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.

Species Phylum/Subphylum Class Order Family
Aplosporella prunicola CBS 121.167 v1.0 Ascomycota Dothideomycetes Botryosphaeriales Botryosphaeriaceae
Botryosphaeria dothidea Ascomycota Dothideomycetes Botryosphaeriales Botryosphaeriaceae
Cucurbitaria berberidis CBS 394.84 v1.0 Ascomycota Dothideomycetes Pleosporales Cucurbitariaceae
Didymella exigua CBS 183.55 Ascomycota Dothideomycetes Pleosporales Didymellaceae
Lentithecium fluviatile v1.0 Ascomycota Dothideomycetes Pleosporales incertae sedis
Myriangium duriaei CBS 260.36 v1.0 Ascomycota Dothideomycetes Myriangiales Myriangiaceae
Polychaeton citri CBS 116435 Ascomycota Dothideomycetes Capnodiales Capnodiaceae
Monascus ruber NRRL 1597 v1.0 Ascomycota Eurotiomycetes Incertae sedis Monascaceae
Symbiotaphrina kochii v1.0 Ascomycota Incertae sedis Incertae sedis Incertae sedis
Ascobolus immersus RN42 v1.0 Ascomycota Pezizomycetes Pezizales Ascobolaceae
Apiospora montagnei NRRL 25634 v1.0 Ascomycota Sordariomycetes Incertae sedis Apiosporaceae
Melanconium sp. NRRL 54901 Ascomycota Sordariomycetes Dothideales Melanconidaceae
Suillus brevipes Basidiomycota Agaricomycetes Boletales Suillaceae
Mixia osmundae IAM 14324 Basidiomycota Mixomycetes Mixiales Mixiaceae
Catenaria anguillulae PL171 Blastocladiomycota Blastocladiomycetes Blastocladiales Catenariaceae
Gonapodya prolifera v1.0 Chytridiomycota Monoblepharidomycetes Monoblepharidales Gonapodyaceae
Conidiobolus coronatus NRRL 28638 Entomophthoromycotina Incertae sedis Entomophthorales Ancylistaceae
Coemansia reversa NRRL 1564 Kickxellomycotina Incertae sedis Kickxellales Kickxellaceae
Umbelopsis ramanniana AG # v1.0 Mucoromycotina Incertae sedis Mucorales Mucoraceae

5 thoughts on “Update on 1KFG”

  1. Dear Joey and all colleagues of the 1KFG project,

    thanks for the update. Really great job. I’m very much amazed about the progress and the exciting news about the completion of the five genomes from the basal clades. May I ask you about the nvovlevment of the nuclearid Fonticula alba Worley et al. (ATCC® 38817™), which is a type strain and available from ATCC. Fonticula alba is a representative of the Nucleariidae, which is a monophyletic sister group to the core fungi, all together buidling up the Holomycota or Nucletmycea. Involvement of Fonticula alba would largely enrich our understanding on the evolution of the fungi apart from protists as separate phylogenetic branch. I’d like to nominate this strain at jgi.doe.gov/fungi. Please feel free to contact me.

    1. Kerstin,

      Hello there. Thanks for the email. I will forward your email to Igor Grigoriev at JGI and see if he would be open to the idea. I am in Amsterdam right now, but I’ll be back in touch soon.

      Cheers,

      joey

      1. Hello Joey,

        thanks for your reply and taking care about my idea to involve Fonticula alba. I’m looking forward to repsonse from Igor Grigoriev.
        I’m also just back from CBS in the Netherlands, where we organized a workshop on zygomycetes (www.zygomycota.eu) preceding the CBS spring symposium in Amsterdam, which you are attending. Unfortunately, due to family obligations (my 2nd son is just 7 months old) I was not able to stay to meet you there. But will be pleased to hear about you next time.

        Have a pleasant stay in Amsterdam…with my best wishes,
        Kerstin

  2. Permission to use the data of the newly released genomes

    I’m very much amazed about the progress and I’m happy to participate in any work. identification of taxa which are worth to be sequenced and to provide DNA/RNA samples as well as expertise fro genomic analyses towards publication.

    We like to include five of the latest released genomes in our comparative phylogenomic analyses. These are:
    Umbelopsis ramanniana (Mucoromycotina, the most basal lineage): http://genome.jgi.doe.gov/Umbra1/Umbra1.home.html
    Coemansia reversa (Kickxellomycotina): http://genome.jgi.doe.gov/Coere1/Coere1.home.html
    Conidiobolus coronatus (Entomophthoromycota): http://genome.jgi.doe.gov/Conco1/Conco1.home.html
    Gonapodya prolifera (Monoblepharidomycota): http://genome.jgi.doe.gov/Ganpr1/Ganpr1.home.html
    Catenaria anguillulae (Blastocladiomycota): http://genome.jgi.doe.gov/Catan1/Catan1.home.html

    Where can we get permission from to do so?
    We are happy to include the people responsible as coauthors or to announce the project and people involved among the acknowledgement according to the rule “the more we are the more fun we have”.
    Could you please give me advice how to solve/organize this issue about our contribution to the scientifc community of the 1 KFG project?

    1. Hi – we need to go through the various PIs for these genomes before it can be agreed upon that these data can be used prior to their publication. There is an effort towards an early diverging fungal lineages manuscript as part of the intended work by most of those who proposed these genomes. Joey, Jason, and JGI will or should soon be in touch on how these projects are emerging and how we can help coordinate the joint effort.

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