Category Archives: Announcements

1KFG@Asilomar

See many of you at Fungal Genetics@Asilomar next week or the JGI user meeting the following week. We are formulating some action plans for more sampling and also preparing a first dataset of 300 genomes for analysis and release. Will prepare update notes from the meetings and the current and future plans for sequencing through the JGI CSP and affiliated projects.

Protocols for fruiting body sampling

Recently 1KFG has begun exploring using fresh fruiting body sampled tissue to obtain DNA rather than requiring pure culture-based samples only. This can be problematic for a variety of reasons including the heterokaryon nature of fruiting tissue, possible contamination with bacteria, insects, or other fungi, and the limitations to return to the exact sample for additional sampling since it will either be destroyed in the sampling or only have a small amount left for a voucher specimen.

All of that noted, we still can only obtain samples of some fungi as fruiting mushrooms. The INRA-Nancy group have applied this approach of sampling fruiting tissues to several mushrooms including the published Tuber genome. So please see the links for  DNA extraction and extracting DNA from fruiting bodies.

If you are interested in contributing samples to the sequencing especially after making collections on a foray, please take note of the guidelines above and see the JGI 1000 Fungal Genomes list to identify where there are missing taxa which could be contributed. Simply fill out a nomination on the page for a species you can or have collected and it will be evaluated and if it passes the requirements, confirmed for nomination.

Grad Students & Postdocs, please also see how you can propose a species for sequencing through the Grad student / Postdoc challenge which will include these fruiting body samples.

Dendrothele bispora genome release

1KFG is pleased to announce the public release of the Dendrothele bispora genome.   D. bispora is classified in the family Marasmiaceae (Agaricales; Agaricomycetes) and is an example of a crust fungus that is closely related to typical mushroom-forming fungi.  As such, it represents an important sampling point in understanding evolutionary transitions among major fungal morphologies.

Dendrothele bispora was contributed to the 1KFG project by David Hibbett and Laszlo Nagy of Clark University, Massachusetts, USA.  As always, please contact the PIs associated with unpublished 1KFG genomes for permission prior to the use of any data in publications.

Dothidotthia symphoricarpi genome release

1KFG is pleased to announce the public release of the Dothidotthia symphoricarpi genome.   D. symphoricarpi is classified in the family Dothidotthiaceae (Pleosporales; Dothideomycetes) and was isolated from branches of Symphoricarpos occidentalis (snowberry).

Dothidotthia symphoricarpi 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 Dothidotthiaceae.  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.

Update on 1KFG Genome Releases

It has been a busy Fall term and there were several genomes that were completed but slipped through our announcements.  So here is a quick update on some genomes that were released recently by JGI and sequenced as part of 1KFG.

Dothideomycetes: Lophiostoma macrostomum (Lophiostomataceae, Pleosporales), Piedraia hortae (Piedraiaceae, incertae sedis) contributed by Manfred Binder and Pedro Crous at CBS Netherlands.

Eurotiomycetes: Monascus purpureus (Monascaceae, incertae sedis), Gymnascella citrina, and Gymnascella aurantica (Gymnoascaceae, Onygenales) contributed by Kerry O’Donnell and Stacy Sink at USDA Peoria.

Sordariomycetes: Anthostoma avocetta (Diatrypaceae, Xylariales) contributed by Kerry O’Donnell and Stacy Sink at USDA Peoria.

Pezizomycetes: Wilcoxina mikolae (Pyronemataceae, Pezizales) contributed by Tom Bruns and Sarah Branco at UC Berkeley.

Xylonomycetes: Xylona heveae (Xylonomycetaceae, Xylonomycetales) contributed by David Hibbett and Romina Gazis at Clark University.

Mucoromycotina: Backusella circina (Thamnidiaceae, Mucorales) contributed by Andrii Grygansky at Duke University

If you are interested in contributing species to the 1KFG project, please visit the nomination page http://genome.jgi.doe.gov/pages/fungi-1000-projects.jsf.  The project is open to worldwide participation and all researchers are welcome.  The time to contribute is now!!

Zopfia rhizophila genome release

1KFG is pleased to announce the public release of the Zopfia rhizophila genome http://genome.jgi.doe.gov/Zoprh1/Zoprh1.home.html.  Zopfia rhizophila is classified in the family Zopfiaceae (Dothideomycetes), but it has unknown ordinal affiliation.  It is associated with roots and rhizomes of asparagus and causes root rots in weakened and wounded plants.

Zopfia rhizophila 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 Zopfiaceae.  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.

Rhizopus microsporus genome release

1KFG is pleased to announce the public release of the Rhizopus microsporus genome http://genome.jgi.doe.gov/Rhimi1_1/Rhimi1_1.home.html.  Rhizopus microsporus is a soil-inhabiting member of the Mucorales (Zygomycota).  It can cause mucoromycosis in immunocompromised humans and seedling blight in rice.  It harbors bacterial endosymbionts, including beta-protoebacteria Burkholderia rhizoxinica and B. endofungorum, which provide the fungus with potent toxins and control its asexual reproduction.  These attributes make R. microsporus into an attractive system to study fungal interactions with bacteria and to decipher reproductive biology of Mucorales.

Rhizopus microsporus was contributed to the 1KFG project by Teresa Pawlowska and Stephen Mondo of Cornell University.  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.

Patellaria atrata genome release

1KFG is pleased to announce the public release of the Patellaria atrata genome http://genome.jgi.doe.gov/Patat1/Patat1.home.html.  Patellaria atrata (Patellariales, Patellariaceae) is a saprotrophic fungus that colonizes preferentially exposed phloem fibers of wood and the decay mode resembles that of a white rot.  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 Patellariales.  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.

Lichtheimia hyalospora v1.0 genome release

1KFG is pleased to announce the public release of the Lichtheimia hyalospora genome http://genome.jgi.doe.gov/Lichy1/Lichy1.home.html.  The genus Lichtheimia belongs to the family Lichtheimiaceae (Mucorales, Mucoromycotina) of the zygomycetous fungi.  Mucorales includes numerous well-known fungi such as Rhizopus and Phycomyces, but L. hyalospora represents the first genomic sequence of the Lichtheimiaceae.  Lichtheimia is a ubiquitous thermotolerant soil zygomycete, which grows between 200C and 550C, with rapid mycelial growth occurring between 37 and 420C. Its thermotolerance enables the fungus to survive the digestive tract of mammals and it is often found in animal intestinal contents and feces. It can cause ‘self-heating’ of animal feed stored under moist conditions.  It was contributed to the 1KFG project by Andrii Gryganski of Duke University and Jason Stajich of University of California at Riverside.  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.