Jason Stajich UC Berkeley [PDF]

Fungal genome evolution. Jason Stajich. UC Berkeley. Page 2. Fitzpatrick DA, Logue ME, Stajich JE, Butler G. BMC Evoluti

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Fungal genome evolution Jason Stajich UC Berkeley

Fitzpatrick DA, Logue ME, Stajich JE, Butler G. BMC Evolutionary Biology 2006

SNAP AUGUSTUS

Genome

Glimmer Genscan BLASTZ BLASTN

ZFF to GFF3

GFF to AA

GFF2 to GFF3 Tools::Glimmer Tools::Genscan SearchIO

Bio::DB::GFF

Rfam tRNAscan

ESTs

exonerate

predicted proteins

SearchIO

GFF2 to GFF3

protein2genome

exonerate est2genome

http://fungal.genome.duke.edu

FASTA all-vs-all

Proteins

SearchIO

protein to genome coordinates

Tools::GFF Proteins

Analysis

Methodology

HMMER

Find orthologs

MCL

GLEAN (combiner) Gene families

Find orthologs

Improve gene predictions

Gene families

Multiple sequence alignment

Gene trees Protein, NT, indel evolutionary rates

• • •

CAFE

Intron position analysis

Lineage specific duplications and losses

Multiple sequence CAFE alignment

Protein & NT evolutionary rates

“Core” conserved genes

Pathogens and non-pathogens Ecological niches, sexual strategies Contrasts of multicelluar and unicellular fungi; morphological forms

Chaetomium globosum (463) Podospora anserina (359) Neurospora crassa (336) Euascomycota Magnaporthe grisea (368) Fusarium graminearum (372) Aspergillus fumigatus (481) Aspergillus terreus (474) Aspergillus nidulans (469) Stagonospora nodorum (403) Saccharomyces cerevisiae (7) Candida glabrata (6) Hemiascomycota Kluyveromyces lactis (6) Ashbya gossypii (7) Debaryomyces hansenii (5) Yarrowia lipolytica (30) Archiascomycota Schizosaccharomyces pombe (214) Phanerochaete chrysosporium (1615) Basidiomycota Coprinus cinereus (1621) Cryptococcus neoformans (1578) Opisthokont Ustilago maydis (86) Zygomycota Rhizopus oryzae (947) Mus musculus (2656) Vertebrates Homo sapiens (2735) Fugu rubripes (2685) Arabidopsis thaliana (2290) Plants 0.1

600

500

Hemiascomycota

400

K.lactis 300 S.cerevisiae Y.lipolytica 200

100

0

U.maydis

Euascomycota

D.hansenii

Basidiomycota

A.gossypii

Mean intron length (bp)

C.glabrata

C.cinereus

P.chrysosporium

C.neoformans

R.oryzae

S.pombe 0

1

2

3

4

5

Mean introns per kb (CDS)

6

7

Saccharomyces

Y. lipolytica

Eurotiomycetes + S. nodsum

Sordariomycetes

S. pombe

C. cinereus

P. chrysosporium

C. neoformans

U. maydis

R. oryzae

Vertebrates

A. thaliana

A

6.61 2.28 0.21 3.80 3.89 3.90 0.52 0.89 1.12 0.07 0.02 5.51 7 30 2290 947 86 1578 1615 1621 214 2745 592 981 359 114 0 0 111 653 258 251 148 0 1 0 32 623 103 111 23 1355 4.01 0.07 1.20 1667 29 500 87 427 191 302 7 162 3.55 1.28 1476 533 0 373 0 9 2.23 3.55 925 1476 588 299 150 328 3.49 474 96 15 3.73 1550 217 91 4.60 1911 294 0

Ashbya gosspyii Kluyveromyces lactis Saccharomyces cerevisiae Candida glabrata Yarrowia lipolytica Schizosaccharomyces pombe Cryptococcus neoformans Cryptococcus neoformans grubii Cryptococcus gattii WM276 Cryptococcus gattii R265 Phanerochaete chrysosporium

Saccharomyces

Hemiascomycota

Basidiomycota changes Hymenomycota

Basidiomycota 500

400

300

Homobasidiomycota

200

100

0

C.neoformans P.chrysosporium

Coprinus cinereus Ustilago maydis Rhizopus oryaze

C.cinereus

U.maydis

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

Million years ago 400

136 Homobasidiomycota 300

200

100

0

141 C.cinereus

ccin 03995 ccin 12432 ccin 12477 ccin 12447 ccin 03760 ccin 08843 ccin 08880 ccin 08948 ccin 08949 ccin 09228 ccin 08947 ccin 08946 ccin 12431 ccin 12515 ccin 08608 ccin 12514 ccin 07535 ccin 07536 ccin 05141 ccin 07531 ccin 04462 ccin 04461 ccin 04460 ccin 07538 ccin 01326 ccin 04884 ccin 07555 ccin 07554 ccin 03994 ccin 12516 ccin 09337 ccin 09357 ccin 09950 ccin 00042 ccin 00039 ccin 00043 ccin 11079 ccin 11073 ccin 12301 ccin 03618 ccin 12868 ccin 12386 ccin 03622 ccin 09244 ccin 08520 ccin 10950 ccin 13218 ccin 13220 pchr 04215 pchr 02481 pchr 02475 pchr 02324 pchr 02322 pchr 02461 pchr 02249 pchr 02248 pchr 02471 pchr 02460 pchr 02469 pchr 02472 pchr 02470 pchr 02468 pchr 02462 pchr 02442 pchr 02441 pchr 02317 pchr 02473 pchr 02477 pchr 02480 pchr 02479 pchr 02474 pchr 02459 pchr 02478 pchr 09197 pchr 08602 pchr 02326 pchr 08048 pchr 08046 pchr 08045 pchr 08047 pchr 02328 pchr 06733 tree 16195 pchr 10861 pchr 07430 pchr 07443

CYP64 was from independent duplication

C. cinereus expansion

Mario Cervini

P. chrysosporium expansion

Tom Volk

Population Genomics • Model systems S. cerevisiae • 25 strains WGS. • Funding for 90 strains of at 2-3X; 10 at 6X: Association mapping

• Focused on pathogenic fungi • Rates of recombination asexual/sexual • Hyper/hypo virulent strains • Genome structural variation

Nuts and Bolts • Genome annotation • Sequence Similarity analysis • Gene lists • Gene and species tree comparisons • Rates of molecular evolution

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