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Comparative Genomics in Basidiomycetes - Analyzing multigene families

Comparative Genomics in Basidiomycetes - Analyzing multigene families. Balaji Rajashekar Anders Tunlid Dag Ahrén. Jason Stajich. Basidiomycete genome data. 58,030. Gene 3. Gene 4. Gene 2. Gene 7. Gene 5. Gene 6. Gene 8. Gene 9. Gene 10. Sequence similarity & clustering. BLASTP.

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Comparative Genomics in Basidiomycetes - Analyzing multigene families

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  1. Comparative Genomics in Basidiomycetes- Analyzing multigene families Balaji Rajashekar Anders Tunlid Dag Ahrén Jason Stajich

  2. Basidiomycete genome data 58,030

  3. Gene 3 Gene 4 Gene 2 Gene 7 Gene 5 Gene 6 Gene 8 Gene 9 Gene 10 Sequence similarity & clustering • BLASTP Gene 1

  4. TribeMCL (Enright et al. NAR 2002) • BLASTP: All against all for the basidiomycete genomes • 58,000 versus 58,000 proteins • Split generated network into families • Data and settings dependent TribeMCL animation

  5. Gene family distribution

  6. Global view of proteins vs genome size

  7. Gene family size distribution

  8. Statistical analyses of gene families CAFE (Bie et al, Bioinformatics 2006) • Model the evolution of gene family sizes • Takes phylogeny into account • Calculates birth and death of genes in all nodes • Identifies families with accelerated gene gain/loss including extinction

  9. Gene family expansions/contractions

  10. Protein families in Laccaria • Protein families analysed by CAFE • 1969 Unique protein families • 7352 Protein families in total

  11. Example of families >25 Laccaria proteins

  12. Identification of significant families

  13. PCA of expression data Mycorrhiza Mycelia Fruiting bodies 11 experiments Protein family 2 Axis 1

  14. Comparative Genomics in Basidiomycetes- Analyzing multigene families Balaji Rajashekar Anders Tunlid Dag Ahrén Jason Stajich

  15. Identification of significant families

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