FungiDB presentation at the 2012 Fungal Pathogens Keystone meeting

1. F ngiD Fungal genomics resources
FungiDB
Jason Stajich
Dept of Plant Pathology and Microbiology
University of California, Riverside
http://lab.stajich.org/ http://fungalgenomes.org/blog http://fungidb.org
twitter: @fungidb @stajichlab @hyphaltip @fungalgenomes

2. Cryptococcus oligo array
• Wash U is no longer printing oligo arrays.
• Texas A&M University can print the array slides at the cost
of ~$40/slide ONLY if there is a pre-order of 100-200
slides.
• The cost for performing microarray experiments will be
available soon.
• Please contact Xiaorong Lin at xlin@bio.tamu.edu if you are
interested in using/ordering Crypto oligo slides.

3. Awash in Fungal Genomes
• Mid-2011: Genomes from 150+ species sequenced and ~400 more in progress/pipeline
• Several multi-strain resequencing projects (Neurospora - Ellison PNAS 2011),
Saccharomyces (Liti Nature 2009), Coccidoides (Neafsey Genome Res 2010) and many in
progress/proposed.
• Many of sequenced genomes were focused around plant, animal pathogens, and some
specific evolutionary questions.
• Now are starting to fill out the tree more to capture the diversity of kingdom and also for
studies of molecular evolution among many related species.
• Also efforts targeting specific questions - pathogens and their relatives; wood rotting fungi;
flagellated and non-flagellated forms; extremophiles; comparison of growth forms (e.g.
yeast forms from phylogenetically very different species)

4. Need to cover more of the phylogenetic diversity: 1000
Fungal genomes project - http://1000.fungalgenomes.org
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5. FungiDB
Strategy queries Genome Browser
Data-mining Synteny
Functional Phylogenomic
Genomics profiles
Data
Annotation &
Function Gene function curation tool

6. Release 1.0 of FungiDB [March 2011]
The following 18 genomes of 17 species are now available via FungiDB:
• Eurotiomycetes; Ascomycota
◦ Aspergillus clavatus
◦ Aspergillus flavus
◦ Aspergillus fumigatus strain Af293
◦ Aspergillus niger
◦ Aspergillus nidulans (Emericella nidulans) strain A4
◦ Aspergillus terreus
◦ Coccidoidies immitis strain RS http://beta.fungidb.org
◦ Coccidoidies immitis strain H538.4
• Sordariomycetes; Ascomyocta
◦ Fusarium oxysporum f. sp. lycopersici
◦ Gibberella zeae (Fusarium graminearum)
◦ Gibberella moniliformis (Fusarium verticillioides)
◦ Magnaporthea oryzae
◦ Neurospora crassa strain OR74A
• Saccharomycotina; Ascomyocta
◦ Candida albicans
◦ Saccharomyces cerevisiae
• Basidiomycota
◦ Filobasidiella neoformans (Cryptococcus neoformans var. grubii) strain H99
◦ Puccinia graminis
• Mucormycotina ("Zygomycota")
◦ Rhizopus oryzae (Rhizopus delemar)

7. Release 2.0 alpha [Jan 2012] - http://alpha.fungidb.org
• 5 Cryptococcus genomes - C.neo JEC21, B3501, H99; C.gattii WM276, R265
• 1 RNA-Seq dataset (O’Meara, Alspaugh) Nrg1
• Tremella mesenterica
• Neurospora crassa
• Curated GO
• 1 RNA-Seq (Stajich lab) hyphal growth timepoints
• Saccharomyces cerevisiae
• Curated GO, Yeast2Hybrid interactions

8. Querying with FungiDB and
the Strategies Web
Development Kit (WDK)

10. Query matrix of types of strategies to use for genes

11. A strategy for drug targets - http://bit.ly/crypto0
C.neoformans genes with
- no hits in other eukaryotes
(excepting fungi), bacteria
- has S.cerevisiae orthologs
that have EC terms
OR orthologs in other fungi
with GO metabolic terms
associated

12. Query for RNA-Seq

18. Sort by fold change

19. http://s.fungidb.org/Cneo_Nrg1KO_1
Sort by fold change

20. http://s.fungidb.org/Cneo_Nrg1KO_1
Sort by fold change

26. Query for ESTs

32. Ortholog comparative, & synteny analyses

44. Gbrowse to examine Synteny and shared
gene structure

45. http://s.fungidb.org/wzIYfQ

46. http://s.fungidb.org/wzIYfQ

47. Examine RNA-Seq support for the exons

52. Querying for phylogenetic profiles
What are Coccidioides genes that are Cocci specific and
have a signal peptide domain indicating they are likely
secreted?

53. Query for Phylogenetic profile

54. Choose only Coccidioides orthologs, not found in Bacteria,
Animals, etc

55. Find those Cocci genes which are only found in
Coccidioides

56. Add constraint that they must also have Signal Peptide domain

57. The complete list, can scroll to see what are their functions
http://bit.ly/fdb_cocciSecreted

58. Annotating Loci, adding gene names and publication links

59. Can add comments by clicking here

60. Comments are structured

64. Take homes
• Use help@fungidb.org or Contact Us link for help queries, but also
• Propose datasets that should be included (key microarray, RNA-Seq, resequencing/SNP,
ChIP-Seq, proteomic datasets, etc)
• Send us an email when you publish or release dataset if you think it should be included.
Even better, we can load it before and make it available in a next release.
• Suggest additional genomes to be covered
• Will be soliciting members of an advisory board to help choose datasets

65. FungiDB Team
Daniel Borcherding David Roos (U Penn)
Raghu Ramamurthy
EuPathDB @UPenn & UGA
Steve Fischer - John Brestelli VBI/Oregon State
Brian Brunk - Debbie Pinney Brett Tyler
Wei Li - Sufan Hu Sucheta Tripathy
Todd Harris
F ngiD Fungal genomics resources
http://alpha.fungidb.org
MoBeDAC
Microbiome of the Built Environment Data Analysis Core
http://mobedac.org/