Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes

Abstract

Fungal type I polyketides (PKs) are synthesized by PK synthases (PKSs) and include well known secondary metabolites such as the anticholesterol drug lovastatin and the potent natural carcinogen aflatoxin. Other type I PKs are known to be virulence factors for some plant pathogens and pigments such as melanin. In this study, a phylogenomic approach was used to investigate the origin and diversity of fungal genes encoding putative PKSs that are predicted to synthesize type I PKs. The resulting genealogy, constructed by using the highly conserved PKS ketosynthase (KS) domain, indicated that: (i). Species within subphylum Pezizomycotina (phylum Ascomycota) but not early diverging ascomycetes, like Saccharomyces cerevisiae (Saccharomycotina) or Schizosaccharomyces pombe (Taphrinomycotina), had large numbers (7-25) of PKS genes. (ii). Bacteria and fungi had separate groups of PKS genes; the few exceptions are the likely result of horizontal gene transfer from bacteria to various sublineages of fungi. (iii). The bulk of genes encoding fungal PKSs fell into eight groups. Four groups were predicted to synthesize variously reduced PKs, and four groups were predicted to make unreduced PKs. (iv). Species within different classes of Pezizomycotina shared the same groups of PKS genes. (v). Different fungal genomes shared few putative orthologous PKS genes, even between closely related genomes in the same class or genus. (vi) The discontinuous distributions of orthologous PKSs among fungal species can be explained by gene duplication, divergence, and gene loss; horizontal gene transfer among fungi does not need to be invoked.

Fig. 1.

Genealogy of type I PKSs, inferred by maximum parsimony analysis of the KS domain. Major clades and subclades are indicated by vertical bars, each of which shares a common organization of domains (those in parentheses are variable in their presence/absence within that clade). Branch length indicates number of inferred amino acid changes. Numbers below branches indicate percentage bootstrap support for each clade. All branches present in a strict consensus of the maximum parsimony trees received bootstrap support. Bold branches indicate putative orthologs, which were inferred as described in Materials and Methods. Monophyletic gains and losses of domains are noted by arrows. Three G. moniliformis PKSs were previously represented by GenBank submissions; these are noted with double asterisks. The accession numbers for all sequences obtained from GenBank are given in Table 1. Three G. zeae and one B. fuckeliana PKSs represented by partial C-terminal fragments of the KS domain were mapped onto the tree that was based on an alignment that included only N-terminalfragments; these are marked with a single asterisk. Alignment was based on 4,862 amino acids from the KS domain; 462 characters were informative, 20 were uninformative, and 4 were constant. Parsimony was performed with 100 random additions. Shown is one of 18 most-parsimonious trees of 17,859 steps, consistency index (CI) = 0.2763, rescaled CI = 0.1491. The maximum parsimony trees generated by coding gaps as either 21st amino acid or as missing were not significantly different from each other or from the tree generated by neighbor joining.

Fig. 2.

Species tree (Upper) depicts the inferred gene duplication and gene losses necessary to account for the distribution of these PKS proteins present in fungal nonreducing PKS subclade III (Lower). Arrows indicate the two gene duplication events, and X indicates the extinction of the ortholog of C. heterostrophus PKS23 in the lineage leading to B. fuckeliana.

Fig. 3.

Venn diagrams showing predicted PKS gene orthologs shared between and among taxa, inferred as described in Materials and Methods. (A) Among the classes Leotiomycetes (represented by B. fuckeliana), Dothideomycetes (C. heterostrophus), and Sordariomycetes (N. crassa, G. moniliformis, and G. zeae). (B) Among the Sordariomycetes: N. crassa, G. moniliformis, and G. zeae.