press release, 19. June 2018

The oak genome unveils the secrets of tree longevity

Scientists have sequenced the genome

An international consortium driven by the French National Institute for Agricultural Research INRA and the French Alternative Energies and Atomic Energy Commission CEA has sequenced the genome of the pedunculate oak. The work recently published in Nature Plants, which also involved three researchers from Central Germany, reveals two main genomic features related to the longevity of this emblematic species. The first is the existence in the genome of a particularly rich and diverse set of genes involved in resistance against pests (fungi, oomycetes, insects, bacteria and viruses). This extended defense arsenal affords trees protection against their dominant predators and is likely a key to their longevity. The second feature revealed by the work is the existence of somatic mutations that can be transmitted to the next generation - a result that raises questions about the importance of somatic mutations (non germ line) in generating genetic diversity in long-lived species.

150 years old oak trees in the Forêt domaniale de Bercé Photo: INRA / Didier Bert
150 years old oak trees in the Forêt domaniale de Bercé
Photo: INRA / Didier Bert
The team from Halle provided to the project large gene expression data from a library. Basis is an own clone of the common oak micro-propagated since years at the UFZ. Photo: UFZ / André Künzelmann
The team from Halle provided to the project large gene expression data from a library. Basis is an own clone of the common oak micro-propagated since years at the UFZ.
Photo: UFZ / André Künzelmann

Trees contribute greatly to our natural and cultural heritage. In addition to being ubiquitous in our most common landscapes, they also provide humans with invaluable services. In past and present human societies, their longevity and ability to withstand environmental changes made them important symbols in sacred, mystical and popular representations of stability, resistance and the perpetuity of life.

A reference genome for one of the 400 oak species
Scientists from France, Sweden, Spain, the USA and Germany jointly investigated the genetic bases of longevity of trees. They started their investigation by sequencing the genome of the common oak using high throughput sequencing technologies. This allowed them to sequence and assemble the 750 million nucleotides, that make up the genome of this wide-spread European species, whose genetic diversity is ten times greater than that of humans.

The annotation of the oak genome, locating and determining the likely function of all genes (done by comparison with other species), showed that it is enriched with transposable elements (DNA sequences that move within the genome) at 51% of total DNA and contains 26,000 genes. Among these genes, 36% are organized in clusters of continuous genes (so called tandem duplicates); this number is much higher than found in other plants at ca. 15 %. The investigators also showed that the number of resistance genes in oaks increased mostly via tandem duplication. The comparison between the genomes of herbaceous species (Arabidopsis, soybean, potato, watermelon…) and perennial woody species (oak, poplar, eucalyptus, peach tree…) demonstrates that this expansion of resistance genes is not specific to oaks, but shared among all tree species investigated. As trees remain living across years, they are continually barraged by pests; these pests likely evolve faster than their tree hosts due to their much shorter generation times. In these conditions the diversity and richness of immunity genes could help trees to cope with a broad range of short-lived microbial enemies and help them to persist and live longer.

Are trees genomic mosaics?
Multi-cellular organisms accumulate somatic mutations as they grow. The extremely long life of trees, often reaching hundreds of years for some species, and the persistence of tissue produced across their lives makes them perfect models to investigate this phenomenon. The team investigated the frequency of somatic mutations by comparing the genomes of samples harvested at the extremities of branches of different ages on a centennial oak tree. This strategy allowed the researchers to identify rare somatic mutations, but also to show that they can be transmitted to the next generation. The next step will be to determine the importance of this mechanism in generating genetic diversity in populations and whether some of these mutations can confer individuals with a selective edge.

From the UFZ-Department Soil Ecology in Halle (Saale), three scientists participated to the international consortium. One of these was financed by the German Centre for Integrative Biodiversity Research (iDiv). They contributed by annotating genes related to the ectomycorrhizal symbiosis between roots and soil fungi, in particular those involved in sugar exchange between the partners. The team from Halle also provided to the project large gene expression data from a library constructed during interaction studies between a number of microorganisms and animals displaying beneficial or detrimental interactions with oak leaves or roots. Basis for this research was an own clone of the common oak micro-propagated since years at the UFZ. "The two traits revealed e.g. the high amount of genes involved in resistance against pests and the high level of transposons and potential of somatic mutations may provide keys to understand how a species with so many different biotic interactions makes it to have one of the broadest geographic distributions among all European forest trees. It reinforces the value of releasing our own oak clone as phytometer among sites in Europe to study how long lived organisms adapt to environmental variations" says Dr. Sylvie Herrmann from the UFZ Halle.

Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé J, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne A, Martin F, Wincker P, Quesneville H, Kremer A, Salse J.: Nature Plants, 2018,

INRA press release:

Further information

Dr. Christophe Plomion
INRA, Universität Bordeaux

Dr. Sylvie Herrmann
UFZ-Department Soil Ecology

UFZ press office

Susanne Hufe
Phone: +49 341 235-1630

In the Helmholtz Centre for Environmental Research (UFZ), scientists conduct research into the causes and consequences of far-reaching environmental changes. Their areas of study cover water resources, biodiversity, the consequences of climate change and possible adaptation strategies, environmental technologies and biotechnologies, bioenergy, the effects of chemicals in the environment and the way they influence health, modelling and social-scientific issues. Its guiding principle: Our research contributes to the sustainable use of natural resources and helps to provide long-term protection for these vital assets in the face of global change. The UFZ employs more than 1,100 staff at its sites in Leipzig, Halle and Magdeburg. It is funded by the federal government, Saxony and Saxony-Anhalt.

The Helmholtz Association contributes to solving major and urgent issues in socie-ty, science and industry through scientific excellence in six research areas: Energy, earth and environment, health, key technologies, structure of matter as well as aviation, aerospace and transportation. The Helmholtz Association is the largest scientific organisation in Germany, with 35,000 employees in 18 research centres and an annual budget of around €3.8 billion. Its work is carried out in the tradition of the great natural scientist Hermann von Helmholtz (1821-1894).
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