Archive for the ‘Genome sequencing’ category

1000 Fungal Genome (1KFG) project: Graduate Student-Postdoc Challenge (2014)

August 6th, 2014

The 1000 Fungal Genome (1KFG) project is a large-scale community sequencing project supported by the Joint Genome Institute (JGI).  The goal of 1KFG is to facilitate the sequencing of fungal genomes across the Kingdom Fungi with the objective to significantly advance genome-enabled mycology.  The sampling guideline is to sequence two species of fungi for every family-level clade of Fungi so that genomic data is representative of phylogenetic diversity of Fungi. In support of this endeavor, 1KFG is pleased to announce the Graduate Student/Postdoc Challenge.  From July 2014-June 30 2015 we will accept nominations to sequence up to 100 species of fungi in support of graduate student and postdoctoral research projects.  Students and postdocs are encouraged to nominate species and submit DNA and RNA samples for genomic sequencing.

 

Follow the link to find out how to nominate species.

 

Mycorrhizal Genomics Initiative – Year 3

July 31st, 2014

In 2003, the Poplar Mesocosm Sequencing project was launched to sequence the genome of three Populus-associated fungi, the ectomycorrhizal (EM) basidiomycete Laccaria bicolor, the arbuscular mycorrhizal (AM) glomeromycete Rhizophagus irregularis (formerly Glomus intraradices), and the poplar leaf rust Melampsora larici-populina. The publication of the genome sequence of L. bicolor was a landmark event for the mycorrhizal community. It has been rapidly followed by the release of the genome of the iconic edible EM Tuber melanosporum, the Périgord black truffle and more recently, by the genome of Rhizophagus irregularis. These genomes have provided unprecedented knowledge about the structure and functioning of the mycorrhizal fungal species and their interactions with their host plants. Genome-wide transcript profilings have also led to the identification of master genes with crucial roles in symbiosis formation, such as those coding for Mycorrhiza-induced Small Secreted Proteins (MiSSPs) controling plant immunity and development.

An international effort, referred as to the Mycorrhiza 25 Genomes Project and then the Mycorrhizal Genomics Initiative (MGI), aiming to unearth the evolution and functioning of mycorrhizal symbioses through large-scale genome sequencing has been launched in 2011. As of writing, this initiative targets a set of 35 fungal species that are able to form various types of mycorrhizal symbioses, i.e., EM, arbuscular, ericoid and orchid mycorrhizae (see my previous posts ‘Mycorrhizal Genomics Initiative‘ and ‘Exploring the Mycorrhizal Genomes‘ ). Sequencing is carried out at JGI and Genoscope in the framework of the JGI Community Science Program, the 1000 Fungal Genomes Project and the TuberEvol project. Comparison of these genomes should facilitate the characterization of the genetic mechanisms that underpin the formation and evolution of ecologically-relevant mycorrhizal symbioses and characterization of genes selectively associated with particular symbiotic patterns.

The fungal species sequenced have been selected based on: (1) their phylogenetic position, (2) their ecological relevance, and (3) their ability to establish different types of mycorrhizal symbiosis. As of today, genomic sequences and gene repertoires are publicly available for 28 mycorrhizal fungi, including 24 ectomycorrhizal species, 3 ericoid species, 2 orchid mycorrhizal species and 1 arbuscular mycorrhizal species (see Table below & see the JGI MycoCosm Mycorrhizal Fungi portal.

Genomes of the sequenced mycorrhizal fungi range in size from about 36 Mb, as in the case of Rhizopogon vinicolor, to a 193 Mb, as in Tuber magnatum (Table). Repetitive DNA, mostly in the form of transposable elements (TE), is responsible for the bulk of the variation. A striking feature is the wide variation in repetitive DNA content (from 3.6 % for H. cylindrosporum to 58.3% for T. magnatum). Predicted gene contents range from about 7500 for T. melanosporum to ~28000 genes for Rhizophagus irregularis.

We are drafting a paper summarizing the main conclusions from the analysis of the first series of mycorrhizal genomes. Stay tune!

 

Species Genome size Gene #
1 Amanita muscaria Koide v1.01 40,699,759 18,153
2 Boletus edulis v1.01 46,637,611 16,933
3 Cenococcum geophilum 1.58 v2.01 177,557,160 14,748
4 Choiromyces venosus 120613-1 v1.01 126,035,033 17,986
5 Cortinarius glaucopus AT 2004 276 v2.01 63,450,306 20,377
6 Gyrodon lividus BX v1.01 43,048,674 11,779
7 Hebeloma cylindrosporum h7 v2.01 38,226,047 15,382
8 Laccaria amethystina LaAM-08-1 v1.01 52,197,432 21,066
9 Laccaria bicolor 81306 v1.01 50,950,722 17,791
10 Laccaria bicolor D101 v1.01 70,029,479 22,538
11 Laccaria bicolor S238N-H70 v1.01 57,049,857 19,903
12 Laccaria bicolor S238N-H82 v1.01 52,023,709 18,706
13 Laccaria bicolor S238N-H82xH70 v1.01 42,115,601 17,045
14 Laccaria bicolor v2.01 60,707,050 23,132
15 Meliniomyces bicolor E v2.03 82,384,847 18,619
16 Meliniomyces variabilis F v1.03 55,857,776 20,389
17 Morchella conica CCBAS932 v1.01 48,213,273 11,600
18 Oidiodendron maius Zn v1.03 46,426,256 16,703
19 Paxillus involutus ATCC 200175 v1.01 58,301,126 17,968
20 Paxillus rubicundulus Ve08.2h10 v1.01 53,011,005 22,065
21 Piloderma croceum F 1598 v1.01 59,326,866 21,583
22 Pisolithus microcarpus 441 v1.01 53,027,657 21,064
23 Pisolithus tinctorius Marx 270 v1.0 71,007,534 22,701
24 Rhizophagus irregularis DAOM 181602 v1.02 91,083,792 30,282
25 Rhizopogon vinicolor AM-OR11-026 v1.01 36,102,320 14,469
26 Scleroderma citrinum Foug A v1.01 56,144,862 21,012
27 Sebacina vermifera MAFF 305830 v1.04 38,094,242 15,312
28 Suillus brevipes v1.01 51,712,595 22,453
29 Suillus luteus UH-Slu-Lm8-n1 v1.01 37,014,302 18,316
30 Terfezia boudieri S1 v1.01 63,234,573 10,200
31 Tricholoma matsutake 945 v3.01 175,759,688 22,885
32 Tuber aestivum1 131,544,163 9,344
33 Tuber magnatum v1.01 192,781,443 9,433
33 Tuber melanosporum v1.01 124,945,702 7,496
34 Tulasnella calospora AL13/4D v1.04 62,392,858 19,659
35 Wilcoxina mikolae CBS 423.85 v1.01 117,288,895 13,093

 

MGI4

March 11th, 2014

ICOM8

March 6th, 2014

JGI User Meeting, Genomics of Energy and the Environment

February 19th, 2014

The JGI User Meeting, Genomics of Energy and the Environment, will be held March 18-20 in Walnut Creek, CA.

This year looks like a particularly exciting meeting, with great speakers and a diversity of interesting topics.  The agenda and other details for this meeting can be found at http://www.jgi.doe.gov/meetings/usermeeting/

myTree of the Month

February 15th, 2014

Understanding the Polyporales Evolution

December 15th, 2013

The Saprotrophic Agaricomycetes Sequencing Consortium, lead by David Hibbett (Clark University) analyzed 10 currently available whole genomes of Polyporales, comparing them to known gene datasets. In a special issue of Mycologia, the consortium reported the phylogenomic and phylogenetic analyses of this ecologically-important group of wood-rotters. They also analyzed several single-copy genes to assess them for their potential as markers of relationships between members of this group.

This analysis yielded new details about the evolutionary relationships between species, which they detailed in several phylogenetic trees of several clades (residual polyporoid clade, plebioid clade, antrodia clade and core polyporoid clade).

December 12th, 2013

Labex ARBRE Annual Meeting

October 16th, 2013

The Annual Meeting 2013 of the Lab of Excellence ARBRE will be held at INRA-Nancy on Monday 21st October, 2013.

The primary objective of this meeting will be to present the projects awarded funding by the Labex call for proposals in 2012.  It will aim to highlight and discuss the most noteworthy achievements during the first year of Labex ARBRE, specific to research units and those in each thematic area (Research, Valuation, Training-Dissemination).  Projects selected for funding from the 2013 call for proposals will also be presented.  The day will end with a strategy discussion moderated by project leaders from each thematic area who will focus on how to strengthen relationships between thematic actions and areas of research.

For the detailed meeting agenda please click here – Agenda

 

Jacques Monod Conference on Bacterial-Fungal Interactions

August 27th, 2013
The deadline for application to the first Jacques Monod Conference on Bacterial-Fungal Interactions entitled :
Bacterial-fungal interactions: a federative field for fundamental and applied microbiology“, is September 15, 2013.
The conference will take place at Roscoff in Britanny (France) from December 8 to 11, 2013.

The Passion Principle

August 15th, 2013

Wilson EO (2013) Letters to a Young Scientist.

New York: Liveright (W.W. Norton). 245 p. ISBN 978-0871403773 (hardcover). US$21.95.

doi:10.1371/journal.pbio.1001629.g001

Read the book review by:  Simberloff D (2013) The Passion Principle. PLoS Biol 11(8): e1001629. doi:10.1371/journal.pbio.1001629

 

 

Comparative Genomics of Eukaryotic Microorganisms

August 6th, 2013

An INRA-JGI Bastille Day tribute!

July 14th, 2013
In the spirit of Bastille Day, I enthuse (in French with English subtitles) about the Joint Genome Institute’s contributions to the field of fungal genomics:
I enjoyed shooting this video at the Fungal Genetics Conference in Asilomar in March 2013. Thanks to David Gilbert from the JGI, we had a lot of fun working with the video crew.

Photo: © france.fr

First Global Biodiversity Conference

June 26th, 2013

Loosing its claws …

June 26th, 2013

Must read …

The Transition from a Phytopathogenic Smut Ancestor to an Anamorphic Biocontrol Agent Deciphered by Comparative Whole-Genome Analysis
[Abstract. Pseudozyma flocculosa is related to the model plant pathogen Ustilago maydis yet is not a phytopathogen but rather a biocontrol agent of powdery mildews; this relationship makes it unique for the study of the evolution of plant pathogenicity factors. The P. flocculosa genome of ~23 Mb includes 6877 predicted protein coding genes. Genome features, including hallmarks of pathogenicity, are very similar in P. flocculosa and U. maydis, Sporisorium reilianum, and Ustilago hordei. Furthermore, P. flocculosa, a strict anamorph, revealed conserved and seemingly intact mating-type and meiosis loci typical of Ustilaginales. By contrast, we observed the loss of a specific subset of candidate secreted effector proteins reported to influence virulence in U. maydis as the singular divergence that could explain its nonpathogenic nature. These results suggest that P. flocculosa could have once been a virulent smut fungus that lost the specific effectors necessary for host compatibility. Interestingly, the biocontrol agent appears to have acquired genes encoding secreted proteins not found in the compared Ustilaginales, including necrosis-inducing-Phytophthora-protein- and Lysin-motif- containing proteins believed to have direct relevance to its lifestyle. The genome sequence should contribute to new insights into the subtle genetic differences that can lead to drastic changes in fungal pathogen lifestyles.]

 

 

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

5th European Plant Science Retreat

April 2nd, 2013

This summer, Ghent university and the VIB will be the host of the annual 5th European Plant Science Retreat (23-27 July). This is a conference and networking event organized by and held for PhD’s in plant research from 11 of the best plant-research institutes around Europe.

Genomics of Fungal Drug Producers

March 2nd, 2013

In a breakthrough paper, Schardl’s group and collaborators have published 15 genomes of diverse species of Clavicipitaceae plant endophytes and parasites in the last issue of PloS Genetics. The Clavicipitaceae (PezizomycotinaSordariomycetes, Hypocreales) includes “ergot” fungi that parasitize ears of cereals and produce  the toxic ergoline derivatives; ergot fungi have historically caused epidemics of gangrenous poisonings, the ergotism, also known as the Saint Anthony’s Fire. The ascomycetous family also includes plant endophytic symbionts that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. They synthesize alkaloids with chemical similarities to biogenic amines that deter insects, livestock, and wildlife from feeding on the fungus or plant. Thanks to this chemical warfare, Epichloae protect their hosts from cattle grazing. The lysergic acid diethylamide (LSD), a semisynthetic ergot alkaloid originally developed as an antidepressant, is the most potent known hallucinogen.

In this study, they sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and the bamboo witch’s broom pathogen (Aciculosporium take), profiled the alkaloids in these species and compared the gene clusters for four classes of alkaloids. The genomes were primarily sequenced by shotgun 454 pyrosequencing, but paired-end and mate-pair reads were used to scaffold several assemblies. Size of the assembled genome among the sequenced strains varied 2-fold from 29.2 to 58.7 Mb, with wide ranges even within the genera Claviceps (31–52.3 Mb) and Epichloë (29.2–49.3 Mb). This genome size variation is mainly resulting from the abundance of repeated elements, which ranged from 4.7 to 56.9%. Annotated genome sequences have been posted at www.endophyte.uky.edu.

In the epichloae, the clusters of genes coding for enzymes of alkaloid biosynthesis contain very large blocks of repetitive elements which promote gene losses, mutations, and even the evolution of new genes. Two striking features emerged from the detailed analysis of alkaloid biosynthesis gene clusters. Firstly, in most alkaloid loci in most species, the periphery of each cluster was enriched in genes that by virtue of their presence, absence, or sequence variations determined the diversity of alkaloids within the respective chemical class. Second, alkaloid gene loci of the epichloae had extraordinarily large and pervasive blocks of AT- rich repeats derived from retroelements, DNA transposons, and MITEs. This finding suggests that these plant-interacting fungi are under selection for alkaloid diversification.

In their conclusions, the authors suggest that this selection of chemotypes is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the ecologically diverse cool-season grasses.

Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, et al. (2013) Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci. PLoS Genet 9(2): e1003323. doi:10.1371/journal.pgen.1003323

Image: Claviceps purpurea -Franz Eugen Köhler, Köhler’s Medizinal-Pflanzen (Wikimedia Commons).

A Cornucopia of Mycorrhizal Genomes

February 23rd, 2013

Mycorrhizal symbioses are nearly universal in terrestrial plants. Based on host plant and characteristic symbiotic structures, several classes of mycorrhizal symbioses are currently recognised, with the two major types being the endocellular arbuscular mycorrhiza (AM) and the intercellular ectomycorrhiza (ECM). Mark Brundrett’s web site provides an excellent introduction to the different types of mycorrhizal symbioses. Briefly,

In AM association, the fungal hyphae penetrates host roots to form intracellular arbuscules and vesicles.

In ECM, colonizing hyphae remain in the intercellular, apoplastic space forming the Hartig net. They do not penetrate the root cells. ECM are mostly form by basidiomycetes (e.g., Amanita, Boletus, Sebacina), but some are formed with ascomycetes (e.g., Tuber, Terfezia).

Additionally, the ericoid mycorrhiza (ERM) has been regarded as the most specific of mycorrhizas because of its limitation to hosts belonging to a restricted number of families of the Ericales and the participation of a small group of ascomycetous fungi (e.g., Helotiales) as mycobionts in the association. Ericoid fungi form hyphal coils in outer cells of the narrow “hair roots” of plants in the family Ericaceae, such as Vaccinium and Calluna.

All orchids are myco-heterotrophic at some stage during their lifecycle and form orchid mycorrhizas with a range of basidiomycete fungi (e.g., Tulasnella). The mycobiont forms coils of hyphae within roots or stems of orchidaceous plants. This type of mycorrhiza is unique because the endophytic fungus supplies the plant with carbon during the heterotrophic seedling stage of orchidaceous plants. The mycorrhizal fungi are often Tulasnellales, a basidiomycetous order that contains plant parasites and saprobes capable of degrading complex carbohydrates, such as cellulose.

Whether these different types of mycorrhizal fungi forming strikingly different anatomical structures and with contrasted biology and ecology differ in their gene repertoires and symbiosis-related gene networks is currently unknown and tackling these major questions is the main impetus of the current Mycorrhizal Genomics Initiative lead by the JGI and INRA (see my previous posts ‘Mycorrhizal Genomics Initiative‘ and ‘Exploring the Mycorrhizal Genomes‘ )

The genome of 30 representatives of these various types of mycorrhizal symbioses are currently sequenced and these tremendous genomic resources are providing new highlights on the biology, genetic and ecology of these symbioses. The findings obtained previously on L. bicolor and T. melanosporum genomes suggested that the ECM condition represents a syndrome of variable traits and that mycorrhizal fungi share fewer functional similarities in their molecular ‘toolboxes’ than anticipated (Plett & Martin, 2011) and this hypothesis is confirmed by the newly available genomes. We see very different symbiosis-upregulated genes in the various mycorrhizal lineages suggesting that these are non-homologous ecologies and that there are many routes to the similar nutritional modes. Several talks and posters at the forthcoming 27th Fungal Genetics Conference in Asilomar will illustrate several breakthroughs obtained by the MGI consortium members.

As of writing, the mycorrhizal species sequenced, assembled and annotated span a wide section of the evolutionary tree of Ascomycota and Basidiomycota, and include ectomycorrhizal, ericoid and orchid symbionts as follows:

Ectomycorrhizal species:

  • Amanita muscaria,
  • Boletus edulis
  • Cenococcum geophilum,
  • Cortinarius glaucopus,
  • Hebeloma cylindrosporum h7  (v2.0),
  • Laccaria amethystina 08-1,
  • Laccaria bicolor (v2.0),
  • Paxillus involutus,
  • Paxillus rubicundulus,
  • Piloderma croceum F 1598,
  • Pisolithus microcarpus 441,
  • Pisolithus tinctorius 270,
  • Scleroderma citrinum FougA,
  • Suillus luteus UH-Slu-Lm8-n1,
  • Terfezia boudieri,
  • Tricholoma matsutake 945.

Orchid mycorrhizal species:

  • Tulasnella calospora AL13/4D
  • Sebacina vermifera MAFF 305830,

Ericoid mycorrhizal species

  • Oidiodendron maius Zn,
  • Meliniomyces bicolor,
  • Meliniomyces variabilis.

As of today, 20 mycorrhizal genomes have been released on the JGI MycoCosm web portal and 10 additional genomes will be publicly released by the end of 2013 (see also our MGI web portal).

In addition to these new genomes/transcriptomes, those of Rhizopogon vinicolor, Gyrodon lividus, Choiromyces venosus, Lactarius quietus, Leccinum scabrum, Thelephora terrestris, Tomentella sublilacina, Tuber aestivum, Tuber magnatum, Rhizoscyphus ericae are expected to be released in 2013.

The genomes of mycorrhizal species released over the last two years, combined with previous studies of the L. bicolor and T. melanosporum genomes, provides a rich foundation for future studies to elucidate the unique features of these ubiquitous plant symbionts. Let’s find the gems in these genetic blueprints!

Photo: Fruiting bodies of the ectomycorrhizal Fly Agaric (Amanita muscaria).