All posts by Joey Spatafora

Professor Department of Botany & Plant Pathology Oregon State University

Aulographum hederae genome release

1KFG is pleased to announce the public release of the Aulographum hederae genome http://genome.jgi.doe.gov/Ahederae2.  Aulographum hederae (Aulographaceae, Microthyriales) is a saprobic Dothideomycetes that occurs on dead leaves of numerous hosts.  It was contributed to the 1KFG project by Manfred Binder and Pedro Crous of Centraalbureau voor Schimmelcultures KNAW, Netherlands, and represents the first genome sequenced for the family Aulographaceae and the order Microthyriales.  As always, please contact the lead contact and PI associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

Suillus brevipes genome released

1KFG is pleased to announce the public release of the Suillus brevipes genome http://genome.jgi.doe.gov/Suibr1/Suibr1.home.htmlSuillus brevipes is an ectomycorrhizal species of Suillaceae (Boletales), and was contributed to the 1KFG project by Sara Branco and Tom Bruns (Bruns Lab) from the University of California at Berkeley.  As always, please contact the lead contact and PI associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

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  As always, please contact the lead contact(s) associated with unpublished 1KFG genomes prior to use in any publication.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

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.