Fungi DB at Keystone meeting
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Fungi DB at Keystone meeting

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FungiDB presentation at the 2012 Fungal Pathogens Keystone meeting

FungiDB presentation at the 2012 Fungal Pathogens Keystone meeting

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Fungi DB at Keystone meeting Fungi DB at Keystone meeting Presentation Transcript

  • F ngiD Fungal genomics resources FungiDBJason StajichDept of Plant Pathology and MicrobiologyUniversity of California, Riversidehttp://lab.stajich.org/ http://fungalgenomes.org/blog http://fungidb.orgtwitter: @fungidb @stajichlab @hyphaltip @fungalgenomes
  • Cryptococcus oligo array• Wash U is no longer printing oligo arrays.• Texas A&M University can print the array slides at the cost of ~$40/slide ONLY if there is a pre-order of 100-200 slides.• The cost for performing microarray experiments will be available soon.• Please contact Xiaorong Lin at xlin@bio.tamu.edu if you are interested in using/ordering Crypto oligo slides.
  • Awash in Fungal Genomes• Mid-2011: Genomes from 150+ species sequenced and ~400 more in progress/pipeline• Several multi-strain resequencing projects (Neurospora - Ellison PNAS 2011), Saccharomyces (Liti Nature 2009), Coccidoides (Neafsey Genome Res 2010) and many in progress/proposed.• Many of sequenced genomes were focused around plant, animal pathogens, and some specific evolutionary questions.• Now are starting to fill out the tree more to capture the diversity of kingdom and also for studies of molecular evolution among many related species.• Also efforts targeting specific questions - pathogens and their relatives; wood rotting fungi; flagellated and non-flagellated forms; extremophiles; comparison of growth forms (e.g. yeast forms from phylogenetically very different species)
  • Need to cover more of the phylogenetic diversity: 1000 Fungal genomes project - http://1000.fungalgenomes.org !"#$%&%()*+#+,- !"#$%&%()*+#+,- .%#$/+%()*+#+,- .%#$/+%()*+#+,- 01"%2%()*+#+,- 01"%2%()*+#+,- D+%E8%,,%()*+#+,- D+%E8%,,%()*+#+,- F+GG%()*%2&4- 3&*+"#4+-,+/,- F+GG%()*%2&4- 3&*+"#4+-,+/,- 547%187+&%()*+#+,- 547%187+&%()*+#+,- 5+*4&%"%()*+#+,- 5+*4&%"%()*+#+,- 5+%2%()*+#+,- 5+%2%()*+#+,- 5*$&%()*+#+,- 5*$&%()*+#+,- 6"78%()*+#+,- 6"78%()*+#+,- F+GG%()*+#+,- F+GG%()*+#+,- 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$"&%()*+#+,- M,284E&%()*%2&4- 0L%74,/%()*+#+,- M,284E&%()*%2&4- 0L%74,/%()*+#+,- M,284E&%()*+#+,- M,284E&%()*+#+,- !E4"*%,287%()*+#+,- !E4"*%,287%()*+#+,- !#"4*2+88%()*+#+,- !#"4*2+88%()*+#+,- N84,,*18%()*+#+,- N84,,*18%()*+#+,- F1**&%()*%2&4- N")K#%()*%*%84*%()*+#+,- F1**&%()*%2&4- N")K#%()*%*%84*%()*+#+,- N),#%74,/%()*+#+,- N),#%74,/%()*+#+,- O*"%7%#")%()*+#+,- O*"%7%#")%()*+#+,- OL%()*+#+,- OL%()*+#+,- F1**&%()*+#+,- F1**&%()*+#+,- !E4"*%()*+#+,- !E4"*%()*%2&4- !E4"*%()*+#+,- .4*")()*+#+,- !E4"*%()*%2&4- .4*")()*+#+,- J"+(+88%()*+#+,- J"+(+88%()*+#+,- D8%(+"%()*+#+,- 0&#%(%K$#$%"%()*%2&4- D8%(+"%()*+#+,- P*Q+88%()*%2&4- 0&#%(%K$#$%"%()*%2&4- O%"2+"+88%()*%2&4- P*Q+88%()*%2&4- 04"8)-.T+"E&E- O1*%"%()*%2&4- O%"2+"+88%()*%2&4- R%%K4E%()*%2&4- 04"8)-.T+"E&E- O1*%"%()*%2&4- 5&+4E+,- R%%K4E%()*%2&4- I+%*488(4,2E%()*+#+,- S84,#%*84/%()*+#+,- 5&+4E+,- I+%*488(4,2E%()*+#+,- N$)#"/%()*+#+,- 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
  • FungiDB Strategy queries Genome Browser Data-mining SyntenyFunctional PhylogenomicGenomics profiles Data Annotation & Function Gene function curation tool
  • 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)
  • 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
  • Querying with FungiDB and the Strategies Web Development Kit (WDK)
  • Query matrix of types of strategies to use for genes
  • 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
  • Query for RNA-Seq
  • Sort by fold change
  • http://s.fungidb.org/Cneo_Nrg1KO_1Sort by fold change
  • http://s.fungidb.org/Cneo_Nrg1KO_1Sort by fold change
  • Query for ESTs
  • Ortholog comparative, & synteny analyses
  • Gbrowse to examine Synteny and shared gene structure
  • http://s.fungidb.org/wzIYfQ
  • http://s.fungidb.org/wzIYfQ
  • Examine RNA-Seq support for the exons
  • Querying for phylogenetic profilesWhat are Coccidioides genes that are Cocci specific andhave a signal peptide domain indicating they are likelysecreted?
  • Query for Phylogenetic profile
  • Choose only Coccidioides orthologs, not found in Bacteria,Animals, etc
  • Find those Cocci genes which are only found inCoccidioides
  • Add constraint that they must also have Signal Peptide domain
  • The complete list, can scroll to see what are their functions http://bit.ly/fdb_cocciSecreted
  • Annotating Loci, adding gene names and publication links
  • Can add comments by clicking here
  • Comments are structured
  • 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
  • FungiDB TeamDaniel 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 TripathyTodd HarrisF ngiD Fungal genomics resources http://alpha.fungidb.org MoBeDAC Microbiome of the Built Environment Data Analysis Core http://mobedac.org/