Thon, M.R. and Sukno, S.A. Gene family evolution in Botrytis cinerea and Sclerotinia sclerotium. 3rd. Botrytis Genome Workshop. Tenerife Spain. Sept 2008.
To better understand the role of gene family expansion and contraction in the adaptive evolution of B. cinerea and S. sclerotiorum, we performed a genome-wide comparative analysis of gene family content. Protein sequences from seven fungal genomes were clustered and all clusters containing five or more proteins were analyzed with the CAFE software package to identify statistically significant changes in gene family size. Since we are interested in the evolution of the Leotiomycetes, we identified the gene families that showed a significant size changes along the branch that represents the divergence of the Leotiomycetes from the lineage shared by the non-Leotiomycete, Stagonospora nodorum. We identified 20 gene families with statistically significant p-values (P < 0.01), of which seven represent gene family expansions, and 13 represent gene family contractions. Three of the seven families that show evidence for expansion have roles in carbohydrate metabolism, suggesting that changes in carbohydrate metabolism occurred during the evolution of this lineage of fungi.
We have also performed a detailed analysis of the G-protein coupled receptor (GPCR) gene families. We used InterProScan and BLASTP to identify GPCRs in the genomes of Botrytis cinerea and S. sclerotiorum. Proteins belonging to six different GPCR families were identified. The PTHll-like proteins make up the largest family of GPCRs, and is comprised of 56 copies in B. cinerea and 48 copies in S. sclerotiorum. The M. grisea PTH11 protein functions in substrate sensing for appressorium development. The large and variable size of this family suggests that it is evolving rapidly, and coupled with its hypothetical role in external substrate sensing, suggests that this family has an important role in the adaptation of these species to their environment.