Sequencing of the oyster mushroom genome

Professor of Microbiology at the Public University of Navarre, Antonio Gerardo Pisabarro de Lucas, is leading an international project to sequence the genome of the oyster mushroom. The project research team is composed of scientists from nineteen universities and research centres from Europe, Canada, Japan, Israel and the United States.

The project, chosen from amongst more than 400 entered for the annual competition of the Joint Genome Institute (JGI) of the United States Department of Energy's Science Office, is one of just over 40 which have the go-ahead, one of the seven coordinated by a European body and the only one led by a Spanish person.

The oyster mushroom, Pleurotus ostreatus, will be the first edible mushroom in the world to be genetically sequenced but, apart from its characteristics that make its consumption beneficial (rich in vitamins and proteins), this fungus is a model for studying the CO₂ cycle – carbon dioxide being one of the principal gases of the greenhouse effect – and holds great potential for use in bioremediation –biodegradation of contaminants –, reasons why, together with other crops such as the yucca or cotton, it has been chosen for genome sequencing by the mentioned North American Genome Institute.

The oyster mushroom and CO₂ balance

The oyster mushroom is actively involved in the re-circulation of carbon at a global level, in as much as this fungus is a lignin-degrading one, lignin being a component of wood of trees and other plants that form part of the second most important store of carbon in the Biosphere. The degradation of this compound is an essential step in the transformation of cellulose - the principal store for carbon – into biofuel.

Moreover, it has to be taken into account that lignin has a chemical composition that is not easy to break down – similar to some of the contaminant compounds that man releases into the environment, such as certain colorants or oils and by-products of the timber industry such as pulp and paper.

Thus, the study of the functioning of the oyster mushroom and of its strategies for adapting to its growth environment and for degrading lignin found in agricultural waste or decomposing wood in the natural environment, may be used for designing systems to enable the elimination of these contaminants from the environment.

The oyster mushroom is also a fungus the cultivation of which is widespread and so the study of its genetic organisation can give pointers to what is needed for many mushrooms not industrially grown in order for them to be produced as industrial crops, such as, for example, Boletus aereus.

More than 10 years of research

The Genetics and Microbiology Team at the Public University of Navarre, of which Professor Pisabarro belongs, has been working with the genetic material of the oyster mushroom since 1994.

Over this period, the Team has established the genetic bases that have made sequencing a viable project and they have managed to sequence about 350 thousand "letters" of the genome of this mushroom, corresponding to 1% of the total genome, a small part but a significant one for estimating the general parameters of the genome such as how many genes there are or how they are organised.

The complete genome for the oyster mushroom has 70 million "letters" or bases, distributed throughout two equivalent copies, given that this fungus has a double copy of each chromosome – as humans do. However, the project of sequencing the complete genome involves the handling of a volume of 280 million letters, given the fact that each one of the two sets of genes has to be read several times in order to ensure a good result. It is like a complicated text that demands an assurance that there are no errors in what has been read.

To understand what this really involves, Pisabarro gives us an example: 70 million letters would be equivalent to a volume of more than 11,500 pages of text. If the pages are normal, folio size and are placed side by side, they would run for a distance of 3.5 kilometres; the letters thereof, written and placed one after the other, would run to 141 km. The genome of the mushroom has twin sets of the genes and, thereby, each set has about 6,000 "pages" on which we estimate there are some 12,000 genes - approximately two genes per page. Thus, the real task now is to determine where each of these genes starts and finishes, what they do and how they do it.

Order 70 million letters

With the selection of the project by the Genomics Institute, it will be this United States-based body that will be responsible for carrying out the sequencing work and computer analysis.

At the Public University of Navarre laboratories the DNA of the oyster mushroom will be isolated and purified and then sent to the Genomics Institute for sequencing. Within one year, approximately, the JGI will have undertaken a first reading of the genome's 70 million letters. And, once again, it will be laboratories at the Public University of Navarre that will order the sequenced fragments and co-ordinate the rest of the project tasks.

From the Navarre university, the resulting computer archive of the sequencing, containing the definitive "pages of letters" for the genetic code, will be then distributed to the other participating laboratories in order to carry out the annotation of the genome sequence – involving the identification of each one of the genes that make up the oyster mushroom, i.e. the genetic constitution of the organism.

Life appeared on Earth some 3,000 million years ago. The evolution undergone by this fungus whose DNA is to be purified, has been through these 3,000 million years, as has the human being. Thus, within its genome there is 3,000 million years of history – the goal of the sequencing of this genome is to unlock and read this history of the organism, so that we might understand its biology and reproduction and enhance its utilization.

Moreover, an understanding of the evolutionary history registered in the genome of the oyster mushroom and its comparison with other histories registered in other genomes that have been – or are currently being – sequenced (human, animal, vegetable and microbian), enables us to obtain an overall and more enriched picture of the evolution of life on Earth.

In the second year of the project, the reading of the genome will be completed and the annotation of the genes perfected. In the end, all the information will be placed at the disposal of the scientific community free of charge. Source : Elhuyar Fundazioa