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Genome mining from fungarium specimens accelerates the mushroom tree of life

In their quest to help create a Fungal Tree of Life, scientists from the Royal Botanic Gardens, Kew have collaborated with colleagues in the UK and USA to successfully extract DNA, viable for whole genome sequencing, from preserved fungal specimens: the oldest of which was eight years old.

The study’s use of pioneering DNA sequencing techniques has demonstrated the continued relevance of fungarium collections in the genomic era with technological advances set to vastly accelerate the completion of a fungal evolutionary tree. The fungarium at the Royal Botanic Gardens, Kew is the largest such collection in the world, with an estimated 1.25 million specimens, yet its genetic richness is only just beginning to be evaluated.

Senior RBG Kew mycologist, Dr Bryn Dentinger, says: “The extraction of viable DNA from dried, historic specimens represents something of a breakthrough for this project. If we could only rely on freshly collected samples, it would take many generations to complete the Fungal Tree of Life. The enormous breadth and depth of mushroom specimens held within the world's biological collections, especially at Kew, offer an unparalleled opportunity to capture genomic data from across the entire range of known fungal diversity.”

Fungi are the unsung heroes of our ecosystems: The major decomposers of our world, they play a vital role in breaking down animal and plant material, releasing nutrients for future generations of plants and animals. Yet in spite of their extraordinary role and diversity, comparatively little is known about them and it is thought that as little as 5% of fungal species have been discovered and described to date. The creation of a Fungal Tree of Life, which features as a main strategic output for RBG Kew, will greatly accelerate the discovery of new fungi and how they relate to one another; fundamental knowledge that will facilitate the exploration of their potential uses, such as a sources of new medicines and industrial enzymes.

Dr Bryn Dentinger continues: “The completion of a fungal evolutionary tree, showing the relationships between all known species will open up a myriad of possibilities, from identifying medicinal properties, unlocking economic potential, to furthering our understanding of the patterns and processes that drive the maintenance of biodiversity.”

The paper, published on 20th May in early view on the Biological Journal of the Linnean Society website, presents the analysis of a dataset derived from sequencing whole genomes from preserved specimens to represent most of the known families of Agaricales, the main group of mushroom-forming fungi. Although Agaricales contains most of the generally known types of mushrooms, such as the cultivated edible mushroom (Agaricus bisporus) and magic mushrooms (Psilocybe spp.), previous studies have failed to generate a clearly resolved phylogenetic explanation for the Agaricales – a major obstacle to successfully interpreting their evolutionary history and relationships. However, this recent study has resulted in a robust and, for the first time, fully supported phylogeny of the Agaricales, providing the first subordinal classification of the group and thus, a resource for testing and exploring the evolution of other families of mushrooms.

Dr Ester Gaya, Kew Research Leader in comparative fungal biology says: “A current limiting factor in the emerging field of phylogenomics is the overwhelming amount of data that needs to be processed and analysed. In this study, we have provided guidance on gene selection for future studies, enabling efficient application of high-throughput sequencing techniques which could unlock the potential of collections-based research in the genomic era”.

This successful analysis of Agaricales demonstrates that unlocking the potential of genetic data within collections could be instrumental in reconstructing the evolutionary fungal tree of life. The accumulation of specimens over many years from all over the world makes collections a rich resource for dense and comprehensive DNA sampling, and collections-based phylogenomics has the potential to fill out the twigs and leaves of this tree at  greater pace than was previously thought possible.


Story source: Kew Royal Botanic Gardens press release, 21 May 2015

Journal Reference: Bryn T. M. Dentinger, Ester Gaya, Heath O'Brien, Laura M. Suz, Robert Lachlan, Jorge R. Díaz-Valderrama, Rachel A. Koch, M. Catherine Aime.Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of lifeBiological Journal of the Linnean Society, 2015; DOI: 10.1111/bij.12553

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