Fungal Genomes

© Else C .Vellinga
Original publication: Mycena News, October 2008

The publication of the human genome in 2001 was a milestone in our understanding of the human genetic make-up. The data shed light on the number of protein-coding genes (20–25 thousand, far fewer than expected), their position and composition, and the rest of the genome, which lies between the genes, and whose significance is still obscure. The data are a treasure trove for biomedical science. For example, they have been widely used to hunt for the genes that cause, or make us susceptible to, particular diseases.

Fig. 1

What exactly is a genome sequence? It is the order, like letters in a text, of four different bases (bases being a particular kind of molecule) in a chain of millions, an order which scarcely varies from one individual to another in the same species. We say that this order is the genetic code of the species and different orders make different species. But the order is more than a name: it is a set of specifications for making the myriad chemical building blocks of life. The bases form the rungs of a twisted ladder which is the structure of the DNA molecule (the “sides” of the ladder, famously called the double helix, are made up of sugars and phosphates). Does this mean that there are two orders, corresponding to the two sides of the ladder? Not really. Eukaryotes have four different DNA bases (adenine, cytosine, guanine, and thymine), which are paired (A-T and C-G) with one member of each pair on a different side (see fig.1). Because of this correspondence, the order of bases on one side of the ladder can be read from the bases on the other side. A part of the ladder that codes for the making of a particular protein or enzyme is called a gene; three bases in a row code for one amino acid, and many amino acids (often hundreds) make up proteins and enzymes. There are patterns in the code that mark the beginning and end of genes and the intervening regions are called “non-coding,” though their significance is not understood. DNA is organized in chromosomes in the cell nucleus, but also in organelles within the cell, like mitochondria, which were once bacteria.

Humans were by no means the first species to have their genome sequenced. Bacteria, with their small genomes, were the forerunners, and the first eukaryotic (non-bacterial) organism was a fungus: baker’s yeast (Saccharomyces cerevisiae) (fig.2). Next came three other genetic models: the first multicellular organism, the nematode Caenorhabditis elegans (colloquially called C. elegans) (1998); the fruit fly Drosophila melanogaster (2000); and the plant model, Arabidopsis thaliana (also in 2000). The Homo sapiens genome was ready in 2001.

The publication of the yeast genome in 1996, with the title Life with 6000 Genes, is still a very interesting read. The functions of many of its genes were not known at that time. In retrospect, the yeast genome seems very compact and low in non-coding regions. The work on that first sequencing project took many years, involved 600 scientists (only 16 of whom became coauthors of the paper), and many institutions worldwide. At that time it was daringly estimated that the human genome sequence would be ready in 2005. The invention of different, faster sequencing techniques, the development of faster computers and novel software, and the rivalry of two teams, sped up the process. The human genome was done in 2001. Now, 12 years after the publication of the first fungal genome, over 70 species of fungi have been completely sequenced—including several strains for quite a few species—and many more are in the pipeline. The choice of species to be sequenced was determined by several factors: those that cause human disease or considerable damage to crops were first, followed by some model organisms like baker’s yeast, Neurospora crassa, and Coprinopsis cinerea (though the data for the ink cap are not yet publicly available). Now, costs have gone down considerably, and the time has come when almost anyone can dream of sequencing his or her favorite fungus (or even him or herself ) starting at $15,000 for material costs. For this amount of money you’ll get very raw data produced in a week or so. Mainstream sequencing, analyzing, and annotating of the data still adds up to around $400,000. Work is scheduled for the false truffle, Rhizopogon salebrosus and the dyer’s puffball, Pisolithus microcarpus, and is well underway for the button mushroom, Agaricus bisporus.

Ascomycetes were the first fungi to be sequenced, as that group harbors many well known human pathogens, including Aspergillus fumigatus, Candida albicans, and Coccidioides immitis. Only a small number of basidiomycetes have been sequenced so far. The crustforming fungus, Phanerochaete chrysosporium, was the first basidiomycete. This might be an unknown for the mushroomer, but it is a species with great industrial potential, both as a decomposer of lignin (that hard component of plants, trees in particular)—making it very useful in the paper and fabric industry—and in hazardous waste remediation. Number two was a human pathogen, Cryptococcus neoformans, another yeast. The disease it causes used to be rather obscure, but patients with AIDS, whose immune systems have been compromised are susceptible to this pathogen.

The corn smut, Ustilago maydis, and most recently an ectomycorrhizal species, Laccaria bicolor, have also been completely sequenced. For all of these, publications can easily be found (see the list under Further Reading), and the data are publicly available on the web. So, for a very varied but extremely limited group of basidiomycetes, the genome data are available.

At first the focus was to figure out what kind of genes there are and what they do. This is certainly a work in progress, as baker’s yeast has 6,000 genes, and Laccaria around 20,000! Besides genes, the rest of the genomes contain lots of noncoding regions, repeated elements, and so-called junk DNA (all of which has to be sorted out, as well). These pieces can still be useful, though we do not know exactly why and how (that “junk” label may be premature).

The next step was to compare the genes of one species with the genes of others, and relate the differences to lifestyle. The four basidiomycetes, which represent totally different lifestyles, provide a good example. For instance, Phanerochaete chrysosporium has many genes involved in the breakdown of lignin, but these genes are lacking in Laccaria bicolor. These comparisons also showed that a species often does not have just one gene to perform such an important task, but several, and these might be derived from a single shared ancestor gene. There are also studies looking specifically at those genes that are involved in the decomposition of plant material. These include ones that code for laccases and different types of peroxidases (lignin peroxidases and manganese peroxidases) and indeed, Laccaria bicolor has not been equipped with genes for peroxidases. Cryptococcus cells are surrounded by a polysaccharide capsule, and this envelope is made by a series of 30 different genes, which are absent in the other basidiomycetes investigated so far. This information might be extremely useful in the battle against this fungus. The smut fungus, Ustilago maydis, has, again, a different lifestyle. In one stage it lives as a saprotrophic yeast, and in another grows inside a corn cob, forming the gall-like “huitlacoche,” an enlarged part of the cob full of smut spores. It is not a very aggressive pathogen and lacks the genes to make the enzymes that degrade the plant cell-wall and give it access to the contents. But its genome sequence did reveal an unsuspected set of small genes that play a role in its virulence. In contrast, the rice blast fungus, Magnaporthe grisea, an ascomycete, is well-provided with genes that encode for cutinases, the enzymes that decompose cutin (the first barrier the plant uses to keep intruders at bay). Comparing the genetic composition of phylogenetically different fungi with similar lifestyles (e.g. the ectomycorrhizal Tuber, an ascomycete, and its basidiomycete counterparts, such as Boletus edulis and Amanita muscaria), is another interesting research field.

Evolutionary histories of species can be determined by comparing complete genomes, but the small number of fungal genomes available means that these studies still have limited power. One such study, which was published a few years ago, was based on 42 different genomes, of which only four represented basidiomycetes. It would be great if whole-genome studies could indicate which single-gene sequences gave the same results as the more reliable genome-wide phylogenies, in order to validate which sequences to use in future phylogenetic studies. Gene phylogenies are not by definition the same as species phylogenies, as depending on the environmental pressure, genes undergo different changes. The current favorites are LSU and a few protein-coding genes for phylogenetic studies, and ITS as a fungal “barcoder.”

Whole genomes can also reveal aspects of evolutionary history that no single gene can. For instance, they reveal where and when genome duplication took place (as happened once in a group of ascomycete yeasts, close to the baker’s yeast), and they also show that a switch in the interpretation of the code of the base sequence “CTG” has occurred—in most species this translates into the amino acid leucine, but a group of Candida species makes serine out of it.

But up to now, only the surface has been scratched. Coming are more in-depth questions concerning gene function. Does a gene work on its own? When is it active? Does it always have the same function, or does it depend on the circumstances? And of course, many more whole genomes will be sequenced. I’m looking forward to seeing the secrets of my own pet fungi, the beautiful parasol mushrooms, revealed!

Further Reading: