Posts Tagged ‘genome’

Alisha owenby lands an NSF DDIG

May 23rd, 2013

From Joey Spatafora Lab blog

[Alisha Owensby, PhD candidate in the lab, was recently awarded an NSF Doctoral Dissertation Improvement Grant (DDIG) for her proposal, “Evolutionary Genomics of Inter-Kingdom Host-Jumping in the Fungal Genus Elaphocordyceps“.  Way to go!  If you follow our blog, you know that Alisha is currently in Nancy, France working in the laboratory of Francis Martin at INRA.  She is working on the genome of Elaphomyces, one of the hosts of Elaphocordyceps.  This is a particularly challenging project as Elaphomyces does not culture and thus the genomic libraries are prepared from DNA and RNA extracted directly from sporocarps and are metagenomic in nature.  The photo is of Alisha working in Francis’ lab doing an RNA extraction.  Just a few more weeks and she’ll be back.  Bring wine and cheese!!]

Photo: Alisha and Nicolas extracting Elaphomyces RNA for RNA-Seq

Genome of the Honey Mushroom Unearthed

May 23rd, 2013

Collins C, Keane TM, Turner DJ, O’Keeffe G, Fitzpatrick DA, Doyle S (2013) Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Towards a New Infection Model System. J Proteome Research, DOI: 10.1021/pr301131t

Abstract

Armillaria mellea is a major plant pathogen. Yet, no large-scale ‘-omic’ data are available to enable new studies, and limited experimental models are available to investigate basidiomycete pathogenicity. Here we reveal that the A. mellea genome comprises 58.35 Mb, contains 14,473 gene models, of average length 1575 bp (4.72 introns/gene). Tandem mass spectrometry identified 921 mycelial (n = 629 unique) and secreted (n = 183 unique) proteins. Almost 100 mycelial proteins were either species-specific or previously unidentified at the protein level. A number of proteins (n = 111) were detected in both mycelia and culture supernatant extracts. Signal sequence occurrence was fourfold greater for secreted (50.2%) compared to mycelial (12%) proteins. Analyses revealed a rich reservoir of carbohydrate degrading enzymes, laccases and lignin peroxidases in the A. mellea proteome, reminiscent of both basidiomycete and ascomycete glycodegradative arsenals. We discovered that A. mellea exhibits a specific killing effect against Candida albicans, during co-culture. Proteomic investigation of this interaction revealed the unique expression of defensive and potentially offensive A. mellea proteins (n = 30). Overall, our data reveal new insights into the origin of basidiomycete virulence and we present a new model system for further studies aimed at deciphering fungal pathogenic mechanisms.]

Photo: Fruiting body of Armillaria mellea © F Martin

Exploring the Mycorrhizal Genomes

September 9th, 2012

 

I hope you are wrapping up a good summer. I’m touching base to update you on our Mycorrhizal Genomics Initiative (MGI).

The list of taxa of mycorrhizal fungi for the first series of analyses aiming to identify symbiotic traits has now been “frozen”. Thanks to Igor Grigoriev’s JGI team, this list includes an outstanding series of annotated genomes and transcriptomes from ectomycorrhizal, ericoid and orchid symbionts:

  • Amanita muscaria Koide
  • Hebeloma cylindrosporum h7  (v2.0),
  • Laccaria bicolor (v2.0),
  • Oidiodendron maius Zn,
  • Paxillus involutus,
  • Paxillus rubicundulus,
  • Piloderma croceum F 1598,
  • Pisolithus microcarpus 441,
  • Pisolithus tinctorius 270,
  • Scleroderma citrinum FougA,
  • Sebacina vermifera MAFF 305830,
  • Suillus luteus UH-Slu-Lm8-n1,
  • Tulasnella calospora AL13/4D,

In addition, the following available transcriptomes will also be mined for symbiotic-related features:

  • Cenococcum geophilum
  • Cortinarius glaucopus,
  • Laccaria amethystina 08-1,
  • Lactarius quietus,
  • Meliniomyces bicolor,
  • Meliniomyces variabilis, and
  • Tricholoma matsutake 945.

Finally, we will add the unpublished genomes of five saprotrophic agaricomycotina (including leaf-litter species) that we will use for identifying potential common genomic features in litter-borne and mycorrhizal fungi:

  • Jaapia argillacea MUCL-33604,
  • Hydnomerulium pinastri MD-312,
  • Plicaturopsis crispa FD-325 SS-3,
  • Hypholoma sublateritium FD-334 SS-4, and
  • Gymnopus luxurians FD-317 M1

JGI has (or will soon) publicly released the web portals with the annotation for the above-mentioned fungal species. Visit the JGI Mycocosm database. In addition, we have released web sites for the corresponding transcriptome annotation at the Mycorhiza Genomics Initiative portal [restricted].

To make good use of this tremendous genomic resource, we are organizing the 2nd MGI Workshop at the INRA-Nancy center in Champenoux (France), on November 13-14, 2012. The aim of the workshop is to bring together the consortium teams for discussing our findings. The format of the workshop will be roughly equally split between informal presentations summarizing the current findings and brainstorming about how to take advantage of the genome sequences to inform our understanding of symbiosis and fungal biology.

On the following days, we will organize a New Phytologist Workshop entitled ‘ Bridging Mycorrhizal Genomics, Metagenomics & Forest Ecology‘. The workshop will also take place at INRA-Nancy over two days (Thursday 15 & Friday 16 November). The aim is to bring together a small group of MGI PI’s, fungal biologists and ecologists (20-25 attendees) to explore the future use of mycorrhizal genomes in order to both maximize the efficacy with which the community utilizes these technological breakthroughs in biology, ecology, phylogenetics, and forestry.

Photo: Larch Bolete (Suillus grevellei) (Boletales), a close relative of the sequenced slippery Jack (Suillus luteus) (© F Martin).

Genome sequence of the insect pathogenic fungus Cordyceps militaris

March 4th, 2012


Species in the ascomycete fungal genus Cordyceps have been proposed to be the teleomorphs of Metarhizium species. The latter have been widely used as insect biocontrol agents. Cordyceps species are highly prized for use in traditional Chinese medicines, but the genes responsible for biosynthesis of bioactive components, insect pathogenicity and the control of sexuality and fruiting have not been determined.

Chengshu Wang’s group from the Shanghai Institutes for Biological Sciences report the genome sequence of the type species Cordyceps militaries in the last issue of Genome Biology. Phylogenomic analysis suggests that different species in the Cordyceps/Metarhizium genera have evolved into insect pathogens independently of each other, and that their similar large secretomes and gene family expansions are due to convergent evolution. However, relative to other fungi, including Metarhizium spp., many protein families are reduced in C. militaris, which suggests a more restricted ecology. Consistent with its long track record of safe usage as a medicine, the Cordyceps genome does not contain genes for known human mycotoxins. This study shows that C. militaris is sexually heterothallic but, very unusually, fruiting can occur without an opposite mating-type partner. Transcriptional profiling indicates that fruiting involves induction of the Zn2Cys6-type transcription factors and MAPK pathway; unlike other fungi, however, the PKA pathway is not activated.

The data offer a better understanding of Cordyceps biology and will facilitate the exploitation of medicinal compounds produced by the fungus.

Zheng et al. (2011) Genome Biology 12: R116

Photo: Chinese Tussah silkmoth pupae colonized by C. militaris (© Zheng et al.)

La Mérule démasquée

July 15th, 2011

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

FungiDB

March 20th, 2011

At the Fungal Genome Tools workshop (26th FGC), Jason Stajich announced the release of FungiDB 1.0 beta. This pre-release version of FungiDB is available for early community review. Please explore the site and contact Jason with your feedback.

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.

Blurred Boundaries

December 4th, 2010

PoplarLaccariaECMOur review paper on the genomes of ectomycorrhizal fungi is available online at the Trends in Genetics site.

Plett JM & Martin F. 2010. Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes. Trends in Genetics. doi:10.1016/j.tig.2010.10.005

Abstract. “Soils contain a multitude of fungi with vastly divergent lifestyles ranging from saprotrophic to mutualistic and pathogenic. The recent release of many fungal genomes has led to comparative studies that consider the extent to which these lifestyles are encoded in the genome. The genomes of the symbiotic fungi Laccaria bicolor and Tuber melanosporum are proving especially useful in characterizing the genetic foundation of mutualistic symbiosis. New insights gleaned from these genomes, as compared to their saprotrophic and pathogenic cousins, have helped to redefine and shape our understanding of the nature of the symbiotic lifestyle. Here we detail the current state of research into this complex relationship and discuss avenues for future exploration.”

Photo: section of Populus/Laccaria ectomycorrhizal root – JM Plett © INRA.

Histoire de Fourmis … suite: Ant Genomes

August 29th, 2010

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Symbioses between plants and fungi, fungi and ants, and ants and plants all play important roles in ecosystems. For those interested by ant ecology and biology, and their interaction with plants, I would recommend reading the paper from Defossez et al. on Ant‐plants and fungi: a new threeway symbiosis‘ published on March 11, 2009 in the New Phytologist. For further ant reading go to the comparative genomics paper published by Bonasio et al. in the 27 August 2010 issue of Science. A collaborative research consortium involving scientists from the US and China report that they have sequenced the genomes of two ant species: Harpegnathos saltator, known as Jerdon’s jumping ant, and the Florida carpenter ant, Camponotus floridanus.

By comparing the genome structure and gene repertoire of the two ant species, and analyzing their transcriptome profiling in different castes, the team obtained clues about gene regulation and epigenetic processes underlying diverse physical and behavioral features in these ant species. They identified up-regulation of telomerase and sirtuin deacetylases in longer-lived H. saltator reproductives, caste-specific expression of microRNAs and SMYD histone methyltransferases, and differential regulation of genes implicated in neuronal function and chemical communication. Their findings provide clues on the molecular differences between castes in ants paving the way for further investigations on everything from brain function and behavior to aging.

Photo: Florida Carpenter Ant (by Alex Wild)

The genome of asongrid

April 18th, 2010

Zebra_finchThe zebra finch (Taeniopygia guttata) is a songbird belonging to the large avian order Passeriformes. As the lovely bird lives in trees, it deserves a slot in this blog. This songbird genome has been sequenced and assembled, and the main results are presented in the 1st of April issue of Nature.

Of the 1.2 gigabase (Gb) draft assembly, 1.0 Gb has been assigned to 33 chromosomes and three linkage groups, by using zebra finch genetic linkage and bacterial artificial chromosome (BAC) fingerprint maps. A total of 17,475 protein-coding genes were predicted from the zebra finch genome assembly using the Ensembl pipeline supplemented by Gpipe gene models. A major result of this study the demonstration that song behaviour engages gene regulatory networks in the songbird brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. This study also suggests rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication.

Warren et al. (2010) The genome of a songbird. Nature 464, 757-762.

Photo: © mediawiki.org

Peach Genome Released: “un jus de première qualité”

April 11th, 2010

Peach flowerThe draft of the genome sequence of Peach (Prunus persica) (cultivar ‘Lovell’) has been released on April 1st by the International Peach Genome Initiative. This consortium, under the direction of Drs Bryon Sosinski, Ignazio Verde and Daniel Rokhsar, includes numerous researchers from countries around the globe including the US, Italy, Spain and Chile.

The genome is available online at the Genome Database for Rosaceae, JGI Phytozome and Istituto di Genomica Applicata (IGA).

Peach (Prunus persica) is considered one of the genetically most well characterized species in the Rosaceae, and it has distinct advantages that make it suitable as a model genome species for Prunus as well as for other species in the Rosaceae. While some Prunus species, such as cultivated plums and sour cherries, are polyploid, peach is a diploid with n = 8 and has a comparatively small genome currently estimated to be ~220-230 Mbp based upon the peach v1.0 assembly.

Assembly v1.0 currently consists of 8 pseudomolecules (scaffolds) representing the 8 chromosomes. The genome sequencing consisted of approximately 7.7 fold whole genome shotgun sequencing employing the Sanger methodology, and was assembled using Arachne. The assembled peach scaffolds cover nearly 99% of the peach genome, with over 92% having confirmed orientation. To further validate the quality of the assembly, 74,757 Prunus ESTs were queried against the genome — only ~2% were missing;  28,689 transcripts and 27,852 genes have been predicted.

Together, with the poplar and euclayptus genomes, the peach genome is being used to identify genes that are critical for deciduous tree growth and development.

Photo: Peach flower (© FM).

Rhizopus oryzae genome published

August 9th, 2009

rhizopusThe genome of the fungus Rhizopus oryzae has been published. R. oryzae is a widely dispersed mold fungus found in soil and decomposing organic material. It can cause fatal infections in people with suppressed immune systems. It belongs to the Mucoraceae in the order Mucorales. As a representative of the paraphyletic basal group of the fungal kingdom called Zygomycetes, R. oryzae is widely used as a model to study fungal evolution. This genome analysis provides the first insights into the genome structure and dynamics of a basal fungal lineage. Whole-genome duplication (WGD) plays an important role in evolution of R. oryzae genome. The post-WGD retention of entire protein complexes and gene family expansions likely enable the mold to rapidly use more complex carbohydrates for energy sources and quickly accommodate major environmental changes in soil or hosts.

The genomic sequence is available at the Broad Institute database: http://www.broadinstitute.org/annotation/genome/rhizopus_oryzae/MultiHome.html.

Ref. Li-Jun Ma et al. (2009) Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication. PLoS Genet 5(7): e1000549.