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 * ** 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 !"#$%&'%()*+#+,- !"#$%&'%()*+#+,- .%#$'/+%()*+#+,- .%#$'/+%()*+#+,- 01"%2%()*+#+,- 01"%2%()*+#+,- D+%E8%,,%()*+#+,- D+%E8%,,%()*+#+,- F+G'G%()*%2&4- 3&*+"#4+-,+/',- F+G'G%()*%2&4- 3&*+"#4+-,+/',- 547%187+&'%()*+#+,- 547%187+&'%()*+#+,- 5+*4&%"%()*+#+,- 5+*4&%"%()*+#+,- 5+%2%()*+#+,- 5+%2%()*+#+,- 5'*$'&%()*+#+,- 5'*$'&%()*+#+,- 6"7'8'%()*+#+,- 6"7'8'%()*+#+,- F+G'G%()*+#+,- F+G'G%()*+#+,- H4**$4"%()*%2&4- H%"/4"'%()*+#+,- H4**$4"%()*%2&4- H%"/4"'%()*+#+,- H4**$4"%()*+#+,- H4**$4"%()*+#+,- I+%8+*#%()*+#+,- I+%8+*#%()*+#+,- J4K$"'&%()*%2&4- F&+1(%*),2/'%()*+#+,- J4K$"'&%()*%2&4- F&+1(%*),2/'%()*+#+,- H*$'G%,4**$4"%()*+#+,- H*$'G%,4**$4"%()*+#+,- J4K$"'&%()*+#+,- J4K$"'&%()*+#+,- M,284E'&%()*%2&4- 0L%74,'/'%()*+#+,- M,284E'&%()*%2&4- 0L%74,'/'%()*+#+,- M,284E'&%()*+#+,- M,284E'&%()*+#+,- !E4"'*%,287%()*+#+,- !E4"'*%,287%()*+#+,- !#"4*2+88%()*+#+,- !#"4*2+88%()*+#+,- N84,,'*18%()*+#+,- N84,,'*18%()*+#+,- F1**'&'%()*%2&4- N")K#%()*%*%84*%()*+#+,- F1**'&'%()*%2&4- N")K#%()*%*%84*%()*+#+,- N),#%74,'/'%()*+#+,- N),#%74,'/'%()*+#+,- O'*"%7%#")%()*+#+,- O'*"%7%#")%()*+#+,- O'L'%()*+#+,- O'L'%()*+#+,- F1**'&'%()*+#+,- F1**'&'%()*+#+,- !E4"'*%()*+#+,- !E4"'*%()*%2&4- !E4"'*%()*+#+,- .4*")()*+#+,- !E4"'*%()*%2&4- .4*")()*+#+,- J"+(+88%()*+#+,- J"+(+88%()*+#+,- D8%(+"%()*+#+,- 0&#%(%K$#$%"%()*%2&4- D8%(+"%()*+#+,- P'*Q+88%()*%2&4- 0&#%(%K$#$%"%()*%2&4- O%"2+"+88%()*%2&4- P'*Q+88%()*%2&4- 04"8)-.'T+"E'&E- O1*%"%()*%2&4- O%"2+"+88%()*%2&4- R%%K4E%()*%2&4- 04"8)-.'T+"E'&E- O1*%"%()*%2&4- 5'&+4E+,- R%%K4E%()*%2&4- I+%*488'(4,2E%()*+#+,- 5'&+4E+,- S84,#%*84/'%()*+#+,- I+%*488'(4,2E%()*+#+,- N$)#"'/'%()*+#+,- S84,#%*84/'%()*+#+,- O%&%78+K$4"'/%()*+#+,- N$)#"'/'%()*+#+,- O%&%78+K$4"'/%()*+#+,- 9- <9- >9- @9- B9- ;99- ;<9- 9:- ;9:- <9:- =9:- >9:- ?9:- @9:- A9:- B9:- C9:- ;99:- Blue = completed or in progress, Red= proposed for Tier One sampling, Green = remaining unsampled families Numbers or Percent of Families in each clade and their current or proposed genome sampling What’s working? What’s not? • 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.