Genomics data integration, analysis, and curation using MycoCosm

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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.

Technology

Genomics data integration,
analysis, and curation using
MycoCosm
Robert Riley
Igor Shabalov
Igor Grigoriev

3 April 2012

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

Fungi in bioenergy

degrade
lignin & White rot
cellulose Phanerochaete
chrysosporium

Biofuel
Lignocellulose Brown rot
Postia precursors
degrade
cellulose placenta

Data integration: MycoCosm

Comparative View

MycoCosm
jgi.doe.gov/fungi
120+ genomes;
5K visitors/month Genome-Centric View

Curation: user annotation

Users may
create improved
gene models

Your name here!
7

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

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

Analysis: genome-centric view

GC content

Sequence
conservation

Gene
catalog
ESTs

PFAM domains

BLAST hits

Alternate gene
models
10

Analysis: evolution of
lignocellulose degradation
CAZy CAZy and lignin-degrading genes
genes

Oxidoreductase
genes

Eastwood et al. Science 2011 Riley et al. in prep

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

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

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Genomics data integration, analysis, and curation using MycoCosm

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

Genomics data integration, analysis, and curation using MycoCosm

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