Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

Abstract

As decomposers, fungi are key players in recycling plant material in global carbon cycles. We hypothesized that genomes of early diverging fungi may have inherited pectinases from an ancestral species that had been able to extract nutrients from pectin-containing land plants and their algal allies (Streptophytes). We aimed to infer, based on pectinase gene expansions and on the organismal phylogeny, the geological timing of the plant-fungus association. We analyzed 40 fungal genomes, three of which, including Gonapodya prolifera, were sequenced for this study. In the organismal phylogeny from 136 housekeeping loci, Rozella diverged first from all other fungi. Gonapodya prolifera was included among the flagellated, predominantly aquatic fungal species in Chytridiomycota. Sister to Chytridiomycota were the predominantly terrestrial fungi including zygomycota I and zygomycota II, along with the ascomycetes and basidiomycetes that comprise Dikarya. The Gonapodya genome has 27 genes representing five of the seven classes of pectin-specific enzymes known from fungi. Most of these share a common ancestry with pectinases from Dikarya. Indicating functional and sequence similarity, Gonapodya, like many Dikarya, can use pectin as a carbon source for growth in pure culture. Shared pectinases of Dikarya and Gonapodya provide evidence that even ancient aquatic fungi had adapted to extract nutrients from the plants in the green lineage. This implies that 750 million years, the estimated maximum age of origin of the pectin-containing streptophytes represents a maximum age for the divergence of Chytridiomycota from the lineage including Dikarya.

Keywords: Gonapodya; carbohydrate active enzymes; evolution; fungal phylogeny; geological time; pectinases; streptophytes.

Fig. 1.—

Phylogeny of fungi based on analysis of data from 40 genomes. Numbers in black are the bootstrap values from ML analysis; the posterior probability from Bayesian analysis was one unless specified otherwise by a numeral following a slash. Numbers in red are the fixation points in RADICAL analysis, and smaller numbers indicate better support for the node, whereas red asterisks indicate nodes so poorly supported that they were not fixed. The sidebars show the number of genes present in each species, out of the 136 genes included in the analysis. Mucor circinelloides and Mortierella verticillata had the largest number, 126 genes each.

Fig. 2.—

Evolution of GH28 pectinase genes within the phylogeny of fungi, based on Notung-rearranged gene tree/species tree reconciliation. Branch thickness is proportional to pectinase copy number. The numerals above the branches are the copy numbers, followed by the number of duplication (D) or loss events (L) associated with the branch, both estimated by “Notung-rearranged analysis.” Within species, duplication and loss events are not counted. Following the genus name is its total number of GH28 gene copies. Pectinase gene expansions were concentrated on branches leading to node 1, which represents the most recent common ancestor of Chytridiomycota and terrestrial fungi, and to node 2, representing the common ancestor of Pezizomycotina.

Fig. 3.—

Chronogram showing the effect on fungal ages of assuming that Chytridiomycota diverged from its sister clade only after pectin evolved in plant cell walls, some 750 Ma. Pectinase gene expansions were concentrated on branches leading to node 1, which represents the most recent common ancestor of Chytridiomycota and terrestrial fungi, and to node 2, representing the common ancestor of Pezizomycotina. At these branches, the letters and numbers before a colon designate a pectinase family in which gene duplications mapped to the branch, followed by the number of duplication (D) events estimated from the Notung-rearranged analysis and then from the Notung-bootstrap analysis. The shaded area shows the estimated age of origin of land plants by recent studies (Steemans et al. 2009; Rubinstein et al. 2010).