Breeding new strains of mushrooms

When it comes to choosing a sexual partner, the options seem endless for fungi. Many of the fungi that sexually reproduce are isagomous, meaning that their reproduction cells do not differ in appearance. The terms ‘male’ and ‘female’ thus do not apply to many members of the fungal kingdom. Instead, their reproduction is a complex process governed by mating types.

“Some species are known for having thousands of different mating type options”, says Thomas Abeel of the department Pattern Recognition and Bioinformatics (Faculty of Electrical Engineering, Mathematics and Computer Science). His research group is specialised in unraveling the workings of complex genomes, amongst which those of fungi.

For microbiologists, the complex reproduction system of fungi is a bit of a bother. “It is extremely difficult to study the genetics of fungi, such as mushrooms,” says Abeel. “Their genomic architecture is quite different from that of humans.”

A new landmark paper

In 2016, Abeel’s research group published an important paper in Nature Scientific Reports in which the team disclosed that each fungus cell contains two or more nuclei containing DNA from its progenitors. In contrast, most organisms – all animals and plants – contain only one cell nucleus in each cell in which DNA from both parents is mixed.

Now the researchers have published another landmark paper together with colleagues from Utrecht University and Wageningen University. They discovered that the genes from the parental DNAs are expressed at different times during mushroom development. The article ‘Nucleus-specific expression in the multinuclear mushroom-forming Agaricus bisporus fungus reveals different nuclear regulatory programmes’, was published in the journal PNAS on 11 April 2018.

“Unravelling this was a tough challenge,” says Abeel. “You can investigate the genetic activity (the production of proteins). But if you want to pinpoint protein production to a specifically parental gene, you need to use very complicated algorithms to analyse your data. That is what our group here specialises in doing.”

Beer and bread

Fungi, such as mushrooms, play an important role in our ecosystem. In nature, they recycle dead plants and animals. As humans, we not only eat fungi, but also use them in making food such as bread and beer, and as bioreactors in the manufacture of drugs and other substances. They also play a direct role in human health since they can cause infections.

The impact of the new discovery is that from now on, any study of mushrooms, such as the quest for the genes involved in mushroom formation, starts with determining the active nucleus – the ‘paternal’ or ‘maternal’ nucleus. This new understanding of the molecular mechanisms in mushroom DNA can be used to breed new strains that can improve the cultivation of edible mushrooms such as the common mushroom.

Much of the article in PNAS originates from the dissertation by Thies Gehrmann, who obtained his PhD on Friday April 6 at TU Delft. For his doctoral research, he developed and applied methods of bioinformatic analysis to understand variations within and between mushroom-forming fungi. The phenomenon described in PNAS is an example of that.