Comparative genomics is a powerful tool to infer the molecular basis of fungal pathogenicity and its evolution by identifying differences in gene content and genomic organization between fungi with different hosts or modes of infection. Through comparative analysis, pathogenicity-related chromosomes have been identified in Fusarium oxysporum and Fusarium solani that contain genes for host-specific virulence. Lateral transfer of pathogenicity chromosomes, inferred from genomic data, now has been experimentally confirmed. Likewise, comparative genomics reveals the evolutionary relationships among toxin gene clusters whereby the loss and gain of genes from the cluster may be understood in an evolutionary context of toxin diversification. The genomic milieu of effector genes, encoding small secreted proteins, also suggests mechanisms that promote genetic diversification for the benefit of the pathogen.
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We thank our colleague Li-Jun Ma for her enthusiasm and tireless efforts for a greater understanding of fungal biology through genomics. We also thank Dr. Ma and Leslie Gaffney for the preparation of Figure 1 . MR acknowledges the support of the Royal Netherlands Academy of Arts and Sciences , the Netherlands Organisation for Scientific Research and the Centre for Biosystems Genomics . HCK acknowledges the support of the United States Department of Agriculture , National Institute of Food and Agriculture , Agriculture and Food Research Initiative and the National Science Foundation, Environmental Genomics program .