Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Sequencing of the oyster mushroom genome

04.10.2006
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.

Participating bodies

Concretely, the universities and institutions taking part in the project are the following: from Spain, apart from the Public University of Navarre, the universities of Seville, Salamanca and Leon are collaborating, as well as the CSIC Centre; from the United States, the University of Wisconsin, Southeast Missouri State University, the universities of Michigan, Texas, Duke and Indiana; from Germany, the universities of Georg-August in Gotinga, Munster and Hannover. Also participating are the universities of Toronto (Canada), Vienna (Austria), Hebrea in Jerusalem (Israel), Federico II of Naples (Italy) and Kyushu (Japan).

Irati Kortabitarte | alfa
Further information:
http://www.elhuyar.com
http://www.basqueresearch.com/berria_irakurri.asp?Gelaxka=1_1&hizk=I&Berri_Kod=1046

Further reports about: Carbon Environment Genetic Genom Navarre Sequencing contaminant fungus

More articles from Life Sciences:

nachricht The irresistible fragrance of dying vinegar flies
16.08.2017 | Max-Planck-Institut für chemische Ökologie

nachricht How protein islands form
15.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

Im Focus: Scientists improve forecast of increasing hazard on Ecuadorian volcano

Researchers from the University of Miami (UM) Rosenstiel School of Marine and Atmospheric Science, the Italian Space Agency (ASI), and the Instituto Geofisico--Escuela Politecnica Nacional (IGEPN) of Ecuador, showed an increasing volcanic danger on Cotopaxi in Ecuador using a powerful technique known as Interferometric Synthetic Aperture Radar (InSAR).

The Andes region in which Cotopaxi volcano is located is known to contain some of the world's most serious volcanic hazard. A mid- to large-size eruption has...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

New thruster design increases efficiency for future spaceflight

16.08.2017 | Physics and Astronomy

Transporting spin: A graphene and boron nitride heterostructure creates large spin signals

16.08.2017 | Materials Sciences

A new method for the 3-D printing of living tissues

16.08.2017 | Interdisciplinary Research

VideoLinks
B2B-VideoLinks
More VideoLinks >>>