Identification and Evolution of Transcription Factors in Stramenopiles · Identification and...

Identification and Evolution of transcription factors in Stramenopiles

Francisco Buitrago Florez, Silvia Restrepo, Diego Riaño Pachón

[email protected]

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Stramenopiles

Golden Algae Diatoms

Phytophthora Saprolegnia

http://en.wikipedia.org/wiki/File:Dinobryon_sp.jpg framptonwiki541a.wikispaces.com

botany.hawaii.edu telegraph.co.uk

telegraph.co.uk

telegraph.co.uk

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Heterotrophic P. infestans S. parasitica

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Biological Question • Mechanisms?

•  Transcription regulation Networks –  Biological Reprogramming N

atur

e P

rece

ding

s : d

oi:1

0.10

38/n

pre.

2011

.640

0.1

: Pos

ted

12 S

ep 2

011

Regulation

Modificado de Komberg 2007, PNAS:104,12995-61. Cortesía Diego Riaño-Pachon, 2011

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1


Regulation

TFs

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1


Regulation

TRs

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Identification?

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Transcription Factors

Courtesy from Diego Riaño

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Reglas

Cortesía Diego Riaño-Pachon, 2011

Rules

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

128 Rules

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Stramenopiles Organism Size Genes Proteins

spurce

P. infestans 237 Mb 18179 18140 BROAD

P. ramorum 65 Mb 15743 16066 DOE-‐JGI

P. capsici 64 Mb

19805 15919 DOE-‐JGI

P. sojae 86 Mb 19027 19276 DOE-‐JGI

S. parasi3ca 53.09 Mb 20113 20088 BROAD

H. parasi3ca 82.05 Mb 14567 14565 BROAD

P. ul3mum 44.91 Mb 15291 12614 BROAD

T. pseudonana 32 Mb 11397 11318 DOE-‐JGI

P. Tricornutum 28 Mb 10489 10389 DOE-‐JGI

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Identification and Clasification

Rules System

Search Hmmscan!

Proteomes

58 Families

Pfam V. 24 In House Models

Assign Family

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Database

StramenoTFDB

Models Genes Proteins

Rules

Expression data

Related Literature Databases

TFs/TRs Families

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Relative Importance of TFs Families

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

!

1!2!3!

4!

5!

6!

1. Oomycetes!(se!mete!O.tauri!que!es!una!planta)!2. Stramenopile!3. Protist!4. Plants!5. Metazoa!6. Fungi!

Metodo:!Between!Groups!

Intervalo:!Coeficiente!de!correlación!de!Pearson.!!

Dendogram

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Orthologs (Ortho-‐MCL)

Aligment (MAFFT)

EvoluXonary Model

(ProtTest)

Maximum Likelihood (RAxML)

Phylogenomic Reconstruccion 781 Genes!

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

PSOJAE: P. Sojae PINFES: P. Infestans PCAPSI: P.capsici PRAMOR: Phytophthora ramourm HPARAS: Hyaloperonospora parasitica PULTIM: Pythium Ultimum SPARAS: Saprolegnia parasitica PTRICO: Phaeodactylum tricornutim TPSEUD: Thalasiossira pseudonana

Autotrophic

Heterotrophic

Animal Pathogens

Plant Pathogens

Phylogenomic Reconstruccion

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Phylogenetical Signal!

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

•  Deep Analysis TFs/TRs families •  Web Interface •  Phylogenetic independent contrasts

(PIC) •  qPCR •  Inference of gene regulatory

networks

Outlook

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

•  Research fund and to the Fund to support Assistance Professors of the faculty of sciences of the Universidad de los Andes

•  Laboratory of Computational and Evolutionary Biology of the Universidad de los Andes - BCE

•  Laboratory of Mycology and Phytopathology of the Universidad de los Andes – LAMFU

•  Javier Felipe Tabima – Phylogenetic Analysis

Acknowledgements

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Thanks! framptonwiki541a.wikispaces.com


telegraph.co.uk

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Questions? framptonwiki541a.wikispaces.com


telegraph.co.uk

Nat

ure

Pre

cedi

ngs

: doi

:10.

1038

/npr

e.20

11.6

400.

1 : P

oste

d 12

Sep

201

1

Identification and Evolution of Transcription Factors in Stramenopiles · Identification and...

Documents

Transcript of Identification and Evolution of Transcription Factors in Stramenopiles · Identification and...