identification and evolution of transcription factors in stramenopiles · identification and...
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Identification and Evolution of transcription factors in Stramenopiles
Francisco Buitrago Florez, Silvia Restrepo, Diego Riaño Pachón
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Stramenopiles
Golden Algae Diatoms
Phytophthora Saprolegnia
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Heterotrophic P. infestans S. parasitica
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Biological Question • Mechanisms?
• Transcription regulation Networks – Biological Reprogramming N
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2011
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: Pos
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Regulation
Modificado de Komberg 2007, PNAS:104,12995-61. Cortesía Diego Riaño-Pachon, 2011
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Modificado de Komberg 2007, PNAS:104,12995-61. Cortesía Diego Riaño-Pachon, 2011
Regulation
TFs
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Modificado de Komberg 2007, PNAS:104,12995-61. Cortesía Diego Riaño-Pachon, 2011
Regulation
TRs
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Identification?
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Transcription Factors
Courtesy from Diego Riaño
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Reglas
Cortesía Diego Riaño-Pachon, 2011
Rules
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Reglas
Cortesía Diego Riaño-Pachon, 2011
Rules
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Reglas
Cortesía Diego Riaño-Pachon, 2011
Rules
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Reglas
Cortesía Diego Riaño-Pachon, 2011
Rules
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128 Rules
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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
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Identification and Clasification
Rules System
Search Hmmscan!
Proteomes
58 Families
Pfam V. 24 In House Models
Assign Family
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Database
StramenoTFDB
Models Genes Proteins
Rules
Expression data
Related Literature Databases
TFs/TRs Families
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Relative Importance of TFs Families
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!
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
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Orthologs (Ortho-‐MCL)
Aligment (MAFFT)
EvoluXonary Model
(ProtTest)
Maximum Likelihood (RAxML)
Phylogenomic Reconstruccion 781 Genes!
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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
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Phylogenetical Signal!
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• Deep Analysis TFs/TRs families • Web Interface • Phylogenetic independent contrasts
(PIC) • qPCR • Inference of gene regulatory
networks
Outlook
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• 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
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Thanks! framptonwiki541a.wikispaces.com
botany.hawaii.edu telegraph.co.uk
telegraph.co.uk
Nat
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Pre
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: doi
:10.
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/npr
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1 : P
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Questions? framptonwiki541a.wikispaces.com
botany.hawaii.edu telegraph.co.uk
telegraph.co.uk
Nat
ure
Pre
cedi
ngs
: doi
:10.
1038
/npr
e.20
11.6
400.
1 : P
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d 12
Sep
201
1