The Fungi

Abstract

The Kingdom Fungi, home to molds, mushrooms, lichens, rusts, smuts and yeasts, comprises eukaryotes with remarkably diverse life histories that make essential contributions to the biosphere, human industry, medicine and research. With the aim of enticing biologists to include fungi in their research, we note that many fungi have haploid genetics, and that those in cultivation are essentially immortal, two features that make it easier to associate traits with genotype, even for complex traits, than with Drosophila or Arabidopsis. The typical fungal genome size of 30–40 Mb is small by eukaryotic standards, which is why fungi have led the way as models for eukaryote genome sequencing with over 100 assembled genome sequences available [1, 2]. For some fungi, DNA transformations, gene knockouts and knockdowns are routine. Species of Ascomycota and Basidiomycota show simple, multicellular development with differentiated tissues. In many species these tissues are large enough to support studies of transcription and translation in the lab and even in nature. About a billion years ago, give or take 500 million years [3], a population of aquatic, unicellular eukaryotes making sporangia containing zoospores each with a single posterior flagellum split into two lineages: one eventually gave rise to animals, the other to fungi. Here we shall summarize the major diversifications of the Fungi by introducing each major fungal branch in the order that it is thought to have diverged (Figure 1) and presenting salient facts about fungal modes of nutrition, reproduction, communication and interaction with other life. Our views are strongly influenced by the Fungal Tree of Life Project [4–6]. Readers interested in learning more about fungi are encouraged to consult any of a number of comprehensive texts [7, 8]. Figure 1 The fungi. Phylogenetic tree, based on [4], showing relationships of many of the fungal lineages fit to geologic time using the program r8s [73] and considering Paleopyrenomycites to be a member of the Ascomycota [3]. Arrows depict changes in morphology ... The exact order of divergence in deep regions of the eukaryotic tree is controversial. On the lineage that leads to the Fungi there are thought to be two other groups; the first to diverge are the nucleariid amoebae [9], and the next the Microsporidia. Microsporidia are either the sister group to the Fungi, or lie within the Fungi, (Figure 1), and they should be included in studies of fungi. They are unculturable, obligate parasites of animals, including humans. They have extremely reduced eukaryotic genomes — with a genome size of ~2.6 Mb and ~2000 genes [10, 11] — remnant mitochondria, and unique morphologies related to parasitism, including a very frightening polar tube used to initiate infection [10].