Posts Tagged ‘transcriptome’

Unraveling the secrets of the mother of plant root endosymbioses

November 17th, 2011

Glomus intraradices, alias G. irregulare, is a widespread arbuscular mycorrhizal fungus (AMF) (Glomeromycota) found in different ecosystems throughout the world, including temperate and tropical locations. As a symbiont G. intraradices is highly effective in mobilizing, taking up and transferring mineral nutrients from soils to plants, and it readily colonizes many plant species including agriculturally important species such as wheat, alfalfa, rice, and key model plants such as Medicago truncatula, Lotus japonicum, and Populus trichocarpa. For these reasons G. intraradices is among the most studied AMF and is the prime ingredient in several commercially available inocula. G. intraradices can also be grown in vitro in dual culture with transformed carrot roots. G. intraradices is also the only species whose spores are available commercially in pure form in large quantities.

From an evolutionary standpoint, the AMF are unique obligate symbionts with coenocytic hyphae (lacking cellular structure) that transport organelles and nutrients over long distances. The concept of an individual does not apply, raising substantial questions about natural selection and population genetics of these highly unusual organisms.

To provide long-awaited insights into the molecular basis of symbiosis-associated traits, the Glomus Genome Consortium investigated the transcriptome from G. intraradices (strain DAOM 197198). From >437,000 ESTs, we generated a set of 25,906 nonredundant virtual transcripts (NRVTs) transcribed in germinated spores, extraradical mycelium and symbiotic roots using Sanger and 454 sequencing. These NRVTs were then used to construct an oligoarray for investigating gene expression.

Take-home points:

  • We identified transcripts coding for the meiotic recombination machinery, as well as meiosis-specific proteins, suggesting that the lack of a known sexual cycle in G. intraradices is not a result of major deletions of genes essential for sexual reproduction and meiosis.
  • Induced expression of genes encoding membrane transporters, such as ammonium and phosphate transporters, and small secreted proteins in intraradical mycelium, together with the lack of expression of hydrolytic enzymes acting on plant cell wall polysaccharides (e.g. cellulases, pectin lyases), are all features of G. intraradices that are shared with ectomycorrhizal symbionts and obligate biotrophic pathogens.

Our results illuminate the genetic basis of symbiosis-related traits of the most ancient lineage of plant biotrophs, hopefully advancing future research on these agriculturally and ecologically important symbionts.

Next challenge: Assembling the highly polymorphic genome sequence of G. intraradices.

Read more …

Parniske M (2008) Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nature Reviews Microbiology 6, 763-775.

Bonfante P, Genre A (2010) Mechanisms underlying beneficial plant-fungus interactions in mycorrhizal symbiosis. Nature Communications 1: 4

Photo: The most beautiful photo of G. intraradices arbuscules, branching profusingly in its host plant cell (Thanks to Yves Piché, Laval University).

Unearthing the truffle genome

February 5th, 2011

np‘The ‘black diamond’, the ‘mysterious product of the earth’, the ‘ultimate fungus’ and ‘la grande mystique’ are some of the common names describing the delectable Périgord black truffle (Tuber melanosporum Vitt.). The culture, harvesting and marketing of this highly prized ectomycorrhizal fungus is a world that retains some of the secrets and intrigue of the past. Truffle cultivation is notoriously difficult, in part because of its cryptic life cycle as an underground symbiont, in which the fungus trades nutrients with oak-tree roots. By the end of the 1960s, there had been some success in devising new methods for producing truffle-infected seedlings under controlled conditions in glasshouses by inoculating plants with truffle cultures and spores. After successful plantation in orchards, reliable information on truffle yields and production is very difficult to obtain as a result of under-reporting of harvests, under-the-table marketing practices and a lack of administration records. It appears, however, that the production of truffles, as with other mushrooms, is erratic from year to year (depending on the weather conditions) and tends to decline as a result of global climate change. Decreasing supply and rising market prices have provided a strong incentive for research on truffle cultivation.’ (from my edito)

The February issue of New Phytologist (189: 3) includes a Special Feature dedicated to the Perigord Truffle genome with 7 papers discussing the transcriptome, the repertoire of transcriptional factors, the carbohydrate metabolism, the aroma biosynthesis and the molecular ecology  of sex of this ultimate fungus. Another raft of companion papers have been published in Fungal, Genetics & Biology.

To date, genomes of two mutualistic fungal symbionts, the basidiomycete L. bicolor and the ascomycete Tuber melanosporum, have been sequenced.  Based on their symbiosis-induced gene networks, evolution of the ectomycorrhizal lifestyle appears to be quite divergent (Plett & Martin, 2011).  To better understand the differences between symbiotic lineages and types of symbiosis, our JGI project is aiming to sequence 25 mycorrhizal fungi from different orders.  As of today, genomic DNA from Amanita muscaria, Cenococcum geophilum, Hebeloma cylindrosporum, Laccaria amethystina, Oidiodendron maius, Piloderma croceum, Paxillus involutus, Pisolithus microcarpus and P. tinctorius is currently being sequenced using next generation sequencing platforms. Sequencing of Boletus edulis, Cantharellus cibarius, Coltricia cinnamomea, Cortinarius glaucopus, Gymnomyces xanthosporus, Lactarius quietus, Meliniomyces bicolor, Paxillus rubicundulus, Ramaria formosa, Rhizoscyphus ericeae, Scleroderma citrinum, Suillus luteus, Sebacina vermifera, Tomentella sublilacina, Tricholoma matsutake, Tulasnella calospora and Terfezia boudieri will follow in 2011.

Thelephoroid Fungi

September 5th, 2010

Thelephora terrestrisWe have just received 500,000 454 TTN ESTs of a series of ectomycorrhizal thelephoroid fungi: Thelephora terrestris, Tomentellopsis submollis and Tomentella stuposa. from the Genoscope. T. terrestris (Earthfan) is a very common ‘contaminant’ of seedlings grown in greenhouses and forest nurseries. The Thelephoraceae are one of the most abundant ectomycorrhizal basidiomycete group in boreal and temperate forests, but they often form fruiting bodies on dead woods. It remains to be determined whether their genome and transcriptome reflect this dual lifestyle.

Photo: Earthfan fruiting bodies © F Martin