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 ~$40/slide ONLY if there is a pre-order of 100-200
slides.
• The cost for performing microarray experiments will be
available soon.
• Please contact Xiaorong Lin at xlin@bio.tamu.edu if you are
interested in using/ordering Crypto oligo slides.
3. Awash in Fungal Genomes
• Mid-2011: Genomes from 150+ species sequenced and ~400 more in progress/pipeline
• Several multi-strain resequencing projects (Neurospora - Ellison PNAS 2011),
Saccharomyces (Liti Nature 2009), Coccidoides (Neafsey Genome Res 2010) and many in
progress/proposed.
• Many of sequenced genomes were focused around plant, animal pathogens, and some
specific evolutionary questions.
• Now are starting to fill out the tree more to capture the diversity of kingdom and also for
studies of molecular evolution among many related species.
• Also efforts targeting specific questions - pathogens and their relatives; wood rotting fungi;
flagellated and non-flagellated forms; extremophiles; comparison of growth forms (e.g.
yeast forms from phylogenetically very different species)
4. Need to cover more of the phylogenetic diversity: 1000
Fungal genomes project - http://1000.fungalgenomes.org
!"#$%&'%()*+#+,- !"#$%&'%()*+#+,-
.%#$'/+%()*+#+,- .%#$'/+%()*+#+,-
01"%2%()*+#+,- 01"%2%()*+#+,-
D+%E8%,,%()*+#+,- D+%E8%,,%()*+#+,-
F+G'G%()*%2&4- 3&*+"#4+-,+/',- F+G'G%()*%2&4- 3&*+"#4+-,+/',-
547%187+&'%()*+#+,- 547%187+&'%()*+#+,-
5+*4&%"%()*+#+,- 5+*4&%"%()*+#+,-
5+%2%()*+#+,- 5+%2%()*+#+,-
5'*$'&%()*+#+,- 5'*$'&%()*+#+,-
6"7'8'%()*+#+,- 6"7'8'%()*+#+,-
F+G'G%()*+#+,- F+G'G%()*+#+,-
H%"/4"'%()*+#+,- H%"/4"'%()*+#+,-
H4**$4"%()*%2&4- H4**$4"%()*+#+,-
H4**$4"%()*%2&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$"'&%()*+#+,-
M,284E'&%()*%2&4- 0L%74,'/'%()*+#+,- M,284E'&%()*%2&4- 0L%74,'/'%()*+#+,-
M,284E'&%()*+#+,- M,284E'&%()*+#+,-
!E4"'*%,287%()*+#+,- !E4"'*%,287%()*+#+,-
!#"4*2+88%()*+#+,- !#"4*2+88%()*+#+,-
N84,,'*18%()*+#+,- N84,,'*18%()*+#+,-
F1**'&'%()*%2&4- N")K#%()*%*%84*%()*+#+,- F1**'&'%()*%2&4- N")K#%()*%*%84*%()*+#+,-
N),#%74,'/'%()*+#+,- N),#%74,'/'%()*+#+,-
O'*"%7%#")%()*+#+,- O'*"%7%#")%()*+#+,-
O'L'%()*+#+,-
O'L'%()*+#+,-
F1**'&'%()*+#+,-
F1**'&'%()*+#+,-
!E4"'*%()*+#+,-
!E4"'*%()*%2&4- !E4"'*%()*+#+,-
.4*")()*+#+,- !E4"'*%()*%2&4-
.4*")()*+#+,-
J"+(+88%()*+#+,-
J"+(+88%()*+#+,-
D8%(+"%()*+#+,-
0&#%(%K$#$%"%()*%2&4-
D8%(+"%()*+#+,-
P'*Q+88%()*%2&4- 0&#%(%K$#$%"%()*%2&4-
O%"2+"+88%()*%2&4- P'*Q+88%()*%2&4-
04"8)-.'T+"E'&E- O1*%"%()*%2&4- O%"2+"+88%()*%2&4-
R%%K4E%()*%2&4- 04"8)-.'T+"E'&E- O1*%"%()*%2&4-
5'&+4E+,- R%%K4E%()*%2&4-
I+%*488'(4,2E%()*+#+,-
S84,#%*84/'%()*+#+,-
5'&+4E+,- I+%*488'(4,2E%()*+#+,-
N$)#"'/'%()*+#+,- 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
5. FungiDB
Strategy queries Genome Browser
Data-mining Synteny
Functional Phylogenomic
Genomics profiles
Data
Annotation &
Function Gene function curation tool
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
52. Querying for phylogenetic profiles
What are Coccidioides genes that are Cocci specific and
have a signal peptide domain indicating they are likely
secreted?
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/