Neurospora as a model for evolutionary...

Neurospora as a model for evolutionary biology.

Jason E. Stajich, Thomas J. Sharpton, Christopher Ellison, Christopher Villalta,

David Jacobson,N. Louise Glass,

Donald O. Natvig,John W. Taylor.

Neurospora experimental evolution!January 2008

Kwangwon Lee “Circadian clock phenotype as a fitness trait” Posters 53 & 54

Dettman, Jacobson & TaylorMycologia 2006

OutbreedingNeurospora

15 phylogeneticspecies

N.crassaclade

N.discretaclade

Chaetomium

Podospora

Neurospora

Cai et al. 2006, Mycol ResMiller et al. 2005. Mol Phyl Evol

Chaetomium

Podospora

N. crassa

N. discretaN. tetrasperma

Habitat difference

bugs.bio.usyd.edu.au

Dung

Cooked plants

Chaetomium

Podospora

N. crassa


Mating difference

Heterothallic

Pseudohomothallic

Heterothallic

Chaetomium

Podospora

N. crassa


Existing Genome Sequence

Broad

Genoscope/CNRS

Broad

Chaetomium

Podospora

N. crassa


New Genome Sequence

Broad

Genoscope/CNRS

Broad

JGI

JGI

FIG. 2. Maximum parsimony phylogram produced from the DMG, TMI and TML loci combined. Taxon labels indicatestrain number and geographic source. Labels to the right of phylogram indicate groups identified by phylogenetic analyses.Bold branches were supported concordantly by the majority of the loci or well supported by at least one locus but notcontradicted by any other locus. Triangles at nodes indicate that all taxa united by (or distal to) it belong to same phylogeneticspecies. Branch support values (MPBP/PP) are displayed for major branches only. A dash indicates the support for the branchwas ,50% MPBP or ,0.50 PP.

DETTMAN ET AL: NEUROSPORA SPECIES DIVERSITY 4432710 JEREMY R. DETTMAN ET AL.

Dettman 2003a Dettman 2006

(Dettman 2003a, Villalta unpublished data)

N. crassa Clade

Phylogeny

Poster 57

CV10 Papua New GuineaCV80 GabonCV56 Haiti

CV57 HaitiCV98 Indonesia

CV93 MexicoCV88 Hawaii

CV82 GabonCV43 Truk

D123 NigeriaD72 Ivory CoastD147 New Mexico

D10 KarnatakaD53 Thailand

D124 VirginiaD63 Haiti

CV79 GabonD78 CongoD77 Congo

D74 CongoD82 Congo

D75 CongoD100 Tamil NaduD106 Tamil Nadu

D103 Tamil NaduD105 Tamil Nadu



D11 KarnatakaD12 KarnatakaD70 Ivory Coast

D110 LouisianaD114 Louisiana


D144 PanamaD60 Haiti

D24 FloridaD94 YucatanD61 Haiti

D69 Ivory CoastD111 LouisianaD112 Louisiana



D19 FloridaD30 Florida

D23 FloridaD59 Haiti

D29 FloridaD90 Yucatan

D88 YucatanD62 Haiti



D140 Ivory CoastD91 Yucatan

D96 Ivory CoastD113 Louisiana


D14 HawaiiD15 Hawaii

D145 UnknownCV55 Haiti

D55 HaitiD57 Haiti

D58 HaitiCV119 HaitiCV156 Mexico

CV152 MexicoCV155 Mexico

CV91 MexicoCV89 MexicoCV148 Mexico


D86 YucatanD89 Yucatan


D87 YucatanD120 MadagascarD121 Madagascar

D1 TaiwanD2 Taiwan

D3 PhilippinesD102 Thailand

D18 QueenslandD4 PhilippinesD31 AnhuiD6 TaiwanD8 JavaD80 CongoD9 Java

D33 Papua New GuineaD84 Hawaii

D101 Tamil NaduD50 Tamil NaduD45 Tamil Nadu

D38 Tamil NaduD129 Karnataka

D132 KarnatakaD135 Karnataka




D137 KarnatakaD139 KarnatakaD128 Karnataka

D122 HondurasD22 FloridaD64 HaitiD21 Florida


D65 Ivory CoastD73 Ivory Coast

D66 Ivory CoastD141 LiberiaD16 Texas

D142 FijiD7 Java

D95 Ivory CoastD83 GabonD76 CongoD79 CongoD81 CongoD34 Papua New Guinea

D51 MalaysiaD52 ThailandD127 Karnataka

D130 KarnatakaD97 Tamil Nadu





D109 Tamil NaduD39 Tamil NaduD133 Karnataka

D32 AnhuiD35 Papua New Guinea

D36 TahitiD146 New MexicoD71 Ivory Coast


D5 Papua New GuineaD67 Ivory CoastD17 Texas

D20 Florida5 changes

N. sitophila

N. perkinsi (PS3)

N. crassa

N. tetraspermaN. hispaniola (PS1)

N. metzenbergi (PS2)

N. intermedia

N. discreta

0.89

86

1.00

89

1.00

68

1.00

91

1.00

89

1.00

96

1.00

84

1.00

96

(Dettman 2003a, Villalta unpublished data)

N. crassa Clade

Phylogeny

Poster 57

CV10 Papua New GuineaCV80 GabonCV56 Haiti

CV57 HaitiCV98 Indonesia

CV93 MexicoCV88 Hawaii

CV82 GabonCV43 Truk

D123 NigeriaD72 Ivory CoastD147 New Mexico


D124 VirginiaD63 Haiti

CV79 GabonD78 CongoD77 Congo

D74 CongoD82 Congo

D75 CongoD100 Tamil NaduD106 Tamil Nadu




D11 KarnatakaD12 KarnatakaD70 Ivory Coast



D144 PanamaD60 Haiti

D24 FloridaD94 YucatanD61 Haiti

D69 Ivory CoastD111 LouisianaD112 Louisiana




D23 FloridaD59 Haiti

D29 FloridaD90 Yucatan




D140 Ivory CoastD91 Yucatan



D14 HawaiiD15 Hawaii

D145 UnknownCV55 Haiti

D55 HaitiD57 Haiti

D58 HaitiCV119 HaitiCV156 Mexico

CV152 MexicoCV155 Mexico





D87 YucatanD120 MadagascarD121 Madagascar

D1 TaiwanD2 Taiwan

D3 PhilippinesD102 Thailand

D18 QueenslandD4 PhilippinesD31 AnhuiD6 TaiwanD8 JavaD80 CongoD9 Java

D33 Papua New GuineaD84 Hawaii

D101 Tamil NaduD50 Tamil NaduD45 Tamil Nadu






D137 KarnatakaD139 KarnatakaD128 Karnataka

D122 HondurasD22 FloridaD64 HaitiD21 Florida


D65 Ivory CoastD73 Ivory Coast

D66 Ivory CoastD141 LiberiaD16 Texas

D142 FijiD7 Java

D95 Ivory CoastD83 GabonD76 CongoD79 CongoD81 CongoD34 Papua New Guinea

D51 MalaysiaD52 ThailandD127 Karnataka






D109 Tamil NaduD39 Tamil NaduD133 Karnataka

D32 AnhuiD35 Papua New Guinea

D36 TahitiD146 New MexicoD71 Ivory Coast


D5 Papua New GuineaD67 Ivory CoastD17 Texas

D20 Florida5 changes

N. sitophila

N. perkinsi (PS3)

N. crassa

N. tetraspermaN. hispaniola (PS1)

N. metzenbergi (PS2)

N. intermedia

N. discreta

0.89

86

1.00

89

1.00

68

1.00

91

1.00

89

1.00

96

1.00

84

1.00

96

N. perkinsi

N. hispaniola

N. metzenbergi

Genome sequences

Assembly size Contigs Genes

39.2 Mb 251 9,841

37.8 Mb 155 10,095

37.3 Mb 176 9,611

34.8 Mb 37 11,048

35.7 Mb 110 9,872

Chaetomium

Podospora

N. crassa

N. discreta

N. tetrasperma

Comparative approach with Mercator improves assemblies

0 0.2 0.4 0.6 0.8 1

Fraction of Assembly

1x106

2x106

3x106

4x106

5x106

Ba

se

pa

irs

Mercator

Broad V7

0 0.2 0.4 0.6 0.8 1


0

1x106

2x106

3x106

4x106

5x106

Ba

se

pa

irs

Mercator

JGI 8X

N.crassa N.discreta

0 0.2 0.4 0.6 0.8 1


0

1x106

2x106

3x106

4x106

5x106

Ba

se

pa

irs

Mercator

JGI 8X

N.tetrasperma

N50orig 664 kbN50merc 2.45Mb

N50orig 2.31 MbN50merc 4.04 Mb

N50orig 976 kbN50merc 2.70Mb

N. crassa Linkage Groups

assembled_4

assembled_1

assembled_2

assembled_7

assembled_6

assembled_3

assembled_8

assembled_9

ncra_LGVII

ncra_LGVI

ncra_LGV

ncra_LGIV

ncra_LGIII

ncra_LGII

ncra_LG_I

assembled_3

assembled_5

assembled_4

assembled_1

assembled_10

assembled_9

assembled_7

assembled2

assembled_6

ncra_LGVII

ncra_LGVI

ncra_LGV

ncra_LGIV

ncra_LGIII

ncra_LGII

ncra_LG_I

N. crassa Linkage Groups

N. tetrasperma(mat A)

N. discreta

Synteny with N. crassa

0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0

N. discreta

N. crassa

N. tetrasperma (mat A)

Repetitive elements (>300bp)

Scale (Megabases)

DeletionInversionContig boundaries

Mating type chromosome synteny

Poster 37

N.tetrasperma (mat A)

N.crassa

N.discreta

N. crassa

N. discreta N. tetrasperma

9903

9611 10096

8427 8684

8221

8047

Gene Conservation in NeurosporaGene content in Neurospora

Poster 36

Histogram of evolutionary rates of orthologs shared between

N. crassa and N. discreta

Evolutionary Rate

Fre

qu

en

cy

0

02

00

40

06

00

80

0

1 2 3 4 5

Search for Adaptively Evolving Genes

(dN/dS)

N.crassa v N. discreta

0 200 400 600 800

02

4

N. crassa Chromosome I position (in 10kb)

dN/dS

0 200 400 600 800

02

4


dN/dS

Distribution of Evolutionary Rates across the N. crassa genome

Evolutionary rates between N. crassa and N. tetrasperma

Evolutionary rates between N. crassa and N. discreta

0 200 400 600 800

02

4


dN/dS

0 200 400 600 800

02

4


dN/dS

Distribution of Evolutionary Rates across the N. crassa genome

Evolutionary rates between N. crassa and N. tetrasperma

Evolutionary rates between N. crassa and N. discretaN.crassa vs N.discreta

N.crassa vs N.tetrasperma

Distribution of Evolutionary Rates across the N.crassa genome

Genes Involved in Adaptation are Enriched For:Sugar Metabolism

DNA Binding/Transcription FactorsMembrane Transport

Adaptation in Neurospora

Dung fungi expanded gene familiesC.globosum P.anserina N.crassa N.tetrasperma N.discreta Family Function

88 72 35 35 36Cellulase and

Cellulose Binding Proteins

24 30 8 7 9Cellobiose

dehydrogenase

67 73 42 49 45Major Facilitator

Superfamily Transporters

16 11 5 5 5 P450

62 91 29 35 33 P450

11 59 32 27 37 HET Domain

Dung fungi expanded gene familiesC.globosum P.anserina N.crassa N.tetrasperma N.discreta Family Function

88 72 35 35 36Cellulase and

Cellulose Binding Proteins

24 30 8 7 9 Cellobiose dehydrogenase

67 73 42 49 45Major Facilitator

Superfamily Transporters

16 11 5 5 5 P450

62 91 29 35 33 P450

11 59 32 27 37 HET Domain

Neurospora expanded gene familiesC.globosum P.anserina N.crassa N.tetrasperma N.discreta Family Function

52 53 69 75 73Transcription

Factor

0 1 7 7 7 C2H2 Zinc Finger

0 0 8 5 7 Signal Peptide

0 0 9 5 8Aldehyde

Dehydrogenase

In Summary

• New N. crassa clade phylogenetic species

• New genomic resources for evolutionary biology of Neurospora

• Better assemblies through comparative analyses

• Genomic rearrangements on Mating chromosome in N. tetrasperma

• Selection and Gene family analyses to identify functional classes that evolving differently

Poster 37

Poster 36

Poster 51

Future directions

• Assembly refinement for N. discreta and N. tetrasperma (JGI)

• Comparative annotation of Neurospora spp. (JGI)

• ESTs from pooled conditions (JGI)

• Mating type chromosome gap closure in N. tetrasperma

• Further identification of genes under selection and expanded gene families

• Traces are in GenBank

NSF

NIH

MIBRS

SWEDEN

BROAD

UNM

Funding Information

UC BerkeleyHome

UNM

FGSC

N.crassa RIP index

RIP index

Freq

uenc

y

0.0 0.5 1.0 1.5 2.0

010

000

3000

050

000

N.tetrasperma RIP index

RIP index

Freq

uenc

y

0.0 0.5 1.0 1.5 2.0

010

000

3000

050

000

N.discreta RIP index

RIP index

Freq

uenc

y

0.0 0.5 1.0 1.5 2.0

010

000

2000

030

000

4000

050

000

6000

0

N.tetraspermaN.crassa N.discreta

RIP Index across Neurospora spp(CpA+ TpG) / (ApC + GpT)

C.globosum has little RIPC.globosum RIP index

RIP index

Freq

uenc

y

0.0 0.5 1.0 1.5 2.0

010

000

3000

050

000

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