Jason Stajich UC Riverside Fungidb Supported by Sloan Foundation

FungiDB and 1000 Fungal genomes Jason Stajich UC Riverside FungiDB supported by Sloan Foundation

• Data coordinating center - Knight, Sogin, Meyer labs • Fungal microbiome support - Stajich Lab (Greg Gu, Steven Ahrendt) --> Scott Bates, Jon Leff Fierer Lab Fungal genome sequencing

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10-15 “Zygos” + Chytrids + Cryptomycota

400-500+ genomes of Fungi http://www.diark.org/diark/statistics http://1000.fungalgenomes.org Addressing the phylogenetic diversity: 1000 Fungal genomes project

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• Some Fungi are hard to get DNA extractions because grow slowly, melanin and complex polysaccharides are mucking up extraction columns,

• Some solutions included in protocols on 1000F genomes site

• JGI requires 34-86 ug of DNA and 10 ug (reduced from 21ug) of RNA for a project

• This appears to be biggest road block - we proposed about 50 species as our Tier I top priority but maybe only 30 were submitted

• Placing key person (M Binder) at CBS to work on Dothideomycetes FungiDB Strategy queries Genome Browser Data-mining Synteny

Functional Phylogenomic Genomics proﬁles Data

Annotation & Function Gene function curation tool

• Eurotiomycetes; Ascomycota ◦ Aspergillus clavatus ◦ Aspergillus flavus ◦ Aspergillus fumigatus strain Af293 ◦ Aspergillus nidulans strain A4 FungiDB 2.0 ◦ Aspergillus niger ◦ Aspergillus terreus ◦ Coccidoidies immitis strain RS ◦ Coccidoidies immitis strain H538.4 • Sordariomycetes; Ascomyocta ◦ Fusarium oxysporum f. sp. lycopersici • 31 genomes - 25 Fungi and 6 Oomycetes ◦ Fusarium graminearum ◦ Gibberella moniliformis (Fusarium verticillioides) ◦ Magnaporthea oryzae • RNA-Seq for 6 species, Microarray for 2 sp, KEGG, EC, ◦ Neurospora crassa strain OR74A ◦ Neurospora tetrasperma and GO annotations for several species ◦ Neurospora discreta ◦ Sordaria macrospora • Taphrinomycotina; Ascomyocta • Ortholog tables with OrthoMCL ◦ Schizosaccharomyces pombe • Saccharomycotina; Ascomyocta ◦ Candida albicans ◦ Saccharomyces cerevisiae • Gene function predictions from InterPro • Basidiomycota ◦ Cryptococcus neoformans var. grubii) strain H99 ◦ Cryptococcus neoformans var. neoformans) strain JEC21 ◦ Cryptococcus neoformans var. neoformans) strain B3501 • Release 2.1 (early Nov) will have 10 additional species ◦ Cryptococcus gattii strain WM276 (including Coprinopsis, Ustilago, Histoplasma, ◦ Cryptococcus gattii strain R265 ◦ Tremella mesenterica Batrachochytrium, Rhizopus) • Oomycetes; Stramenopiles ◦ Phytophthora capsici ◦ Phytophthora infestans ◦ Phytophthora ramorum ◦ Phytophthora sojae ◦ Pythium ultimatum ◦ Hyaloperonospora arabidopsidis

Combining queries

• Results from one query combined with a second one.

• Can be intersection, union, or left or right overlaps

Future directions

• How will more Fungal genomes help amplicon-based studies?

• For shotgun metagenomic plans in fungal communities

• Do we need to focus on more low-coverage genome assemblies for Fungi to ﬁll in the gaps better? Acknowledgements

Marine Biological Lab - VAMPS Stajich lab @UCR lab Mitch Sogin Peng Liu Sue Huse Brad Cavinder Anna Shipunova Anthony Amend Soﬁa Robb Univ of Colorado at Boulder - QIIME Keith Seifert Steven Ahrendt Rob Knight Divya Sain Sco Bates Yizhou Wang Gail Ackerman Yi Zhou Jesse Stombaugh

FungiDB Programmers Argonne Naonal Lab - MG-RAST Daniel Borcherding Folker Meyer Raghu Ramamurthy Daniel Braithwaite Edward Liaw Travis Harrison Greg Gu Kevin Keegan Andreas Wilke EuPathDB @UPenn & UGA David Roos, Jessica Kissinger, Chris Stoeckert Steve Fischer - John Brestelli Brian Brunk - Debbie Pinney Wei Li - Sufen Hu