Posts Tagged ‘Genome sequencing’

F1000 nominations

December 18th, 2012

Great news!!! A new nomination tool for the 1000 Fungal Genome Project has been released (http://genome.jgi-psf.org/pages/fungi-1000-projects.jsf) to entire research community.  Any JGI registered user can click on MycoCosm tree nodes at (jgi.doe.gov/fungi), choose ‘Nominate’ to suggest new fungal species for sequencing and provide DNA/RNA samples to fill the gaps in the Fungal Tree of Life.  The nominations can be made all year around; after review the approved candidates will be added to the list of JGI projects.

The guiding principle for sampling in F1000 is at the end of the project to have 2 representatives from all fungal families or family-level clades. This will require a lot of coordination across several JGI CSP projects, e.g. our Mycorrhizal Genome Initiative, the Forest Soil Metatranscriptome Project and the Saprotrophic Agaricomycotina project, and interactions with the community and systematics experts of given groups. The current nomination will help in selecting the most interesting suggestions from our community.

Photo: Mycena sp. belongs to a large genus of small saprotrophic mushrooms. Mycena galopus will be sequenced within the framework of the Forest Soil Metatranscriptome Project (CSP570) © F Martin

The Genome Encyclopedia of Fungi

October 18th, 2009

jgiBecause of the importance of fungi to Department of Energy (DOE) mission areas such bioenergy production, bioremediation and carbon cycling, the Joint Genome Institute has decided to develop a formal Fungal Genomics Program. In bioenergy projects alone, for example, fungal genome data have been used not only to ensure the health of crops that serve as biomass feedstocks (e.g., Poplar/Melampsora interaction) but also provide enzymes that can break down the biomass. Currently, the vast majority of fungi whose genomes have been sequenced are ascomycetes and basidiomycetes. The result of this bias is that we don’t have a grasp of the enzymatic and metabolic diversity found in the fungal kingdom. The JGI has thus developed a Fungal Genomics Program headed by Igor Grigoriev. The program’s first project, launched October 1, is the Genome Encyclopedia of Fungi (GEF). The program aims to explore fungi’s ecological diversity and breadth across the Tree of Life. One thrust area will be devoted to basidiomycetes. Another thrust area of this program will aim to sequence genomes across the fungal tree of life.  Additional thrust areas will be aimed at in depth sequencing of other fungal groups that are key to DOE mission areas, such as the Dothideomycetes.

hc2Years 2009 and 2010 will be devoted to building and piloting a fungal genome sequencing pipeline that scales – from DNA sample preparation to automated annotation to comparative genomics tools. Five genomes will initially sequenced per month. Within the candidate basidiomycetes for sequencing there are several soil fungi involved in wood degradation and ectomycorrhizal symbiosis, including Gloeophyllum trabeum (brown-rot), Fomitiporia mediterranea (white-rot), and Hebeloma cylindrosporum (symbiont). These multiple genomes will allow a thorough comparative analysis of the genome traits underlying the fungal lifestyles.

Microbial genomics: meeting the challenges and fulfilling the dream

August 15th, 2009

Nature BiotechnologyIn the July issue of Nature Biotechnology, Nikos Kirpides from JGI published a challenging paper entitled “Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream” where he discussed the past and future of microbial genomics. More than two-thirds of the 4,800 currently reported genome projects are microbial and the number of genomes and pangenomes will tremendously increase in the years to come. Unfortunately, several underlying problems hinder additional growth of the field and, even more importantly, compromise the ability of biologists to use and interpret the available data. This includes: (i) Genome publication and data release policy violating a longstanding scientific precept, i.e. examine the actual data, (ii) bias in the selection of species for genome projects, (iii) poor funding for the maintenance of biological databases, (iv) the lack of dedicated professionals for gene catalog curation, and (v) the lack of standard in genomics. As strongly recommended by  Nikos Kirpides “a systematic and comprehensive exploration of the planet microbial world  cannot be achieved by the efforts of individual researchers but requires the establishment of effective national and international collaborations.”

In the Heart of Truffle Country

August 10th, 2009
Perigord Black Truffle (© C Murat)

Perigord Black Truffle (© C Murat)

There are gnarled vines and patches of woodland, and fortified hill villages. We are in the heart of the White Truffle country in Alba (Piemonte). The smell of fresh produce is hanging in the air. There’s one pervasive scent that’s quite unlike any other – rich, earthy and pungently aromatic: the Tartufo Bianco (White Truffle) aroma.

The next Tuber Genome Workshop will take place on October 12-14, 2009 in Alba during the Truffle Festival. The meeting will begin on Monday at 14:00 am and will end on Wednesday at 12:00 pm. The aim of the workshop is (1) to establish the current status of the Tuber melanosporum genome project and (2) to bring together  collaborators for discussing the post-genomics activities of the consortium. The new Tuber magnatum genome sequencing project will be launched at this meeting.

The format of the workshop will be roughly equally split between informal presentations (summarizing the current findings), what we hope will be spirited discussion and brainstorming about how to take advantage of the Tuber genomic sequences to inform our understanding of symbiosis and fungal biology.

Tremella genome released

August 9th, 2009

Tremella mesentericaKnown as the golden jelly fungus, Tremella mesenterica is commonly found on rotting wood, especially gorse, as a parasite of wood decay fungi. It belongs to the Basidiomycota (Agaricomycotina, Tremellomycetes, Tremellales, Tremellaceae). Its genome has been sequenced and recently released by the JGI. The genome is ~28Mb and the JGI annotation group predicted 8,313 genes. This fungus is among the species studied for getting a better understanding of wood degradation mechanisms and how it differs in jelly fungi from the more distantly related Agaricomycotina, such Pleurotus ostreatus or Coprinopsis cinerea.