The US Department of Energy Joint Genome Institute leads the world in sequencing of fungal genomes and contributes 40% of genome projects worldwide. JGI web-based fungal genomics portal MycoCosm integrates fungal genomics data and analytical tools in one place to provide access to over 100 fungal genomes sequenced at JGI and elsewhere. Users may explore fungal genomes in the context of both comparative genomics and genome-centric analysis. MycoCosm promotes user community participation in data submission, annotation and analysis, and has over 4500 unique visitors/month or 35000+ visitors/year.

1. Genomics data integration,
analysis, and curation using
MycoCosm
Robert Riley
Igor Shabalov
Igor Grigoriev
3 April 2012

2. US DOE Joint Genome Institute
Mission: Genomics user facility in
support of DOE missions in:
bioenergy biogeochemistry
carbon cycling
Programs: Fungal, Plant,
Microbial, & Metagomics
Genome sequencing
using latest technology
Illumina HiSeq2000 PacBio Example: JGI fungal sequencing

3. Fungi in bioenergy
degrade
lignin & White rot
cellulose Phanerochaete
chrysosporium
Biofuel
Lignocellulose Brown rot
Postia precursors
degrade
cellulose placenta

4. Data integration: MycoCosm
Comparative View
MycoCosm
jgi.doe.gov/fungi
120+ genomes;
5K visitors/month Genome-Centric View

5. Data Integration: External Links

6. From GenBank to MycoCosm

7. Curation: user annotation
Users may
create improved
gene models
Your name here!
7

8. Curated genes
1
100
10
10000
1000
Hebcy1
Hypsu1
Treme1
Agabi_varbis…
Paxin1
Phaca1
Plicr1
Jaaar1
Phlgi1
Bjead1_1
Botbo1
Phlbr1
Organism
Gansp1
Wolco1
Conpu1
Cersu1
PleosPC9_1
Gymlu1
SerlaS7_9_2
Aurde1
Punst1
Glotr1_1
Fomme1
PleosPC15_2
Pospl1
Fompi1
Trave1
Statistics on manual curation of gene models
by increasing number of curations
Schco2
Stehi1
Hetan2
Phchr1
Curation: user annotation
Lacbi2
Dacsp1
Agabi_varbur…
SerlaS7_3_2
Dicsq1
5
0
10
15
20
25
30
Curators
8

9. Curation: user annotation
Example: user finds a more sensible gene model
Promote to
gene catalog
Compare
to ESTs
Transcript page
Protein page
Cluster viewer
9

10. Analysis: genome-centric view
GC content
Sequence
conservation
Gene
catalog
ESTs
PFAM domains
BLAST hits
Alternate gene
models
10

11. Analysis: comparative view
11

12. Analysis: evolution of
lignocellulose degradation
CAZy CAZy and lignin-degrading genes
genes
Oxidoreductase
genes
Eastwood et al. Science 2011 Riley et al. in prep

13. Summary
MycoCosm
• Integrates functional and comparative
genomic data and analytical tools for
energy and environment fungi
• Offers tools for community annotation,
data repository, and manual curation
• Facilitates comparative genome
analysis

14. Acknowledgments
Igor V. Grigoriev Robert Otillar
Henrik Nordberg Alex Poliakov
Igor Shabalov Igor Ratnere
Andrea Aerts Frank Korzeniewski
Mike Cantor Xueling Zhao
David Goodstein Tatyana Smirnova
Alan Kuo Daniel Rokhsar
Simon Minovitsky Inna Dubchak
Roman Nikitin
Robin A. Ohm