1. Phylogenetic analysis To infer and study evolutionary history of homologous gene families Manuel Ruiz (CIRAD, Data Integration team) Alexis Dereeper (IRD) Nathalie Chantret (INRA) Jean-François Dufayard (CIRAD, Data Integration team)

2. Species evolutionary history Species phylogeny, and molecular phylogeny Species phylogeny

3. Species evolutionary history Species phylogeny Species phylogeny, and molecular phylogeny Molecular evolutionary history Molecular phylogeny

4. Species evolutionary history Species phylogeny Species phylogeny, and molecular phylogeny Molecular evolutionary history Molecular phylogeny Modeling (trees) Modeling (sequences, trees)

5. Species phylogeny, and molecular phylogeny Wheat Rice Tomato Sequence 1 (wheat) Sequence 2 (rice) Sequence 3 (tomato) To infer evolutionary gene history... Permits to infer evolutionary species history ? What signal is supported by sequences ? Are speciations the only important events ?

6. Species phylogeny, and molecular phylogeny Wheat Rice Tomato Duplication Sequence 1 (wheat) Sequence 2 (rice) Sequence 3 (tomato) Sequence 4 (wheat) Sequence 5 (rice) Sequence 6 (tomato)

7. Species phylogeny, and molecular phylogeny Wheat Rice Tomato Gene losses Sequence 1 (wheat) Loss (rice) Sequence 3 (tomato) Loss (wheat) Sequence 5 (rice) Loss (tomato)

8. Species phylogeny, and molecular phylogeny Wheat Rice Tomato Losses Sequence 1 (wheat) Sequence 3 (tomato) Sequence 5 (rice)

9. Species phylogeny, and molecular phylogeny Wheat Rice Tomato Tree reconciliation Sequence 1 (wheat) Loss (rice) Sequence 3 (tomato) Loss (wheat) Sequence 5 (rice) Loss (tomato) Sequence 1 (wheat) Sequence 3 (tomato) Sequence 5 (rice)

10. Definitions Sequence 1 (wheat) Sequence 2 (rice) Sequence 3 (tomato) Sequence 4 (wheat) Sequence 5 (rice) Sequence 6 (tomato) Similarity: mathematical measure of similarity between two sequences (quantitative concept). Coverage: relative or absolute length along which two sequences are comparable. Homology: two molecules are homologous if they have derived from a common ancestral molecule (qualitative concept). Orthologous genes : genes derived from a common ancestor and diverged after a speciation event, they belong to different species. Paralogous genes : genes derived from a common ancestor and diverged after a duplication event, they can belong to the same species. In silico In vivo

11. Starting data 4 sequences from the reference transcriptome of Oryza sativa 1 mapped consensus sequence, for each individual (10 crop african rice et 1 wild african rice). Os2g25612Os3g52163Os4g66669 RC1 RC2 RC3... RS7

12. Alignment and cleaning: Align similar portions between sequences, and select conserved bloc in order to support the homology hypothesis. Workflows Clustering: Retrieve homologous gene families Spot paralogies anterior to the Oryza sativa / Oryza glaberima divergence. Oryza sativa transcriptome: Sequence1_SATIVA Sequence2_SATIVA... Consensus Oryza glaberima / Oryza barthii: Sequence1_RC1 Sequence2_RS1... Phylogenetic reconstruction: Find a tree likely to explain the alignment in a given model of evolution. Analyse: Display, rooting, reconciliation Interspecifique / inter-genderIntraspecifique / intra-gender

13. Alignment and cleaning: Align similar portions between sequences, and select conserved bloc in order to support the homology hypothesis. Workflows Clustering: Retrieve homologous gene families Spot paralogies anterior to the Oryza sativa / Oryza glaberima divergence. Oryza sativa transcriptome: Sequence1_SATIVA Sequence2_SATIVA... Consensus Oryza glaberima / Oryza barthii: Sequence1_RC1 Sequence2_RS1... Phylogenetic reconstruction: Find a tree likely to explain the alignment in a given model of evolution. Analyse: Display, rooting, reconciliation Interspecifique / inter-genderIntraspecifique / intra-gender Similar sequences from distant species: Sequence1_MAIZE Sequence2_SORBI... BLAST on public databanks: Search homologous genes from several distant species Clarify the dates for duplication events

14. Homologous search in public databanks BLAST :