By: Alison Cranage, Science Writer at the Wellcome Sanger Institute
All our lives depend on plants and fungi. Genome sequencing is beginning to uncover their incredible diversity, yet only a tiny fraction of the millions of species which inhabit the planet have been analysed. The Earth BioGenome Project, which aims to sequence the DNA of all complex life, will be cataloguing and sequencing all plants and fungi, together with all animals and protozoa.
The Royal Botanic Gardens, Kew is home to the largest and most diverse collection of plants and fungi in the world. They are a key partner in the Darwin Tree of Life Project to sequence the genomes of all eukaryotic life in the UK – providing scientific expertise and extensive plant and fungi collections.
The genomes of all fungi
Baker’s yeast (Saccharomyces cerevisiae) was the first eukaryote to have its whole genome sequenced back in 1996. Since then, over 1,500 species of fungi have had their genome sequenced. There are about 140,000 species known to science, with an average of 2,000 new species described every year. The total number of fungi species is estimated to be between 2.3 and 3 million.
Genome sequences are already helping people capitalise on some of the unique properties of fungi. They are widely used in industry for the large-scale production of a diverse array of chemicals – from food to pharmaceuticals.
We spoke to Dr. Ester Gaya, Senior Mycology Researcher at Kew Gardens, about some of the untapped resources of fungi.
“Many antibiotics come from fungi. Researching fungal diversity could lead to the discovery of new sources of antibiotics and medicines.
“In industry the genomes of several fungal species are being studied because of their ability to produce ‘mycodiesel’. It may be we can produce fuel sustainably and on an industrial scale.
“There is also research into how we can use fungi for bioremediation. Some species have the ability to consume and break down environmental pollutants – so they could be used to clean up oil spills, for example.”
Not all fungi are beneficial. Many species are harmful to humans. For example Pneumocystis jirovecii causes a type of pneumonia and Candida albicans causes thrush. These, together with hundreds of other harmful species, have had their genomes sequenced – helping researchers design better treatments and surveillance systems.
Other fungi species target plants, including key food crops. Researchers are studying their genomes to understand how their pathogenicity works – understanding which genes are active, will enable researchers to develop new ways to tackle them and improve crop yield.
Inside the Fungarium
Plants underpin all aspects of our everyday life – from the food we eat to the air we breathe. Like fungi, only a tiny fraction of plant species on the planet have had their genome sequence determined.
Most plant species with genomes sequenced to date are crops, including the major cereals – rice, wheat and maize, as well as fruits and vegetables. Commercially important crops that make our favourite drinks like coffee, grapes and hops have also had their genomes sequenced. Studying these genomes helps enhance yield, as well as shedding light on the mechanisms of taste and quality.
Studying the genomes of relatives of crop species is also important. These plants harbour important genetic diversity, often lost in the domesticated crops that dominate world agriculture. 75 per cent of the world’s food supply depends on just 12 species of plants. Their wild relatives harbour essential genetic diversity which can be used for breeding resilience to disease and to climate change.
Plants are a hugely diverse group of organisms, from trees with 5,000 year lifespans to unicellular green algae. Their uses are equally diverse, from medicines to biofuels and materials.
Plant sciences have a vital role in addressing some of the most critical global challenges, such as climate change and food security. Plant science can provide the fundamental research required to protect biodiversity, as well as mitigate and adapt to climate change. Whole genome sequence data will enable researchers to drive the understanding of plant development and evolution and their potential contribution to sustainable agriculture. And new, detailed insights from genome sequences may help us understand medicinally important compounds.
There is no doubt the project comes with challenges. The quality and amount of material available for DNA sequencing will be an issue. This is particularly a problem for microscopic fungi, as many cannot be cultivated outside their natural habitat. This makes it difficult to gather enough material for DNA sequencing. Getting good quality DNA from historical plant and fungal samples, like those housed at Kew, may also be difficult – though it is an area that is rapidly improving.
There are an estimated 1,500 plant species native to the UK, with a total of 400,000 around the world. Nearly all UK species have been catalogued and have seeds stored by Kew. The project is likely to discover new species of both plants and fungi though.
“In fungi there are what we call ‘dark taxa’ ” says Dr. Gaya. “They’re hidden to the naked eye. And before the advent of DNA sequencing we didn’t have the tools to discover them.”
Scientists at the University of Exeter discovered a whole new phylum of fungi in 2011 – it was a whole new branch, right at the base of the fungal tree of life. The microscopic fungi were found living in a pond on the University campus.
We have only just started to scratch the surface of these remarkable groups of organisms.