1KFG genomes releases for May 3, 2013

Two new genomes were released today by JGI as part of the 1000 Fungal Genome (1KFG) Project:  Polychaeton citri v1.0 (http://genome.jgi.doe.gov/Pcitri) and Lepidopterella palustris v1.0 (http://genome.jgi.doe.gov/Lpalustris).  These are both members of the class Dothideomycetes and were contributed to the project by researchers Pedro Crous, Manfred Binder, and Janneke Bloem from the Centraalbureau voor Schimmelcultures in the Netherlands.  Annotation and editing privileges remain password-protected but all other tools are now available to the general public.  As always, please contact the lead contact(s) associated with unpublished 1KFG genomes prior to use in any publication.

Update on 1KFG

1000 Fungal Genomes (1KFG) is off and running.  The first year required a bit of “priming of the pump” but we have made some significant progress recently and nominations for new genomes are increasing rapidly.  Nineteen genomes have been completed as part of the Early Diverging Fungi (EDF) and 1KFG CSPs.  They are both included here as they are directly related efforts that started as EDF CSP and transformed into 1KFG.  The majority of isolates completed to date are from Ascomycota.  The rationale for focusing initially on Ascomycota was because significant progress had been made on Basidiomycota as part of the Saprobic Agaricomycotina Project (SAP) led by David Hibbett and the Mycorrhizal Genome Project led by Francis Martin.  1KFG, however, is open to all clades within Kingdom Fungi so nominate and provide samples for undersampled, sub-ordinals clades at jgi.doe.gov/fungi.  Stay tuned as 1KFG will be providing weekly updates on progress in sequencing, annotations, releases and nominations of fungi.

Continue reading Update on 1KFG

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.

Sampling Strategy for 1000 Fungal Genome Project

Sampling 1000 Fungal Genomes.

The overarching goal of the 1000 Fungal Genome Project (F1000) is to inform all areas of fungal biology by providing broad, genomic coverage of Kingdom Fungi (Fungi). The sampling design is based on a phylogenetic framework developed by the Assembly the Fungal Tree of Life Project (Hibbett et al. 2007) and is focused on covering all major subordinal groups (clades) of Fungi. Currently there are approximately 140 orders of Fungi and over 550 families. The F1000 goal over the next five years is to facilitate the sampling of fungal genomes so that at least two representatives are sequenced from every family or family-level clade of Fungi. This focus on “family or family-level” clade is meant as a guiding principle with the understanding that deliberate discussions involving taxonomic experts will be required to best integrate the current understanding of evolutionary relationships of Fungi and to the best select realistic exemplars.

Tier One of the project was developed as part of the Community Sequencing Proposal (CSP) to the Joint Genome Institute (JGI). As part of the F1000 CSP, it was necessary to propose an initial sampling list for year one. Tier One sampling focuses on unsampled families of groups (classes of Fungi) with existing genomic resources and with existing biological resources in culture collections. As the project matures, the goal is to develop a Research Coordination Network to organize the greater mycological and fungal biology communities to inform all phases of the project including sampling, curation of data, research and analytical, training and publications.

Below is a figure from the F1000 CSP that attempts to capture the current family level of sampling across the Fungal Tree of Life. Accurately documenting this activity is challenging so caution is advised when interpreting these data. This figure is not provided for use in any other research proposals or manuscripts. A more precise list is being developed and will be communicated in the near future.  To examine the species sampling list for Tier One, please visit the “1000 fungal genomes” link under “Fungal Resources & Blogs” located in the right-hand panel of this site.

Family level sampling of fungal genomes across the Fungal Tree of Life. a) phylogenetic tree of current classification. b) bar graphs of absolute number of families represented in genomic sampling by class or subphylum. c) bar graphs of percentage of families represented in genomic sampling by class or subphylum. Blue = completed or in progress, Red = proposed for Tier One sampling, Green = remaining unsampled families. A=Ascomycota, B=Basidiomycota. *The four Tier One classes represent the most phylogenetically diverse classes of nonlichenized fungi.

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.

Sequencing unsampled fungal diversity