Stajich phyloseminar 2011 06-29

Fungal phylogenomics: Getting lost in the moldy forest

Jason E Stajich
Dept of Plant Pathology & Microbiology
University of California, Riverside
http://lab.stajich.org
http://fungalgenomes.org/blog
http://fungiDB.org
twitter{stajichlab,hyphaltip,fungalgenomes,fungidb}

Fungi have diverse forms, ecology, and associations

Cryptococcus neoformans X. Lin Coprinopsis cinerea Ellison & Stajich Aspergillus niger. N Read Glomus sp. Univ Sydney Rozella allomycis. James et al

Puccinia graminis J. F. Hennen Batrachochytrium dendrobatidis
Laccaria bicolor Martin et al. Neurospora crassa. Hickey & Reed Phycomyces blakesleansus T. Ootaki
J. Longcore

Ustilago maydis Kai Hirdes Amanita phalloides. M Wood Xanthoria elegans. Botany POtD Rhizopus stolonifera. Blastocadiela simplex Stajich & Taylor

Fungi are an old group of organisms
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Awash in Fungal Genomes

• Mid-2011: Genomes from 150+ species sequenced and ~400 more in progress/pipeline

• Several multi-strain resequencing projects (Neurospora - Ellison PNAS 2011),
Saccharomyces (Liti Nature 2009), Coccidoides (Neafsey Genome Res 2010) and many in
progress/proposed.

• Many of sequenced genomes were focused around plant, animal pathogens, and some
specific evolutionary questions.

• Now are starting to fill out the tree more to capture the diversity of kingdom and also for
studies of molecular evolution among many related species.

• Also efforts targeting specific questions - pathogens and their relatives; wood rotting
fungi; flagellated and non-flagellated forms; extremophiles; comparison of growth forms
(e.g. yeast forms from phylogenetically very different species)

Genome sizes of fungi are 8Mb-100Mb = easy(ish) to
sequence Melampsora, Blumeria,
Puccinia
Genome size of fungi

(many Transposable
100

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80

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60

Mushrooms Francis Martin
Flickr:/fmartin1954/2338045504/
http://en.wikipedia.org/wiki/File:Barleypowderymildew.jpg
40

Ashbya, Malassezia, Candida
other yeasts
20

http://www.biologie.uni-osnabrueck.de/Genetik/index.php?menuid=12

Need to cover more of the phylogenetic diversity: 1000
Fungal genomes project
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9:- ;9:- <9:- =9:- >9:- ?9:- @9:- A9:- B9:- C9:- ;99:
Blue = completed or in progress, Red= proposed for Tier One sampling,
Green = remaining unsampled families Numbers or Percent of Families in each clade and their current or proposed genome sampling

Tools to access this data

• Genome databases at sequencing centers and NCBI

• Comprehensive and integrated systems are not as well developed in Fungi, but some
examples of excellent tools highlighted at http://tools.fungalgenomes.org/

• Ensembl Fungi, MicrobesOnline, JGI’s Mycocosm, Comparative Fungal Genomics, and
some targeted to specific clades e.g. Saccharomyces (SGD), Aspergillus (AspGD),
Candida (CGD)

• We have launched FungiDB - http://fungidb.org to support integrating functional
genomics data for data mining as well as standard ‘Gene’ pages for genes.

Searching with FungiDB:
A strategy for drug targets

C.neoformans genes with
- no hits in other eukaryotes
(excepting fungi), bacteria
- has S.cerevisiae orthologs
that have EC terms
OR orthologs in other fungi
with GO metabolic terms
associated

Searching with FungiDB:
A strategy for reannotation
2885 C.neoformans genes with desc “"conserved hypothetical
protein” but 1327 can be assigned name from ortholog in any
fungus with EC #, GO terms, or Pfam domains

Gene page and genome browser
Synteny Views

Data mining interface

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Using comparative genomics towards understand
pathogen evolution

• How do traits like pathogenecity evolve?

• Can comparative genomics indicate meaningful differences that can lead to
understanding the basis for pathogenesis?

• Contrasting genomes of pathogens with non-pathogens can suggest recent genomic
changes that might be testable in the lab

• Gene duplication is thought to be important source for evolutionary innovation - What
role might gene family size change play in adaptation?

Models for comparing gene family size changes

• A model for gene family size change that incorporates the birth-death process of gene
families which follow a power law distribution (Hahn et al, Genome Res 2005)

• Implemented in a program called CAFE to find unexpectedly large lineage or clade-
specific changes in gene family sizes (Hahn Lab @Indiana Univ) (De Bie et al,
Bioinformatics 2006)

• Can screen genome family sizes across multiple species to find expectedly large
changes (based on counts) which can be verified using gene tree-species tree
reconciliation approaches like Notung (Chen, Durand, Farach-Colton, J Comp Bio 2000)

Short Life
Coccidioides Granuloma

• Fungal pathogen Doctorfungus.com

Spherule
M. McGinnis

genomics: Gene families Endospores Long Life
and appetite differences

Human pathogen Coccidioides

• Coccidioides (Valley fever) - 2 species C. immitis and C. posadasii

• Is a primary human pathogen - infects healthy people
(most human pathogenic fungi are opportunistic)

• Endemic in US Southwest, Mexico

• Requires laboratory BSL3 and is a Select Agent

• Genomes of 2 species (Sharpton et al Genome Res 2009) and then 18 strains
(Neafsey et al Genome Res 2010)

• Comparative analyses of Coccidoides spp

Human pathogen Coccidioides Life cycle

S/
Hypha Spherule Endospores

Coccidioides ecology
Soil?

Short Life
Granuloma

D octorfungus. com
M. McGinnis

Spherule
Endospores Long Life

pocket mice?

Two species of Coccidioides are allopatric

C.immitis

C.posadasii

EVOLUTION
Fisher et al, 2000

Studying the evolution of a pathogen

• Comparing sequences from two Coccidioides species, closely
related outgroup, and more distant ougroups species:

• Evidence for recent positive selection

• What gene family differences can be identified that distinguish
phenotypic groups (mammalian pathogens from non-
pathogens)

• Evidence for recent introgression which contains candidate
genes for pathogenesis

Gene family changes

• Another mechanism for adaptation may be changes in copy
number of a gene family

• Gene duplication is a source of novelty allowing for changes
in the function of one copy if the other maintains original
function

• Expansions of copy number may also be an easy way to get
more protein for a particular process

• How important is copy number change in adaptation?

Genome samples from fungi
Dictyostelium
Monosiga Choanoflagellida
Caenorhabditis
Metazoa
Drosophila
Homo
Batrachochytrium ‘Chytrid’
Spiromyces Zygomycota
Kickxellomycotina
Opisthokont ‘Chytrid’
Olpidium
Rhizopus Mucormycotina
Fungi Glomus Glomeromycota
Puccinia
Cryptococcus Basidiomycota
Coprinopsis
Schizosaccharomyces Taphrinomycotina
Yarrowia
Saccharomyces
Ascomycota Candida Saccharomycotina
Morchella
Cochliobolus
Cladonia
Pezizomycotina Aspergillus
Coccidioides
Magnaporthe
Pezizomycotina
Neurospora
Fusarium
Botryotinia

Aspergillus clavatus
Aspergillus fumigatus
Aspergillus flavus Animal Pathogen
Aspergillus oryzae (Opportunistic)
Aspergillus terreus
Eurotiales Aspergillus niger Animal Pathogen
Aspergillus nidulans (Primary)
Penicillium marneffei
Blastomyces dermatitidis
Eurotiomycetes Plant Pathogen
Histoplasma capsulatum 186AR
Histoplasma capsulatum 217B
Histoplasma capsulatum WU24
Paracoccidioides brasiliensis
Onygenales Coccidioides immitis
Coccidioides posadasii
Uncinocarpus reesii
Fusarium graminearum
Sclerotinia sclerotiorum
200 100 0
Mya

Few protein domains for eating plant material in animal
pathogens Animal Pathogen

Peptidase_M35

Peptidase_M36
(Opportunistic)

Peptidase_S8
Pec_lyase_C

Subtilisin_N
Cellulase
Cutinase
Tannase
Loss of plant

CBM_1

NPP1

APH
Animal Pathogen
saprophytic (Primary)
enzymes Anid 6 6 6 2 4 13 2 3 3 0 9
Plant Pathogen
Afum 17 5 5 2 5 10 2 5 2 1 9

Ater 15 6 6 2 8 13 2 6 2 1 29

Hcap 0 0 0 0 2 2 2 6 1 0 20

Uree 0 0 0 0 1 2 15 19 4 2 33

Cimm 0 0 0 0 1 1 13 16 7 2 38

Cpos 0 0 0 0 1 1 14 16 7 2 32

Ncra 18 1 1 4 3 6 3 6 2 0 6
Sharpton, Stajich, et al, Genome
Fgra 12 7 9 9 12 8 11 24 1 1 15 Res. 2009

Domains for eating animal material? Animal Pathogen

Peptidase_M35

Peptidase_M36
(Opportunistic)

Peptidase_S8
Pec_lyase_C

Subtilisin_N
Cellulase
Cutinase
Tannase
CBM_1

NPP1
Animal Pathogen

APH
(Primary)

Anid 6 6 6 2 4 13 2 3 3 0 9
Plant Pathogen
Afum 17 5 5 2 5 10 2 5 2 1 9

Ater 15 6 6 2 8 13 2 6 2 1 29

Hcap 0 0 0 0 2 2 2 6 1 0 20

Uree 0 0 0 0 1 2 15 19 4 2 33

Cimm 0 0 0 0 1 1 13 16 7 2 38

Cpos 0 0 0 0 1 1 14 16 7 2 32

Ncra 18 1 1 4 3 6 3 6 2 0 6

Fgra 12 7 9 9 12 8 11 24 1 1 15 Sharpton, Stajich, et al, Genome
Res. 2009

Keratinases in Onygenales
SignalP

Subtilisin_N

• Onygenales are Keratinophilic

• Domains: Peptidase S8, Subtilisin domains

• Large expansion of putative keratinases in Onygenales

Peptidase S8 expansion
I
in Onygenales
14 copies in Coccidioides
1 in Histoplasma
II

III

Population genomics

• Revealed no loci with evidence for
balancing selection - so little
evidence for long standing host-
pathogen battle as in Plasmodium.

• Sliding window FST analysis
revealed some regions of reduced
divergence and followup revealed a
regions of recent intergression.
Directionality looks to be mostly
from Cp and into Ci.

• One gene implicated in
pathogenesis, MEP4, is found in
introgressed region

Towards identifying genes underlying adaptation

Sharpton et al. Genome Res 2009
Neafsey et al, Genome Res 2010

• Coccidioides is found in desert soil and associated with animals - perhaps has a long term
animal association without inducing response from the host.



• Loss of genes involved in plant product metabolism suggests nutritional shift in Onygenales
from relatives in Eurotiales




• Expansion of only a few gene families, seem to be involved in metabolism - none are
Coccidioides specific though.





• From population genetics analysis - failed to find regions under balancing selection suggesting
there is not a long-term arms race between host and pathogen.





• From population genetics analysis - failed to find regions under balancing selection suggesting
there is not a long-term arms race between host and pathogen.

• Evidence for introgression between the species and perhaps imported novel alleles that are
important for adaptation in both species to their animal hosts.


Batrachochytrium dendrobatidis (Bd)- a major cause of
amphibian decline

Bd is a Chytrid
http://cisr.ucr.edu/chytrid_fungus.html
fungus
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Bd genome sequence projects

• 2 strains sequenced at JGI and Broad; allow whole genome comparison between strains

• Found that genome is diploid, but with large regions with loss of heterozygocity (LOH)

• Identified gene family changes that might suggest mechanisms of pathogenecity

• Greater understanding of what the early fungus was like

• With collaborators we are sequencing 20 more strains for population genomics to better
understand population dynamics, trace origin of diversity, and understand the LOH as
independent or shared events.

Bd grows intercellularly

Formally described by Joyce Longcore (U Maine) (Mycologia 1999)

Rick Speare, Lee Berger, Alax Haytt
James Cook University, Townsville, Australia

http://www.jcu.edu.au/school/phtm/PHTM/frogs/chpr1/fc13.htm

Phylogenomic profiling

• For each gene in the the target (Bd) genome, look to see which have homologs in other
fungi, animals, plants

• Classify genes by its profile as to when it must have arisen based on identified homologs

• Also compare well-studied organisms (S. cerevisiae, N. crassa) to see which genes were
missing

• For Bd/Chytrids several trends appeared

• Missing: some cell wall genes, spindle-pole body

• Present in Bd but not other non-chytrid fungi: Flagella, some signaling pathways,
effector like proteins

• Some expansions of gene families

Fungal cell wall evolution- a view from earliest branches

Ergosterol Yeast Cell Wall

What is the fungal cell wall
made of? Sugar polymers

Some fungi also have
Selitrennikoff CP, AEM 2001 α (1,3) glucan

Evolution of β (1,3) glucan synthase

Evolution of FKS1 !"'&
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B. dendrobatidis cell wall biochemical analysis

Cellulose
β (1,3)- β(1,6)- α(1,3)-
β(1,4)- Chitin
glucan glucan glucan
glucan

X X X ✓ ✓

A putative cellulose synthase gene can be found in genome of Bd
but also found in N. crassa and other Fungi with JP Latgé, M. Fisher

B. dendrobatidis cell wall biochemical analysis

Cellulose
β (1,3)- β(1,6)- α(1,3)-
β(1,4)- Chitin
glucan glucan glucan
glucan

X X X ✓ ✓

A putative cellulose synthase gene can be found in genome of Bd
but also found in N. crassa and other Fungi with JP Latgé, M. Fisher

100X higher MIC for Caspofungin than C. albicans with N.A.R Gow & M. Fisher

Expansion of CBM18 domain - Chitin binding gene family
0 100 200 300 800 900 1000
400 500 600 700
Length - aa

BD_03764 C C C DE 471-aa
TL
BD_05538 O E D DE DL
*
746-aa

BD_05531 O D 439-aa
LL

** BD_07015 O E D DE 503-aa

BD_08806 O D DE 503-aa

* ** BD_05161 O D DE 444-aa Deactylase Like
BD_05540 O E D DE 478-aa

BD_05533 D DE 368-aa

BD_05536 D DE 321-aa

BD_06123 A TYR
*
635-aa

BD_06122 A TYR 673-aa Tyrosinase Like
BD_06121 A B B B A TYR 771-aa

* BD_00259 K K K K K H G 577-aa
Lectin Like 1033-aa
BD_01761 F M I X L J J J J H G
* BD_00264 F N M H H G 621-aa

** BD_00271 F N M H H G 577-aa

* * BD_00287 F N M M H H G 636-aa

BD_00289 N I I 334-aa

Abramyan & Stajich, submitted

BD_06121 - A
TL .60 A BD_06121 - A
DL * BD_06123 - A
BD_06122 - A
LL * B BD_06121 - B

** * BD_06121 - B
BD_06121 - B
* = 1.0 * C BD_03764 - C
* BD_03764 - C
** ≥ .90 BD_03764 - C
BD_05538 - D
BD_08806 - D

.85 * BD_05540 - D
BD_07015 - D

* D ** BD_05161 - D
* BD_05536 - D
BD_05531 - D
BD_05533 - D
* E BD_05538 - E
* BD_05540 - E
BD_07015 - E
BD_00271 - F
F
* BD_00264 - F
* BD_00287 - F
BD_01761 - F
X
Domain tree shows **
G ** *
BD_01761 - X
BD_00264 - G
BD_00287 - G
BD_00271 - G
** BD_00259 - G

clade-specific grouping ** *
BD_01761 - G
BD_00271 - H
BD_00264 - H
BD_00287 - H
H BD_00287 - H
BD_00259 - H
* BD_00264 - H
BD_00271 - H

Domains evolved from mostly *I
BD_01761 - H
BD_01761 - I
BD_00289 - I

tandem duplications with some BD_00289 - I
BD_01761 - J

*J
BD_01761 - J

intergene duplications. BD_01761 - J
BD_01761 - J

*K *
BD_00259 - K
** BD_00259 - K
BD_00259 - K
** L * BD_00259 - K
BD_00259 - K
BD_01761 - L
BD_00287 - M
* BD_00271 - M
.81 M ** BD_00264 - M
BD_01761 - M
.86 BD_00287 - M
BD_00289 - N
** N BD_00264 - N
* BD_00271 - N
BD_00287 - N
BD_08806 - O

O * BD_05538 - O
* BD_05531 - O
BD_05161 - O
** * BD_07015 - O
BD_05540 - O
SP_07646
SP_07647
SP_03958


CBM18 expansion

• Largest copy number of CBM18 in all fungi, and most number of domains (11) in a single
locus

• Evidence for positive selection among copies of the domains based on codon analyses

• CBM18 thought to bind chitin, could be involved in binding its own chitin to cloak the cells
from the host immunity

• Could also bind chitin-related molecules in animals attach more firmly to the animal cells


Tyrosinase expansions in Bd and other fungi
Allomyces

Synthesis of
melanin, H.Whistler via Liu et al BMC Evol Biol 2006

pigments
and other
polyphenols
Hajime Muraguchi via
Stajich et al PNAS 2010

E.Medina

But are these changes important?

• Just observing big families in a genome is nice, but does it mean that changes are really
related to recent adaptation?

• The branches on some gene trees are short, indicating duplications are recent

• A better is to polarize the changes to the Bd branch by having a closer species than
50-100 Mya...

• So is there a species closer to Bd we can use? ...

Homolaphylictis polyrhiza JEL142 is a close(ish) relative
F. graminearum
1
N. crassa
1
B. cinerea

454 genome sequencing 1
U. reesii

C. immitis

MAKER genome annotation 1
1
1
T. rubrum

A. benhamiae
OrthoMCL gene families 1 1
M. canis

0.58 A. nidulans
1
P. tritici-repentis

C. cinerea
1
C. neoformans
1 *
U. maydis
1
P. graminis
1

P. blakesleeanus

A. macrogynus

S. punctatus

1 H. polyrhiza JEL142
1
B. dendrobatidis
! "! #
Joneson et al, Submitted

Contrasting some family sizes among the Chytrids
M36 S41 Tyrosinase CBM18

Allomyces 31 0 16 3

Spizellomyces 3 3 3 3

Hp 3-5 3 15 5

Bd 38 32 12 14-16

Fungalysin
Serine protease
Serine protease expansions in
Fungalysins - thought to be Coccidoides and relatives maybe
keratinases (break down keratin in related to breaking down on
an amphibian skin...) animal matter

H. polyrhiza won’t grow on frog skin; doesn’t cause
mortality in frogs

Hp- frog skin intact Bd- frog skin degraded


A) GLEANP3 001910 B)
1
GLEANP3 010940
GLEANP3 058130
0.8
GLEANP3 058330
GLEANP3 058280
Fungalysin GLEANP3 038010 0.6

GLEANP3 035340
M36 GLEANP3 045390 0.4

GLEANP3 016580
up in sporangia GLEANP3 040970 0.2

GLEANP3 030000
no expression GLEANP3 068250 0
zoospore sporangia
GLEANP3 037130
diff GLEANP3 027740
GLEANP3 075460
up in zoospore GLEANP3 019170
1
GLEANP3 075190
GLEANP3 066500
0.8
GLEANP3 075130
GLEANP3 041170
0.6
GLEANP3 035280
GLEANP3 018720
GLEANP3 048430 0.4

GLEANP3 046850
Aspergillus fumigatus outgroup 0.2

Rhizopus oryzae outgroup
GLEANP3 078890 0
0.1 zoospore sporangia

Rosenblum et al PNAS 2008

Bd summary

• Comparisons to close species can polarize some differences in lineage specific
expansions

• Findings of M36, S41 expansions seem to be recent to Bd and could be a functional
link to pathogenesis

• Expansion of Tyronsinase from counts is less compelling, but gene tree analyses
suggests recent expansions on Bd-Hp branch

• Lack of FKS1 in early Chytridiomycota lineages suggests a more recent origin of this
gene than origin of the Fungi and predicts timing of some changes in fungal cell wall
composition

• CBM18 expansion may be related to adhesion, future experiments to test this

• Future: We are employing a population genomic approach, resequencing 24 strains of Bd
and hope to understand more about origins and variation in the genome from these data.

Summary

• Unraveling the evolution of pathogens can be tricky, more so when mode of
pathogenesis is not obvious (e.g. not just a toxin gene)

• Comparative genomics at the scale of gene and gene families can suggest changes that
may be important in adaptation of a species.

• Connecting these molecular changes to pathogenecity is still needed to understand the
role these expansions may play - but provides rich experimental fodder for the
laboratory.

Acknowledgements
Coccidioides B. dendrobatidis
Tom Sharpton {UCSF} John Taylor {UC Berkeley} John Abramyan {UCR}
Dan Neafsey {Broad Institute} Edgar Medina {Universidad de Los Andes,
Bridget Barker, Marc Orbach, Steve Rounsley {U Colombia}
Arizona} Christina Cuomo {Broad Institute}
Tim James {U Michigan}
Suzanne Joneson, Tom Poorten, Erica
Stajich lab @UCR lab
Rosenblum {U Idaho}
Steven Ahrendt
Igor Grigoriev {JGI}
Divya Sain
H. polyrhiza
Yizhou Wang
Suzanne Joneson, Erica Rosenblum {U Idaho}
Yi Zhou
Shin-Han shiu {Michigan State}
Jessica De Anda Burroughs Wellcome Fund Grant Programs
Joyce Longcore {U Maine}
Annie Nguyen
Tim James {U Michigan}
W.M. KeckBiomedical Sciences
Foundation Career Awards for Medical Scientists
http://lab.stajich.org
Five-year awards for physician scientists provide $700,000 to bridge advanced postdoctoral/fellowship
training and the early years of faculty service. This award addresses the on-going problem of increasing

http://mobedac.org
the number of physician scientists and will help facilitate the transition to a career in research. Proposals
must be in the area of basic biomedical, disease-oriented, translational, or molecular, genetic, or
pharmacological epidemiology research.

Collaborative Research Travel Grants http://fungidb.org
Provide up to $15,000 in support for researchers from degree-granting institutions to travel to a labo-

Stajich phyloseminar 2011 06-29

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