Evolutionary genomics of symbiotic fungi
Abstract: Ectomycorrhizae is a mutualistic association between roots of woody plants and a diverse range of soil fungi. The fungi exchange soil derived mineral nutrients for photosynthetic sugars from the host plant. The mycorrhizal symbioses are commonly found in all forest ecosystems and have a major ecological and economical importance. I have used comparative genomics, DNA microarrays and computational approaches to gain insights into the evolution of the ectomycorrhizal symbiosis in two fungi Laccaria bicolor (Basidiomycetes; Agaricales) and Paxillus involutus (Basidiomycetes; Boletales). L. bicolor is the first symbiotic fungus to have its genome sequence determined. The genome assembly contains 65 million base pairs with about ~20,000 predicted protein-encoding genes. Here, I report the analysis of L. bicolor genome and its comparison with the genomes of four other basidiomycetes including the saprotrophic species Coprinopsis cinerea and Phanerochaete chrysosporium, the human pathogen Cryptococcus neoformans and the plant pathogen Ustilago maydis. The compared genomes cover about 550 million years of evolution. A total of 58,030 protein sequences from these five basidiomycetes were clustered into 7352 protein families. The evolution of protein families were analysed for accelerated rates of gain and loss along specific branches of a phylogenetic tree using a stochastic birth and death model. Analysis of the genome sequence of L. bicolor in comparison to other analysed basidiomycetes revealed large genome size, large number of protein families, larger size of protein families, many lineage specific and expanded families, and large number of recent duplicates. The evolution of two large and expanded protein families in L. bicolor having significant homology to protein kinases and Ras GTPases superfamilies were analysed in more detail. The analyses showed these families to contain many paralogs that have arisen through recent duplication events. The comparative analyses of gene families showed that the evolution of symbiosis in L. bicolor has been associated with the expansion of large multigene families. The functions of many of these families are unknown but many of them are differentially expressed during symbiosis. In the second part of my thesis, I have analysed duplicated and rapidly evolving genes that could be associated with symbiotic adaptations in the ectomycorrhizal fungus P. involutus. Strains of P. involutus forming ectomycorrhiza showing various degree of host-specificity were analysed by comparative genomic hybridizations using a cDNA microarray representing 1076 putative unique genes. Approximately 17% of the genes investigated on the array were detected as rapidly and presumably non-neutrally evolving within Paxillus. Among these genes, there were several hydrophobins. Hydrophobins are small, secreted hydrophobic cell surface proteins having several roles in growth and development of fungi. The evolutionary mechanisms responsible for generating sequence and expression divergence among members of the hydrophobin multigene family in P. involutus were examined in more detail.
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