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Discoveries in the fungal kingdom: RUB researchers decode genome with new technique

09.04.2010
PLoS Genetics: efficient "next generation" sequencing

Using "next generation" techniques researchers at the Ruhr-Universität together with international colleagues have decoded the genome of the fungus Sordaria macrospora. By doing so, they have gained insights into the way that fungi live and evolve.


Young fruiting bodies and vegetative hyphae of the fungus Sordaria macrospora. Illustration: Kathryn M. Lord, Sandra Bloemendal, Chris E. Jeffree, Ulrich Kück, Nick D. Read

Sordaria macrospora is able to cope with multiple copies of the same genes, which lead to cell death in other fungi due to immune-like reactions. They also found genes from distant relatives, suggesting that so-called horizontal gene transfer has been taking place over the course of evolution.

In addition, they were able to show that the new techniques can be used effectively to sequence genomes of complex organisms at low cost. The researchers led by Prof. Dr. Ulrich Kück report in the current issue of PLoS Genetics.

Fungi: major ecological and economic importance

With an estimated 1.5 to 6 million species which form their own kingdom alongside plants and animals, the importance of fungi can hardly be overestimated: some grow on dead organic matter, help in the decomposition of plant and animal waste products and thus contribute to the global carbon cycle. Others are important as pathogens, and many fungi are used in biotechnology, to produce antibiotics, enzymes or foodstuffs. In addition, fungi have for decades played a major role in fundamental research when it comes to identifying genetic factors that are also important in other organisms such as humans. "This is due, among other things, to the fact that although fungal genomes are about 100 times smaller than the human genome - 40 million base pairs in the genome of Sordaria macrospora, 3,000 million in the human genome - they still encode a similarly large number of genes: approximately 11,000 genes in Sordaria macrospora, about 25,000 in humans", explained Prof. Kück. The first genome of a eukaryote, which was fully sequenced in1996, was that of the unicellular fungus Saccharomyces cerevisiae, known as baker's or brewer's yeast. This took ~600 researchers six years.

New sequencing techniques: assembling many tiny building blocks

Because of its complexity, until recently, genome sequencing was extremely expensive and usually the reserve of specialised sequencing and bioinformatics institutes. Some years ago, however, "next generation" techniques were developed that significantly reduce costs by using high-throughput methods. All techniques, including the previously used standard techniques (Sanger sequencing), deliver sequence reads with a maximum of 1,000 base pairs. For this reason, genome sequences always have to be assembled from many individual sequences. The new techniques deliver considerably more sequences than Sanger sequencing in the same time, however the individual reads are considerably shorter (36 to 450 base pairs). In order to be able to piece together these short reads to form a genome, newly developed programs on powerful computers are required. Bochum's researchers have used the servers of the RUB data centre to assemble the Sordaria macrospora genome out of nearly 100 million individual sequences. "The methods thus developed will be of great significance in future training programs for master and Ph.D. students and thus provide up to date practical courses with a focus on bioinformatics" explained Prof. Kück.

Surprises in the genome of Sordaria macrospora

The genome sequence of Sordaria macrospora had a number of surprises in store for the researchers: the genome contains multiple copies of genes which serve in other fungi to distinguish between "self" and "non-self", analogous to the rejection of foreign tissue in medical transplants. Unlike Sordaria macrospora, other fungi only have one copy of these genes in their genomes. The presence of multiple copies inevitably leads to incompatibility reactions, which in serious cases result in the death of the affected cells. How Sordaria macrospora copes with several of these gene copies in one genome is still unclear. Furthermore, the genome of Sordaria macrospora contains several genes that were probably taken over by means of "horizontal gene transfer" from another, only very distantly related fungus, and which expand the biochemical repertoire of Sordaria macrospora.

International cooperation and various sponsors

A collaboration of researchers from eight universities in four countries, led by Dr. Minou Nowrousian and Prof. Dr. Ulrich Kück (Department of General and Molecular Botany) made the implementation of this project possible. Thus, the DNA for the sequencing was isolated in Bochum, and DNA sequencing in the USA and Germany led to the sequence data, from which the corresponding genome sequence was assembled. Researchers from Bochum (Dr. Minou Nowrousian, Dr. Ines Engh, Dr. Jens Kamerewerd and Prof. Dr. Ulrich Kück) and research groups from the USA, England and France were involved in the bioinformatic analysis. The project was made possible by funding from the German Research Foundation (DFG) within the framework of the SFB480 (chair Ulrich Kück), by individual project funding from the DFG, as well as funding from the Protein Research Department (PRD, chair Klaus Gerwert).

Bibliographic record

Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, Halliday K, Kamerewerd J, Kempken F, Knab B, Kuo HC, Osiewacz HD, Pöggeler S, Read ND, Seiler S, Smith KM, Zickler D, Kück U, Freitag M (2010) De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genetics 6 (4): e1000891. doi:10.1371/journal.pgen.1000891

Further information

Dr. Minou Nowrousian, Prof. Dr. Ulrich Kück, Department of General and Molecular Botany Faculty of Biology & Biotechnology of the Ruhr-Universität Bochum, 44780 Bochum, tel.: 0234/32-26212, e-mail: Minou.Nowrousian@rub.de, ulrich.kueck@ruhr-uni-bochum.de

Dr. Josef König | idw
Further information:
http://www.ruhr-uni-bochum.de/allgbotanik/
http://c4-1-8.serverhosting.rub.de/public/ -

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