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:

bioenergycarbon cycling

biogeochemistry

PacBioIllumina HiSeq2000

Genome sequencing

using latest technology

Programs: Fungal, Plant,

Microbial, & Metagomics

Example: JGI fungal sequencing

Fungi in bioenergy

LignocelluloseBiofuel

precursors

White rot

Phanerochaete

chrysosporium

degrade

lignin &

cellulose

Brown rot

Postia

placentadegrade

cellulose

Data integration: MycoCosm

MycoCosm

jgi.doe.gov/fungi

120+ genomes;

5K visitors/month Genome-Centric View

Comparative View

Data Integration: External Links

From GenBank to MycoCosm

7

Curation: user annotation

Your name here!

Users may

create improved

gene models

8

Curation: user annotation

0

5

10

15

20

25

30

1

10

100

1000

10000

Heb

cy1

Hypsu1

Trem

e1

Agabi_varbis…

Paxin1

Phaca1

Plicr1

Jaaar1

Phlgi1

Bjead1_1

Botbo1

Phlbr1

Gansp1

Wolco1

Conpu1

Cersu1

PleosPC9_1

Gym

lu1

SerlaS7_9_2

Aurde1

Punst1

Glotr1_1

Fomme1

PleosPC15_2

Pospl1

Fompi1

Trave1

Schco2

Steh

i1

Hetan2

Phchr1

Lacbi2

Dacsp1

Agabi_varbur…

SerlaS7_3_2

Dicsq1

Statistics on manual curation of gene models

Organism

Cura

ted g

enes

Cura

tors

by increasing number of curations

9

Curation: user annotation

Example: user finds a more sensible gene model

Compare

to ESTs

Promote to

gene catalog

Transcript pageProtein page

Cluster viewer

10

Analysis: genome-centric view

Sequence

conservation

GC content

Gene

catalog

ESTs

BLAST hits

PFAM domains

Alternate gene

models

11

Analysis: comparative view

Analysis: evolution of

lignocellulose degradationCAZy

genes

Oxidoreductase

genes

CAZy and lignin-degrading 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

Henrik Nordberg

Igor Shabalov

Andrea Aerts

Mike Cantor

David Goodstein

Alan Kuo

Simon Minovitsky

Roman Nikitin

Robin A. Ohm

Robert Otillar

Alex Poliakov

Igor Ratnere

Frank Korzeniewski

Xueling Zhao

Tatyana Smirnova

Daniel Rokhsar

Inna Dubchak