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U.S. DEPARTMENT OF
SJGI Fungal Genomics Program ENERGY
DOE JOINT GENOME INSTITUTE Contact: Igor Grigoriev <ivgrigoriev@Ibl.gov>
OFFICE OF SCIENCE ENERGYAbstract
Genomes of energy and environment fungi are in focus of the
Fungal Genomic Program at the US Department of Energy Joint
Genome Institute (JGI) Its key project, the Genomics Encyclopedia
of Fungi, targets fungi related to plant health symbiontss, pathogens,
and biocontrol agents) and biorefinery processes (cellulose
degradation, sugar fermentation, industrial hosts), and explores
fungal diversity by means of genome sequencing and analysis Over
50 fungal genomes have been sequenced by JGI to date and
released through MycoCosm (wwwjgi doe gov/fungi), afungal web-
portal, which integrates sequence and functional data with genome
analysis tools for user community Sequence analysis supported by
functional genomics leads to developing parts list for complex
systems ranging from ecosystems of biofuel crops to biorefineries
Recent examples of such parts' suggested by comparative
genomics and functional analysis in these areas are presented
here
Genomic Encyclopedia of Fungi
=Plant Feedstock Health
=Bicrefinery
J= Fungal Diversity
Energy & Environment Fungi
Plant symbionts Lignocellulose Sugar
and pathogens degradation FermentationFuture Grand Challenges
1. 1000 fungal genomes
Sampling fungal diversity
2. Model fungi
MODELING Deep sampling over 1000 of conditions
3. Fungal ecosystems:
- Bioenergy crops symbionts & pathog
FUNCTION Biorefinery parts list
- Fungal metagenomes
SEQUENCE
Fungal Systems of Systems in wild
isolates & groups interaeting organisSymbionts
Laccaria bicolor:
Ectomycorrhyzal symbiont of poplar .
Ma rtn at al, Nature 2000 -Y -
-sm Xanthoria parietina
lichenfungus
/PI Paid It-rlPlant Health
Plant Pathogens
1141 IUE*IUIIEIUERII EIFIm lI 1IIII
No l mm mi n n~m im imnm inii mum lm uu lu s
Q4 ilmlm i inlim l
i H I Dispensome of
DIII mmqTSmEr Mycosphaerellgram n cola
"InWImmsniNuueL Goodwin, Kama et al
..ma
II P llm l
I.na V~
i n nh .uIntegrated genomic and transcriptomic analysis reveals mycoparasitism
Comparative analysis of 12 Dothideomycetes Ohm et a, rn prep as the ancestoral life style of Tnohoderma
Kubicek et aBiorefinery
Thermophiles
* -i-~
-i
Thermophilic biomass-degrading fungi
Mycehophthora thermophla and Thlelavia
terrestns are the first with completely
finished genomes, new candidate for cell
factories with secreted thermostable
enzymesBerka, Tsang, et al
Release bf reducing sugars Im sal, e- by exracellular bnym
MycoCosm: 60+ fungal genomes
Genome-Centric View v -
Comparative View ..Phylogenetic groups
www.jgi.doe.gov/fungi
Lignocellulose Degra
- . - --dation
CAZy and FOLy
in Basidiomycetes
Tandem duplication of
peroxidases in Trametes_IOrthologs Transcrnptomes
Comparative genomics and
-t- - a transcriptomics of -
and xylose growers reveal candidate -
genes for S cerevseae strain "
improvement a
Gasch,etal
Riley, et alFungal Diversity
Genome-centric View
Supports functional genomics, user data deposition and curationComparative View
Enables analysis of groups of fungia- - :- Eurotiomcetes
-- ,-..a,
Biocontrol
-
Xylose Fermenters
-Iii
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Grigoriev, Igor V. JGI Fungal Genomics Program, report, March 14, 2011; Berkeley, California. (https://digital.library.unt.edu/ark:/67531/metadc831115/m1/2/: accessed March 29, 2024), University of North Texas Libraries, UNT Digital Library, https://digital.library.unt.edu; crediting UNT Libraries Government Documents Department.