All posts by Jason Stajich

Assistant Professor, Plant Pathology & Microbiology, University of California, Riverside

Macroventuria anomochaeta genome release

1KFG is pleased to announce the public release of the Macroventuria anomochaeta van der Aa genome.   M. anomochaeta is classified in the family Didymellaceae (Ascomycota; Dothideomycetes; Pleosporales), and is one of two sequenced genome from this family. This isolate was found on decaying canvas in the desert in South Africa.

Macroventuria anomochaeta was contributed to the 1KFG project by Pedro Crous and Manfred Binder at CBS-KNAW.  As always, please contact the PIs associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

Trematosphaeria pertusa genome release

1KFG is pleased to announce the public release of the Trematosphaeria pertusa CBS 122368 genome.   T. pertusa is classified in the family Trematosphaeriaceae (Ascomycota; Dothideomycetes; Pleosporales), and is the first sequenced genome from this family. It is commonly associated with aquatic freshwater habitats and decay of submerged wood.

Trematosphaeria pertusa was contributed to the 1KFG project by Pedro Crous and Manfred Binder at CBS-KNAW.  As always, please contact the PIs associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

Karstenula rhodostoma genome release

1KFG is pleased to announce the public release of the Karstenula rhodostoma CBS 690.94 genome.   K. rhodostoma is classified in the family Melanommataceae (Ascomycota; Dothideomycetes; Pleosporales) and is one of two sequenced genomes from this family. It is a saprotroph found growing on dry branches of alder buckthorn (Rhamnus frangula).

Karstenula rhodostoma was contributed to the 1KFG project by Pedro Crous and Manfred Binder at CBS-KNAW.  As always, please contact the PIs associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

Saccharata proteae genome release

1KFG is pleased to announce the public release of the Saccharata proteae CBS 121410 genome.   S. proteae is classified in the family Saccharataceae (Ascomycota; Dothideomycetes; Botryosphaeriales), is also known as Phyllachora proteae or Botryosphaeria proteae, and is the first sequenced genome from this family. It is commonly associated with leaf tip die-back and spots of Protea and Leucospermum plant species.

Saccharata proteae was contributed to the 1KFG project by Pedro Crous and Manfred Binder at CBS-KNAW.  As always, please contact the PIs associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

Sporormia fimetaria genome release

1KFG is pleased to announce the public release of the Sporormia fimetaria genome and annotation http://genome.jgi.doe.gov/Spofi1/  S. fimetaria  is classified in the family Sporormiaceae (Pleosporales; Dothideomycetes).  It is a  coprophilous fungus  isolated from dung of many mammals.

Sporormia fimetaria  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 Sporormiaceae.  As always, please contact the lead contact and PIs associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

Dissoconium aciculare genome release

1KFG is pleased to announce the public release of the Dissoconium aciculare genome and annotation http://genome.jgi.doe.gov/Daciculare.  D. aciculare  is classified in the family Dissoconiaceae (Dothideomycetes).  It is reported to be hyperparasitic on powdery mildew while some members of the Capnodiales order are plant pathogens or commensals.

Dissoconium aciculare  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 Dissoconiaceae.  As always, please contact the lead contact and PIs associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

Lophiostoma macrostomum genome release

1KFG is pleased to announce the public release of the Lophiostoma macrostomum CBS 122681 genome and annotation http://jgi.doe.gov/Lmacrostomum.  L. macrostomum  is classified in a new family Lophiostomataceae (Dothideomycetes).  It is associated with occur on submerged as well as terrestrial wood, but also occurs on leaf litter.

Lophiostoma macrostomum  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 Lophiostomataceae.  As always, please contact the lead contact and PIs associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

Pleomassaria siparia genome release

1KFG is pleased to announce the public release of the Pleomassaria siparia  genome http://genome.jgi.doe.gov/Plesi1/Plesi1.home.html.  Pleomassaria siparia (Pleomassariaceae) is a saprotrophic ascomycete in birch woodland and scrub in Europe and East Asia. Plant pathologists now monitor the presence of this species in periods of drought or following windbreaks more closely. Pleomassaria siparia seems to extend its range to the North where new disease agents of forest trees are registered increasingly. It has been suggested that the anamorph (Prosthemium betulinum) can endure lower temperatures and is used for hibernation. This fungus grows on broken twigs and branches of birch trees, but its role as a potential pathogen is not studied.

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 order Pleomassariaceae.  As always, please contact the lead contact and PIs associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

Rhizophagus irregularis (Glomus intraradices) genome release

The long road of sequencing a Glomus genome has borne the fruit of a recently released genome for Rhizophagus irregularis (Glomus intraradices) http://genome.jgi.doe.gov/Gloin1/Gloin1.home.html.  R. irregularis is an  arbuscular mycorrhizal fungus which forms symbiotic relationship with plant roots in important crop plants (Soybean, Rice, Maize, Poplar trees). The genome was sequenced through the JGI Mycorrhizal sequencing CSP.  It was contributed by collaborators at INRA, Oak Ridge National Lab,  and  Université de Toulouse. As always, please contact the lead contact and PIs associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

Also see “The long hard road to a completed Glomus intraradices genome” for some background in the previous description of the work that needed to be done.

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.