Archive for the ‘Bioinformatics’ 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

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).

Comparative Genomics of Eukaryotic Microorganisms

August 6th, 2013

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.

March 13th, 2013

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).

Mycorrhizal Genomes Medley

November 1st, 2012

In less than two weeks, mycorrhizasts will gather at the INRA in Nancy, to enjoy an exciting workshop on the mycorrhizal genomes. So much novel and unexpected information is emerging from these genome and transcriptome exploration. That’s like exploring a Terra Incognita.

Below is the agenda;

2nd Mycorrhizal Genomics Initiative (MGI) Workshop

INRA-Nancy, November 13 & 14, 2012

Tuesday 13 November

  • 9:00 – 9:15     Opening remarks
  • 9:15 – 9:40     Exploring the genome diversity of mycorrhizal fungi. Project status. By F Martin
  • 9:40 – 10:00   The MycoCosm database & Fungal Genomics at JGI. By I Grigoriev
  • 10:00 – 10:30 Annotation and analysis of ECM genomes. By A Kuo
  • 11:00 – 11:20 Identifying transposable elements and other repeated elements in mycorrhizal genomes. By C Murat
  • 11:20 – 11:40 A new approach to infer protein function based on whole genomes and phylogenetic information. By L.G. Nagy
  • 11:40 – 12:00 Analysis of multigene families and duplications in mycorrhizal genomes. By E Morin
  • 12:00 – 12:20 CAZYmes and FOLymes in mycorrhizal genomes. By B Henrissat
  • 12:20 – 12:40 The secretome in mycorrhizal genomes. By C Fourrey
  • 14:00 – 14:20 The MGI transcriptome databases. By E Tisserant
  • 14:20 – 14:40 Identifying symbiosis-regulated genes by RNA-Seq. By A Kohler

14:40 – 15:30 Genome descriptions by species

  • Paxillus involutus & P. rubicundulus By A Tunlid & M Gardes
  • Hebeloma cylindrosporum By G Gay & J Doré
  • Amanita muscaria & A. thiersii By A. Pringle/J Hess

16:00 – 18:00 Genome descriptions by species

  • Laccaria amethystina By F Martin
  • Piloderma croceum By  M Tarkka et al.
  • Suillus luteus By J Colpaert et al.
  • Scleroderma citrinum By A Deveau
  • Pisolithus tinctorius & P. microcarpus By A Kohler
  • Sebacina vermifera By A Zuccaro
  • Tulasnella calospora By M Girlanda

18:00 – End

Wednesday 14 November

9:00 – 11:00   Genome descriptions by species

  • Cenococcum geophilum By M Peter
  • Oidiodendron maius By S Perotto et al.
  • Meliniomyces bicolor, M. variabilis By G Grelet
  • Tuber species By C Murat & R Ballestrini et al.
  • Terfezia boudierii By Y Sitrit

11:00 – 11:30 New Mycorrhizal Genomes Projects

CSP2012 #570 – Metatranscriptomics of Forest Soil Ecosystems: C Murat, M Buée, F Martin

CSP2013 #978 – MGI: Exploring the Symbiotic Transcriptomes: A Kohler, F Buscot, A Tunlid, F Martin

11:30 – 12:30 Discussions: MGI: Papers & Future activities

Photo: One of the sequenced ectomycorrhizal basidiomycete, the Amethyst Deceiver (Laccaria amethystina) (© F Martin)

The Pizza Mushroom Genome

October 9th, 2012

The publication describing the genome from the Button Mushroom (Agaricus bisporus) was published online today  in the early Edition of the journal, the Proceedings of the National Academy of Sciences (PNAS). This paper represents a culmination of five years of work by many people from multiple institutions in France, U.S.A., U.K., The Netherlands, Finland and Germany. This was truly an amazing team effort between the JGI teams and the international consortium. Let’s see if the news coverage of this genome study is as good as the one received for the Black Truffle genome. After all, the Portobello mushroom is one of the most commonly and widely consumed mushrooms in the world.

Below is the abstract of our PNAS paper:

[Abstract. Agaricus bisporus is the model fungus for the adaptation,persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.]

Read: Morin et al. (2012) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proceedings of the National Academy of Sciences, Early Edition.

Press releases:

JGI: Adaptable Button Mushroom Serves Up Biomass-Degrading Genes Critical to Managing the Planet’s Carbon Stores

INRA: Le génome du champignon de Paris décrypté

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).

Les champignons au charbon

August 22nd, 2012

Évolution : un champignon préhistorique serait à l’origine de l’arrêt de la formation du charbon

Voici le communiqué de presse de l’INRA sur notre article dans Science sur l’évolution des mécanismes de dégradation de la lignocellulose chez les champignons du groupe des Agaricomycotina: [“L’apparition, il y a environ 300 millions d’années, d’un champignon capable de détruire efficacement le bois pourrait en partie expliquer l’arrêt de la formation de charbon à base de débris végétaux à cette même période. C’est l’une des conclusions d’une étude menée par des chercheurs de l’Inra, du CNRS et des universités de Lorraine et d’Aix-Marseille dans le cadre d’un consortium international. L’étude a permis également de comprendre le processus de dégradation du bois par les champignons contemporains, ce qui devrait fortement intéresser le secteur des bioénergies.] … en savoir plus

Floudas et al. (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336: 1715-1719.

 

Photo: Young fruiting body of  Fomitopsis pinicola (Red Banded Polypore) (© F Martin).

JGI Summer 2012 Primer

August 2nd, 2012

The summer edition of the U.S Department of Energy (DOE) Joint Genome Institute (JGI) newsletter The Primer is now available for download: http://bit.ly/JGI-Summer-Primer-2012

…featuring articles and images:

Features include:

  • A summary of the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting
  • Comparative Genomics of White Rot Fungi Providing Insight into Selective Ligninolysis
  • The Omics Response to the Deepwater Oil Spill
  • Assembling the Switchgrass Genome
  • Single-cell Genomics @ the DOE JGI
  • Save the Date for the 8th Annual Genomics of Energy & Environment Meeting MARCH 25-29, 2013 in WALNUT CREEK, CA
  • Other Publication Highlights

 

 

8th JGI Users Meeting

August 2nd, 2012


Plant Science For Future Needs

June 11th, 2012

The Linnean Centre invites plant scientists to Uppsala for a two-day conference October 11th and 12th, 2012. The conference aims to tackle upcoming challenges like climate change and food security by setting a foundation for future collaborations between different sub-disciplines of plant science. Eight scientific sessions with plenary presentations, short talks and posters will highlight prevailing directions and novel findings.

NOTE: Registration deadline 31st of August, 2012.

Confirmed speakers are:

  • Vincent Colot, Ecole Normale Supérieure Paris
  • Thomas Kraft, Syngenta Seeds
  • Cris Kuhlemeier, Bern University
  • Gary Loake, University of Edinburgh
  • Francis Martin, INRA, Nancy
  • John McKay, Colorado State University
  • Kalien A. Mooney, UC Irvine
  • Michele Morgante, University of Udine

More information about the plenary speakers can be found here.

 

JGI Spring 2012 Primer

May 29th, 2012

The Spring 2012 edition of the DOE Joint Genome Institute (DOE JGI) newsletter The Primer is now available for download:
http://1.usa.gov/JGI-Primer-Spring-2012
and features highlights from the DOE JGI Genomics of Energy & Environment Meeting #7.

Videos of the talks from Meeting #7 are posted here:
http://bit.ly/JGI_Mtg7Videos


Be sure to Save the Date for meeting #8 the week of March 25-29, 2013.

Planaria Matrix

April 28th, 2012

A great image from PLoS Computanional Biology: ‘ The correct regeneration of complex morphology after amputation in planaria requires precise coordination of global patterning information and individual stem cell activity. This image illustrates the algorithmic information that is processed by cells and tissues to restore missing structures.’ See Lobo and Beane (e1002281)

 

Image Credit: Image produced by Daniel Lobo and Wendy Beane.

 

Rust in the limelight

April 20th, 2012

Image by Benjamin Petre and Stephane Hacquard on the cover of the March 2012 issue of Molecular Plant Microbe Interactions. Congrats to Steph, David, Seb and coauthors for their paper: ‘A Comprehensive Analysis of Genes Encoding Small Secreted Proteins Identifies Candidate Effectors in Melampsora larici-populina (Poplar Leaf Rust)‘.

Uredinia formed by the rust fungus Melampsora larici-populina 7 days after inoculation on susceptible poplar leaves (severe and weak infection are pictured above and below the midrib, respectively). The panels below show immunofluorescence localization of small secreted proteins at the periphery of distinct infection structures in poplar leaves.

JGI Fungal Jamboree

March 19th, 2012

The annual JGI Fungal Jamboree will start on Monday 19th at the Marriott Hotel in Walnut Creek. During the workshop, attendees will:

  • provide an update on their JGI program’s development during the last year and future plans,
  • discuss several important questions, including: (1) How to address current bottlenecks for future scale-up (target selection, DNA samples, analysis, publications)? (2) How to reach new groups of users and coordinate with other large genomics initiatives (e.g., 1K Chinese Fungal Genomes)? (3) What products in addition to sequencing JGI should be working on for mycologists? (4) What informatics/analytical needs should be addressed?
  • discuss strategic partnerships.

I will report on our two fungal programs, i.e. the Mycorrhizal Genomics Initiative and the Metatranscriptomics of Forest Soils.

    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.)