Molecular Evolution of Genes Involved in Quinic Acid Utilization in Fungi

Fungi use diverse organic compounds for their growth and development.  Neurospora crassa  can use quinic acid as its sole carbon source for its growth because of presence of a quinic acid utilization (QUT) cluster of genes in its genome. Using bioinformatics methods we examined a total of 285 completely sequenced fungal genomes comprised of 282 unique species and found there were 117 fungal species having all 7 QUT genes in their genomes. Most species in the classes of Dothideomycetes, Eurotiomycetes, Leotiomycetes and Sordariomycetes have QUT genes, however, among 53 species in Saccharomycetes only 3 species have all 7 QUT genes. There were linage specific losses of QUT genes, such as species in Eurotiomycetes class Onygenales order lacked most of QA utilization genes. Our survey revealed that species in Agaricomycetes, Basidiomycota, Chytridiomycetes, Exobasidiomycetes, Malasseziomycetes, Microsporidia, Schizosacharomycetes, and Tremellomycetes did not have QA utilization genes. Using concatenated protein sequences encoded by 7 QUT genes, a robust phylogenetic tree to infer the evolution of the QUT cluster genes was constructed. In addition, we also found QUT genes from recently sequenced genome of cork oak ( Quercus suber ), however, our analysis suggests that these QUT sequences are likely from a contaminated fungal species.