1 L U N D U N I V E R S I T Y Comparative Genomics in Basidiomycetes - Analyzing multigene families Balaji Rajashekar Anders Tunlid Dag Ahrén Jason Stajich

2 L U N D U N I V E R S I T Y Basidiomycete genome data Protein coding genes Genome size (Mb) Laccaria bicolor20, Coprinopsis cinerea13, Phanerochaete chrysosporium10, Cryptococcus neoformans Ustilago maydis ,030

3 L U N D U N I V E R S I T Y Sequence similarity & clustering BLASTP Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Gene 6 Gene 7 Gene 8 Gene 9 Gene 10

4 L U N D U N I V E R S I T Y TribeMCL (Enright et al. NAR 2002) TribeMCL animation BLASTP: All against all for the basidiomycete genomes 58,000 versus 58,000 proteins Split generated network into families Data and settings dependent

5 L U N D U N I V E R S I T Y Gene family distribution LaccariaCoprinopsisPhanerochaeteCryptococcusUstilago Families present Families not present Total7352

6 L U N D U N I V E R S I T Y Global view of proteins vs genome size

7 L U N D U N I V E R S I T Y Gene family size distribution

8 L U N D U N I V E R S I T Y 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 L U N D U N I V E R S I T Y Gene family expansions/contractions Branch Divergence time (MYA) ExpansionNo changeContractionsAverage expansion

10 L U N D U N I V E R S I T Y Protein families in Laccaria 5383 Protein families analysed by CAFE 1969 Unique protein families 7352 Protein families in total

11 L U N D U N I V E R S I T Y Example of families >25 Laccaria proteins Protein familyLacCoprPhaeCrypUstPfam accessionPfam description Significantly Expanded 1* PF00400WD domain, G-beta repeat 2* PF00069, PF07714Protein kinase domain, Protein tyrosine kinase Unique PF00931, PF05729NB-ARC domain, NACHT domain 17*

12 L U N D U N I V E R S I T Y Identification of significant families

13 L U N D U N I V E R S I T Y PCA of expression data Protein family 2 11 experiments Mycelia Mycorrhiza Fruiting bodies Axis 1

14 L U N D U N I V E R S I T Y Comparative Genomics in Basidiomycetes - Analyzing multigene families Balaji Rajashekar Anders Tunlid Dag Ahrén Jason Stajich

15 L U N D U N I V E R S I T Y Identification of significant families

16 L U N D U N I V E R S I T Y