Comparative genomicsof fungi: studying

adaptation throughgene family evolution

Jason StajichUniversity of California, Berkeley

Gene family evolution• How do fungi adapt to a niche? How do

they acquire new functions and new genes?

• Neofunctionalization

• Horizontal Transfer

• Duplication and innovation

• Are genome-wide patterns of duplicationor loss useful to understand adaptation?

Gene family sizes followpower law distribution

Multicopy genesSugar transporters

P450 Enzymes

single copy genesPRP8 (splicing)

CDC48 (cell cycle ATPase)

Models of gene familyevolution

• Need a Null model for comparison of genefamily size

• Birth-Death model for gene family sizeevolution

• CAFE: Computational Analysis of FamilyEvolution

• Compare observed to expected patternsof family size

Hahn et al, Genome Res 2005Demuth et al, PLoS One 2006

Case study: mammals

Demuth JP, De Bie T, Stajich JE, Cristiani N, Hahn MW. PLoS One 2006

6%difference

Methods: Gene families• Functional Annotation “Free”

• Build gene families from protein sequencesimilarity (FASTP), clustered with MCL

• Identify families that are unusually large or smallwith CAFE

• Build gene trees to validate and study mode andtempo of duplication.

• Protein Domain distribution

• Pfam domain counts

FASTAall-vs-all

MCL

Gene families

CAFE

Family 1 P < 0.001 Branch A

Family 2 P < 0.001 Branch B

Family 3 P=0.02 BranchC,E

Family 4 P=0.03 Branch D

10 1 2

14 18 2

7 1 1

6 1 12

6 1 8

3 1 1

+

Family count

Spec

ies

Phylogeny of sequenced fungi

Fitzpatrick DA, Logue ME,Stajich JE, Butler G. BMC

Genomics 2006

Basidiomycota

Eurotiomycetes

Long Life

Short Life

SpheruleEndospores

Granuloma

Doctorfungus.comM. McGinnis

Coccidioides: Evolution of apathogen

Gene Family Evolutionin the Onygenales

ML phylogeny from 1148concatenated genes

46890 unambiguous AA sitesafter removing gaps.

Onygenales Familyexpansions

2 1

0 1

3 3

4 2

3 2

3 2

7 13

7 14

4 13

2 2

Peptidase M35

Keritinase

Keratinases in Onygenales

• Onygenales are Keratinophilic

• Domains: Peptidase S8, Subtilisin domains

• Large expansion of putative keratinases inOnygenales

Subtilisin_N

SignalP

Keratinase expansionin Onygenales

13/14 copies inCoccidioides

1 in Histoplasma

Expansion of 7

Metalloproteinase expansion

MEP

4

MEP

5

MEP

6

MEP

3

MEP

7

MEP

2

MEP

8

MEP1 is a previously described Virulencefactor (Hung et al. 2005)

Family contractions inOnygenales

1 3 7 18

1 0 2 0

5 5 13 17

11 5 11 3

6 8 16 15

6 4 15 7

0 1 2 0

0 1 2 0

0 1 2 0

0 2 3 0

Tan

nase

Cut

inas

e

Cel

lula

se

Cel

lula

seBi

ndin

gD

omai

n

Carbohydratemetabolism

• Domains absent or contracted inOnygenales fungi

• Tannase, Cutinase

• Pectin Lyase, Cellulase, Cellulase BindingDomain, Pectinesterase

• Alpha-L-arabinofuranosidase

• Glycosyl hydrolase

• HET domain

Summary

• Onygenales fungi have lost many domainsrelating to saprophytic growth on plantmatter

• Few expansions, but at least one family isrelated to a known virulence factor

• MEP genes are good Cocci specificexpansion

Basidiomycota changes

U.maydisC.cinereusP.chrysosporiumC.neoformans

P450 CYP64P450 enzymes involved in synthesis and cleavage ofchemical bonds. Drug metabolism in animals.

CYP64: Step in Aspergillus spp aflatoxin pathwayP. chrysosporium implicated in lignin and hydrocarbondegradation.

CYP64 was fromindependentduplication

C. cinereus expansion P. chrysosporium expansion

Tom VolkMario Cervini

Local duplications createdCYP64 expansion

Interpretation ofCYP64 expansion

Million yearsago

Hydrophobin Family

• Self assembling proteins involved in fungalcell wall

• Part of what makes a mushroom

• 8 Cysteine residues critical to function

• Help spores stay airborne resisting water

P.chr C.cin C.neo U.may

21 33 0 2

Local Duplications

C. cinereus

P. chrysosporium

Summary•Local duplications are a major mode of family

expansion in two Homobasidiomycetes

• Independent expansion of families

•Convergent evolution

•High gene turnover in some families?

James et al. Nature 2006 Bruns TD. Nature 2006

Chytrid family changes• Expansions

•More Polysaccharide deacyetalase (2x) and Chitinbinding domains than most fungi

• 12 Chitin synthases, but R.oryzae has 23+, Mostother fungi have 1-5.

• Bd Contractions or small families in fungal ancestor

•No Glucan synthase (FKS1) homolog.

• Few Sugar transporters and Major FacilitorSuperfamily. No Acetate transporter.

•Of 9 P450 genes, 2 pairs are adjacent.

Discussion• Gene content differences not just

orthologous genes need to be consideredwhen describing species divergence.

• Losses may be more informative in someclades.

• Family size change can be a useful startingpoint for comparing species.

• Models that incorporate phylogeneticcontext are critical.

Acknowledgments

Miller Institutefor Basic Research in Science

Indiana UniversityMatthew Hahn

UC BerkeleyThomas Sharpton

John Taylor

Duke UniversityFred Dietrich

Sequencing CentersFGI, Broad Institute

DOE - JGITIGR

Stanford GTCBaylor College of

Medicine