Neurospora as a model for evolutionary...
Transcript of 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
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
N. discretaN. tetrasperma
Mating difference
Heterothallic
Pseudohomothallic
Heterothallic
Chaetomium
Podospora
N. crassa
N. discretaN. tetrasperma
Existing Genome Sequence
Broad
Genoscope/CNRS
Broad
Chaetomium
Podospora
N. crassa
N. discretaN. tetrasperma
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(Dettman 2003a, Villalta unpublished data)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
D107 Tamil NaduD42 Tamil Nadu
D99 Tamil NaduD98 Tamil Nadu
D11 KarnatakaD12 KarnatakaD70 Ivory Coast
D110 LouisianaD114 Louisiana
D117 LouisianaD115 Louisiana
D144 PanamaD60 Haiti
D24 FloridaD94 YucatanD61 Haiti
D69 Ivory CoastD111 LouisianaD112 Louisiana
D118 LouisianaD119 Louisiana
D116 LouisianaD143 Louisiana
D19 FloridaD30 Florida
D23 FloridaD59 Haiti
D29 FloridaD90 Yucatan
D88 YucatanD62 Haiti
D85 YucatanD56 Haiti
D27 FloridaD28 Florida
D140 Ivory CoastD91 Yucatan
D96 Ivory CoastD113 Louisiana
D68 Ivory CoastD13 Louisiana
D14 HawaiiD15 Hawaii
D145 UnknownCV55 Haiti
D55 HaitiD57 Haiti
D58 HaitiCV119 HaitiCV156 Mexico
CV152 MexicoCV155 Mexico
CV91 MexicoCV89 MexicoCV148 Mexico
CV90 MexicoCV153 MexicoCV154 Mexico
D86 YucatanD89 Yucatan
D93 YucatanD92 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
D44 Tamil NaduD46 Tamil Nadu
D48 Tamil NaduD49 Tamil Nadu
D47 Tamil NaduD134 Karnataka
D137 KarnatakaD139 KarnatakaD128 Karnataka
D122 HondurasD22 FloridaD64 HaitiD21 Florida
D25 FloridaD26 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
D131 KarnatakaD41 Tamil Nadu
D43 Tamil NaduD126 Karnataka
D136 KarnatakaD125 Karnataka
D108 Tamil NaduD40 Tamil Nadu
D109 Tamil NaduD39 Tamil NaduD133 Karnataka
D32 AnhuiD35 Papua New Guinea
D36 TahitiD146 New MexicoD71 Ivory Coast
D37 KarnatakaD54 Thailand
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
D10 KarnatakaD53 Thailand
D124 VirginiaD63 Haiti
CV79 GabonD78 CongoD77 Congo
D74 CongoD82 Congo
D75 CongoD100 Tamil NaduD106 Tamil Nadu
D103 Tamil NaduD105 Tamil Nadu
D107 Tamil NaduD42 Tamil Nadu
D99 Tamil NaduD98 Tamil Nadu
D11 KarnatakaD12 KarnatakaD70 Ivory Coast
D110 LouisianaD114 Louisiana
D117 LouisianaD115 Louisiana
D144 PanamaD60 Haiti
D24 FloridaD94 YucatanD61 Haiti
D69 Ivory CoastD111 LouisianaD112 Louisiana
D118 LouisianaD119 Louisiana
D116 LouisianaD143 Louisiana
D19 FloridaD30 Florida
D23 FloridaD59 Haiti
D29 FloridaD90 Yucatan
D88 YucatanD62 Haiti
D85 YucatanD56 Haiti
D27 FloridaD28 Florida
D140 Ivory CoastD91 Yucatan
D96 Ivory CoastD113 Louisiana
D68 Ivory CoastD13 Louisiana
D14 HawaiiD15 Hawaii
D145 UnknownCV55 Haiti
D55 HaitiD57 Haiti
D58 HaitiCV119 HaitiCV156 Mexico
CV152 MexicoCV155 Mexico
CV91 MexicoCV89 MexicoCV148 Mexico
CV90 MexicoCV153 MexicoCV154 Mexico
D86 YucatanD89 Yucatan
D93 YucatanD92 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
D44 Tamil NaduD46 Tamil Nadu
D48 Tamil NaduD49 Tamil Nadu
D47 Tamil NaduD134 Karnataka
D137 KarnatakaD139 KarnatakaD128 Karnataka
D122 HondurasD22 FloridaD64 HaitiD21 Florida
D25 FloridaD26 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
D131 KarnatakaD41 Tamil Nadu
D43 Tamil NaduD126 Karnataka
D136 KarnatakaD125 Karnataka
D108 Tamil NaduD40 Tamil Nadu
D109 Tamil NaduD39 Tamil NaduD133 Karnataka
D32 AnhuiD35 Papua New Guinea
D36 TahitiD146 New MexicoD71 Ivory Coast
D37 KarnatakaD54 Thailand
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
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
Fraction of Assembly
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
Fraction of Assembly
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
N. crassa Chromosome I position (in 10kb)
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
N. crassa Chromosome I position (in 10kb)
dN/dS
0 200 400 600 800
02
4
N. crassa Chromosome I position (in 10kb)
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