Archive for November, 2012

JGI Fall 2012 Primer

November 11th, 2012

The Fall 2012 edition of the DOE JGI newsletter, The Primer is now posted: http://bit.ly/JGI-Fall-Primer-2012

Highlights include:

Photo: Maze-like pore surface of the polypore Trametes versicolor. Wood-decayers in the Polyporales are primary target for sequencing within the framework of the MycoCosm program. © F Martin.

myTree of the Month

November 2nd, 2012

In the ground of the Chaumont-sur-Loire castle, Rainer Gross has created sculptures in blackened wood. They are inspired by the roofs of the Chaumont-sur-Loire castle. One of these sculptures lies under a few centuries-old cedar and can be seen from the Loire river, which in turn can be viewed through an opening in the sculpture. These works seem to take root in the very landscape from which their materials were sourced. Rainer Gross “depicts the ambiguity of Man within Nature and the paradox of being both a product of Nature and yet independent from it“.

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)