Tag Archives: f1000

Nominations for 1000 fungal genomes

We are excited to be entering the next phase of the F1000 project. After a modest start, we now have more than 50 genomes in the pipeline. So far more than 25% of the current 626 Families have at least one genome sequenced and 80 families already have at least two genomes sampled. Nominations for additional species for the next phase of the F1000 project are now open on the JGI website supporting the Fungal 1000 genomes project.

You can login and post your nominations by providing information. The F1000 committee will insure this fits the 2 genomes per family rules. The justification must provide some supporting information on how this fungal genome fits in the DOE mission and that it is indeed increasing the phylogenetic diversity of sampling. If the phylogenetic position of the group is ambiguous or inconsistent with the current taxonomy please provide additional supporting information (phylogenetic trees, publications) that can support the idea that this is increasing the diversity of sampling from the Fungal tree. The nominator must provide the RNA and DNA in quantities necessary for the project following JGI guidelines. From their page the selection criteria includes:

Criteria for Selection:

  • Phylogenetic diversity – the selected fungal project must be from a family with one or no sequenced members. If you are aware of sequencing projects in progress for similar species, please let us know.
  • DOE mission relevance – alternative fuel, carbon cycling, bioremediation. Pathogens or commensals studied in the context of human health or disease are not allowed. These proposals will be rejected.
  • Commitment and likelihood to provide DNA and RNA of required quantity and quality for the nominated fungus (see JGI Sample Preparation Requirements). Desired: proof of previously isolated materials, such as gel images of DNA preps, Bioanlyzer traces of RNA preps, citations describing nucleic acid solutions for sequencing, ITS and/or large subunit sequences, access to a wet lab.
  • Ability of the nominator to oversee project from supplying materials, through analysis and publication. Desired: publication records.
  • Biological questions researcher hopes to answer with the proposed genome.

In addition you can help us track the genomes which are underway by making sure your projects are linked through GOLD or directly out on the site.

Please note that nomination and successful submission of biological materials is only the first step. The nominator should also be able to show follow through to analyze the genome data and work towards generating publications. The F1000 consortium will work together with you as collaborators where possible but it is expected the nominator(s) will be project leads analyzing the genome data once it is annotated and released.

1000 Fungal genomes project is underway

Our proposal to sequence 1000+ Fungal genomes was funded by the DOE’s JGI. This site represents a gathering of the information about the project and will link to additional resources tracking the progress of the project.

With an estimated 1.5 million species, Fungi represent one of the largest branches of the Tree of Life.  They have an enormous impact on human affairs and ecosystem functioning, owing to their diverse activities as decomposers, pathogens, and mutualistic symbionts.  And perhaps more than any other group of nonphotosynthetic organisms, fungi are essential biological components of the global carbon cycle.  Collectively, they are capable of degrading almost any naturally occurring biopolymer and numerous human-made ones.  As such, fungi hold considerable promise in the development of alternative fuels, carbon sequestration and bioremediation of contaminated ecosystems.

The use of fungi for the continued benefit of humankind, however, requires an accurate understanding of how they interact in natural and synthetic communities.  The ability to sample environments for complex fungal metagenomes is rapidly becoming a reality and will play an important part in harnessing fungi for industrial, energy and climate management purposes.  However, our ability to accurately analyze these data relies on well-characterized, foundational reference data of fungal genomes.

To bridge this gap in our understanding of fungal diversity, an international research team in collaboration with the Joint Genome Institute of the Department of Energy has embarked on a five-year project to sequence 1000 fungal genomes from across the Fungal Tree of Life.  The team comprises Joseph Spatafora (Oregon State University), Jason Stajich (University of California at Riverside), Kevin McCluskey (Fungal Genetics Stock Center), Pedro Crous (Centraal Bureau voor Schimmelcultures, Netherlands), Gillian Turgeon (Cornell University), Daniel Lindner (USDA Forest Service), Kerry O’Donnell and Todd Ward (USDA ARS), Antonis Rokas (Vanderbilt University), Louise Glass (University of California at Berkeley), Betsy Arnold (University of Arizona), Francis Martin (INRA, France) and Igor Grigoriev (JGI DOE).  The overall plan is to fill in gaps in the Fungal Tree of Life by sequencing at least two reference genomes from the more than 500 recognized families of Fungi.  In doing so, this project has the core goal of providing reference information to inform research on plant-microbe interactions, microbial emission and capture of greenhouse gasses, and environmental metagenomic sequencing.