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Evolution of gene family size change in fungi
1. Evolution of gene family
size change in fungi
Jason Stajich
University of California, Berkeley
Gene family evolution
10000
N.crassa
A.gossypii
R.oryzae
A.oryzae
A.terreus
C.cinereus
U.maydis
1000
Frequency of Family size
100
10
1
1 10 100
. The phylogenetic tree. Branch lengths t are given in millions Family size
2. Outline
• Gene family size change - a model
• Cornucopia of fungal genomes
• Methodology for comparing family size
• Lineage specific expansions
3. Gene family evolution
• Gene duplications are the crucible of new
genes and thus new functions
• Many comparative approaches focus only
on identifiable one-to-one orthologs.
• Signature of adaptive evolution can be
confounded in multi-gene families
• How important is lineage-specific
expansion in adaptive changes?
4. Identifying family
expansions
• Previous work only considered pairwise
• Ad hoc comparison of gene family sizes
• C.elegans-C.briggsae - GPCR family
expansions (Stein et al, PLOS Biology 2004)
• A. gambiae-D. melanogaster - Mosquito
specific family expansions related to
symbiotic bacteria (Holt et el, Science 2002).
• Need a null model
5. Gene family sizes follow
power law distribution 10000
N.crassa
single copy genes A.gossypii
R.oryzae
PRP8 (splicing) A.oryzae
CDC48 (cell cycle ATPase) A.terreus
C.cinereus
U.maydis
1000
Frequency of Family size
100
Multicopy genes
Sugar transporters
P450 Enzymes
10
1
1 10 100
Family size
6. Phylogenetic evaluation of
gene family size change
• Previous methods only used ad hoc
statistics
• Explicit model for gene family size change
according to a Birth-Death models
• Apply BD to family size along phylogeny
using probabilistic graph models
• CAFE - Computational Analysis of gene
Family Evolution Hahn et al, Genome Res 2005
De Bie, et al Bioinformatics 2006
Demuth et al, submitted
7. CAFE Gene family evoluti
e phylogenetic
ers an ideal null
•
del inUse a way
this Probabilistic
Graph Model for:
ave undergone
od furthermore
• Ancestral states
ny upon which
• Birth and Death rate
likelihoods can-
(lamda)
milies, because
•
wer likelihoods changes
Per branch
•
bias”). Instead,
P-values
atistics to calcu- Figure 2. The phylogenetic tree. Branch lengths t are given in milli
on one of the of years. The branch numbers used in this study are shown in circles
ional P-value is
Hahn et al, Genome Res 2005
mily (with fixed
To define gene families, we took all of the genes in all f
ihood than the
12. Genome annotation
• Many of the fungal genomes were only
assembled genomic sequence.
• Automated annotation pipeline was built to
generate to get systematic gene prediction.
• Several gene prediction programs were
trained and results were combined with
GLEAN (Liu, Mackey, Roo, et al
unpublished) to produce composite gene
calls.
17. Methods: gene family
identification
• All-vs-All pairwise sequence searches
(FASTP)
• Cluster genes by similarity using Markov
CLustering (MCL) algorithm
• Identify families with unusually large size
changes along phylogeny with CAFE
• Use 37 fungal genomes from 5 major clades
18. FASTA
Family count
all-vs-all
10 1 2
14 18 2
Species
7 1 1
6 1 12
MCL
6 1 8
+ A B C D E
3 1 1
Gene
families
CAFE
18 U. maydis
Family 1 P < 0.001 Branch A 5 C. gattii R265
5 gattii
23 Basidiomycota 5 C. gattii WM276
Family 2 P < 0.001 Branch B 5 Cryptococcus
5 C. neoformans JEC21
5 neoformans
Branch
Family 3 P=0.02 23 Hymenomycota 5 C. neoformans var grubii
C,E
163 P. chrysosporium
136 Homobasidiomycota
Family 4 P=0.03 Branch D 141 C.cinereus
400 300 200 100 0
19. Families with significant expansions
49 significant Vitamin & Cofactor transport Methytransferase
families Lactose & sugar transport Cytochrome P450: CYP64
Amine transport Cytochrome P450: CYP53,57A
Transporters Myo-instol, quinate, and Cytochrome P450
glucose transport
Kinases Oligopeptide transport Kinase
P450
ABC transporter Subtilase family
Oxidation
MFS, drug pump, & sugar NADH flavin oxidoreductase
transport
Transport Aldehyde dehydrogenase
Monocarboxylate & sugar Aldo/kedo reductase
transport
ABC transport Multicopper oxidase
Amino acid permease AMP-binding enzyme
20. Transporters
• Of 45 significant families, 22 were related
to transport
• Vitamin and amino acid transport
• Sugar and sugar-like transporters
• Multidrug and efflux pumps
• ABC transporters (ATP Binding Cassette)
22. Transporter expansions
• Sugar related, Drug pump, and Major
Facilitator Superfamily
• Aspergillus spp, Fusarium spp, S. nodorum
• Euascomycota
Fusarium
• Vitamin transport Aspergillus
• C. neoformans, Fusarium S. nodorum
• A. nidulans (Biotin)
• Saccharomyces expansions independent! C. neoformans
23. Sugar transporter use in
phytopathogens
• Sugar transporters are
used to extract nutrients
from host
• Haustorium:
specialized structure
for plant parasitism Haustorium
• Many sugar
transporters highly and
specifically expressed Robert Bauer http://tolweb.org/
in haustoria
25. P450 CYP64
P450 enzymes involved in synthesis and cleavage of
chemical bonds. Drug metabolism in animals.
CYP64: Step in Aspergillus spp aflatoxin pathway
P. chrysosporium implicated in lignin and hydrocarbon
degradation.
18 U. maydis
5 C. gattii R265
5 gattii
23 Basidiomycota 5 C. gattii WM276
5 Cryptococcus
5 C. neoformans JEC21
5 neoformans
23 Hymenomycota 5 C. neoformans var grubii
163 P. chrysosporium
136 Homobasidiomycota
Million years
141 C.cinereus
ago 400 300 200 100 0
27. Local duplications created
CYP64 expansion
pchr_24
9k 10k 11k 12k 13k 14k 15k 16k 17k 18k 19k 20k 21k 22k 23k 24k
GLEAN models
GLEAN_02414 GLEAN_02415 GLEAN_02416 GLEAN_02417
Probability 1 Probability 0.999937 Probability 0.646357 Probability 0.990598
Pfam domains
p450 p450 p450 p450
Cytochrome P450 evalue:1e-28 Cytochrome P450 evalue:6e-26 Cytochrome P450 evalue:6.3e-23 Cytochrome P450 evalue:9e-07
28. Interpretation of
CYP64 expansion
18 U. maydis
5 C. gattii R265
5 gattii
23 Basidiomycota 5 C. gattii WM276
5 Cryptococcus
5 C. neoformans JEC21
5 neoformans
23 Hymenomycota 5 C. neoformans var grubii
163 P. chrysosporium
136 Homobasidiomycota
141 C.cinereus
Million years 400 300 200 100 0
ago
Angiosperm diversification
29. Hydrophobin Family
P.chr C.cin C.neo U.may
21 33 0 2
• Self assembling proteins involved in fungal
cell wall
• Part of what makes a mushroom
• 8 Cysteine residues critical to function
• Help spores stay airborne resisting water
33. Cryptococcus sugar
1,000.
and internal structures of C. neoformans are shown by means of a modified India ink preparation. Magnification, ca.
transporters
• 3x as many sugar
transporters in C.
neoformans (~50) than
other basidiomycetes
• “sugar coated killer”
2291
• Capsule is a mixture of
glucose, xylose, and
mannose.
• Transporters could be
Zerpa et al, 1996
important in capsule
synthesis
35. Acknowledgments
Sequencing centers
Matthew Hahn (Indiana) Broad Institute
Jeff Demuth Joint Genome Institute
Génolevures
Sang-Gook Han
Stanford University
TIGR
Tijl De Bie Welcome Trust Sanger Centre
Nello Cristianini (NIH and NSF)
Aaron Mackey
Ian Korf
Mario Stanke
Fred Dietrich (Duke)