrophic ectomycorrhiza in Boletales. Analysis of the ‘soon-to-be released’ genomes from the ECM Boletales, Paxillus involutus and Pisolithus microcarpus, will facilitate the study of this lifestyle transition which tremendously impacted the fungi’s role in the global carbon cycle.

The non-aggressive lineage, S. lacrymans var. shastensis, residing naturally in North America and Asia, has also been sequenced at JGI. This should help in understanding the evolution from  the non-aggressive to aggressive  Serpula strains.

Eastwood et al. (2011) The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi. Science DOI: 10.1126/science.1205411.

Biofuels study gives clue to forest ecosystems. University of Oxford News & Stories.

Understanding Dry Rot Fungus to Make Fuel. New Energy & Fuel.

Breaking down cellulose without blasting lignin: “Dry rot” genome offers lessons for biofuel pretreatment. The JGI News.

 

Photo: Serpula lacrymans resupinate fruiting body © G Elsner

 

First Mutualist Effector, the Laccaria MiSSP7

July 14th, 2011

Great day!!! Our paper on the first secreted effector from a symbiotic ectomycorrhizal fungus, Laccaria bicolor is available online at Current Biology New Articles.

As you know, tree roots form a nutrient-acquiring, ectomycorrhizal mutualistic symbiosis with soilborne fungi.  Symbiosis development requires a cross-talk involving signals and unknown proteins.  In this paper, we present MiSSP7, a symbiosis-upregulated gene from the ectomycorrhizal fungus L. bicolor that is indispensable for development of symbiosis.  MiSSP7 is secreted by the fungus, imported into the plant cell via endocytosis due to an RXLR-like motif that binds plant PI-3-P, targeted to plant nuclei of compatible host root cells where it alters the transcriptomic fate of the plant cell.  L. bicolor transformants with severely reduced expression of MiSSP7 do not enter into symbioses with poplar roots.  We conclude that MiSSP7 is a genuine symbiotic effector protein and this provides unparalleled opportunities to determine how ectomycorrhizal fungi manipulate their hosts to establish symbioses.

Coincidentally, Natalia Requena and her colleagues from the Karlsruhe Institute of Technology (KIT) also publish in Current Biology New Articles the first report of an arbuscular mycorrhizal fungal effector, SP7. The symbiont Glomus intraradices also secretes a protein that interacts with the pathogenesis-related transcription factor ERF19 in the plant nucleus, contributing to develop the biotrophic status of arbuscular mycorrhizal fungi in roots by counteracting the plant immune program.

These very cool findings call into question the very nature of the mycorrhizal mutualistic relationships; perhaps it is very similar to some pathogenic interactions. They use effectors to live in ‘‘pretend harmony’’ with their host.

Our work on MiSSP7 benefited tremendously from a very efficient collaboration with Brett Tyler and Shiv Kale at Virginia Tech and Ale Pardo and Minna Kemppainen at Quilmes University in Argentina.

Kloppholz S, Kuhn H, Requena N (2011) A Secreted Fungal Effector of Glomus intraradices Promotes Symbiotic Biotrophy. Current Biology, 10.1016/j.cub.2011.06.044.
Plett JM, Kemppainen M, Kale SD, Kohler A, Legué V, Brun A, Tyler BM, Pardo AG, Martin F (2011) A Secreted Effector Protein of Laccaria bicolor Is Required for Symbiosis Development. Current Biology, 10.1016/j.cub.2011.05.033.

Photo: MiSSP7 immunolocalisation in poplar ectomycorrhiza. © JM Plett – INRA.

 

 

Hiking in the Ecrins Range

July 14th, 2011

Glacier Blanc is Barre des Ecrins north side glacier. This is the biggest glacier in Ecrins range.

This image was shot along the scenic path (2700m) leading to the Ecrins hut, above the Glacier Blanc. We were thrilled when we happened upon this wonderful scene near the Pointe du Serre Soubeyran, after hours of hiking. Here, I found my first opportunity to shoot mountain landscapes with the new Singh-Ray LB ColorCombo filter (LB Warming Polarizer and LB Color Intensifier) on my Canon EOS 550D.

The Ecrins-Oisans is a very preserved mountain ranges of Southeastern France in the famous ‘Les Ecrins’ National Park. An integral tour of the Ecrins-Oisans Mountains between wild valleys, traditional hamlets and imposing panoramas is a must-go.

454 vs. Illumina for microbiota amplicon profiling

July 14th, 2011

To survey the soil bacterial and fungal communities in forest ecosystems, we have extensively used 454 Titanium pyrosequencing (Buée et al., 2009, Uroz et al., 2010), but we are currently comparing this approach to the paired-end Illumina read sequencing of the rRNA internal transcribed spacer (ITS). We are expecting the first datasets in a few weeks. The later approach sounds very promising, but in their recent analysis of the intestinal microbiota Claesson et al. (2010) showed that this approach has still important limitations. A very large proportion of the Illumina 16 rRNA reads could not be classified down to genus level as a result of their shorter length and higher error rates beyond 60 nt. Let’s see what we get with the ITS. See abstract below.

[Abstract. High-throughput molecular technologies can profile microbial communities at high resolution even in complex environments like the intestinal microbiota. Recent improvements in next-generation sequencing technologies allow for even finer resolution. We compared phylogenetic profiling of both longer (454 Titanium) sequence reads with shorter, but more numerous, paired-end reads (Illumina). For both approaches, we targeted six tandem combinations of 16S rRNA gene variable regions, in microbial DNA extracted from a human faecal sample, in order to investigate their limitations and potentials. In silico evaluations predicted that the V3/V4 and V4/V5 regions would provide the highest classification accuracies for both technologies. However, experimental sequencing of the V3/V4 region revealed significant amplification bias compared to the other regions, emphasising the necessity for experimental validation of primer pairs. The latest developments of 454 and Illumina technologies offered higher resolution compared to their previous versions, and showed relative consistency with each other. However, the majority of the Illumina reads could not be classified down to genus level due to their shorter length and higher error rates beyond 60 nt. Nonetheless, with improved quality and longer reads, the far greater coverage of Illumina promises unparalleled insights into highly diverse and complex environments such as the human gut].

Claesson et al. (2010) Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res. 38:e200. Epub 2010 Sep 29.

Buée et al. (2009) 454 pyrosequencing analysis of soil fungal diversity as affected by forest management. New Phytologist 184: 452–459.

Uroz et al. (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environmental Microbiology Reports 2: 281–288.

The Potato Genome … j’aime les patates !!!

July 12th, 2011

There are several genomes of plants or fungi published every week, but the paper describing the Potato (Solanum tuberosum) genome and its analysis in this week issue of Nature is worth a post.

Getting a draft of the potato genome was indeed a real challenge as S. tuberosum is a heterozygous autotetraploid with four highly variable copies of each chromosome. This is also the first sequenced genome of an asterid, a major clade within eudicots … and most importantly, that’s the needed ingredient for making my favorite crispy French fries!!!

The Potato Genome Sequencing Consortium (PGSC) was initiated in early 2006 by the Plant Breeding Department of Wageningen University & Research in the Netherlands and has developed into a global consortium of 26 research groups, including the BGI.

The potato genome has 12 chromosomes and is estimated to be 840 million base pairs. To facilitate its WGS sequencing, the PGSC sequenced the doubled monoploid DM1-3 516R44 (DM) potato derived from a diploid landrace of potato in order to simplify and complement the sequencing of the diploid line RH89-039-16 (RH).

The 96.6 Gb of raw sequence was generated using the Illumina Genome Analyser and 454 pyrosequencer platforms, as well as conventional Sanger sequencing technologies. The genome was then assembled using SOAPdenovo4, resulting in a final assembly of 727 Mb.

The draft assembly contains ~62% repeated elements with long terminal repeat retrotransposons (LTRs) comprising the majority of the transposable element classes, representing 29.4% of the genome. The consortium also generated 31.5 Gb of RNA-Seq data from 32 DM and 16 RH libraries representing all major tissue types, developmental stages and responses to abiotic and biotic stresses. Reads were mapped against the DM genome sequence and in combination with ab initio gene prediction, protein and EST alignments, 39,031 protein-coding genes were predicted, including 2,642 asterid-specific and 3,372 potato-lineage-specific genes. Genes encoding transcription factors, self-incompatibility, and defence-related proteins were prominent in the asterid-specific genes and likely contribute to the unique characteristics of asterids.

Potato is susceptible to a wide range of pests and pathogens (e.g. Phytophthora infestans, the culprit of the Irish Potato Famine) and the identification of R genes conferring disease resistance is a main focus of plant pathologists. The DM assembly contains 408 NBS-LRR-encoding genes, 57 Toll/interleukin-1 receptor/plant R gene homology (TIR) domains and 351 non-TIR type. A high rate of pseudogenization has been observed in this R genes. More than one third of these NBS-LRR genes are pseudogenes owing to indels, frameshift mutations, or premature stop codons. It is tempting to speculate that this rapid pseudogenization parallels the rapid evolution of effector-coding genes observed in Phytophthora infestans.

Transcript profiling was used to study the molecular mechanisms controlling the stolon-to-tuber transition. This developmental event coincides with strong upregulation of genes associated with protein storage (patatin), starch biosynthesis, and defense against pests and pathogens (Kunitz protease inhibitor genes).

This draft genome will undoubtly provide a unique resource for genetic improvement of the most important vegetable crop. It will also facilitate the genomic analysis of other tasty members of the Solanaceae family, tomato, pepper, and eggplant.

 

Nature News: All eyes on the potato genome.

Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature doi:10.1038/nature10158