The genome of a 234-year-old oak tree, young as ever

A study carried out by researchers at the University of Lausanne (UNIL) and the SIB Swiss Institute of Bioinformatics has revealed that the genome of an emblematic tree of the University campus, the Napoleon oak (see Box 1), has changed little during its first 234 years of existence. This surprising result, published in Nature Plants, suggests that the tree is capable of protecting itself from an accumulation of harmful genetic mutations.

Box 1. From Napoleon to the Napoleome

Legend has it that the Napoleon oak was planted by the Loys family, owners of the estate situated on today's campus grounds, to commemorate the emperor's visit. Napoleon stopped at Saint-Sulpice on 12 May 1800 to inspect his troops.

Since then, the tree - which is more than 30 metres tall - has become a symbol of the University of Lausanne.

The interdisciplinary "Napoleome" project is the result of a joint venture between eight professors at UNIL and SIB and was launched in 2012. The aim is to sequence the entire genome of the pedunculate oak.

Box 2. A possible mechanism: saving up on stem cells

The stem cells of plants (which have the potential for reproduction) are contained in apical meristems - or buds - located at the end of branches. Cell division allows the tree to grow. By studying the growth of annual plants, a group of researchers in Bern found that some stem cells in the apical meristem were rapidly ignored in a lateral bud, dividing just five or seven times, i.e. very few. Other cells, which continue to multiply, produce stems.

A first in the field of plant biology

The Napoleome project's originality (see Box 1) lies in its analysis of the genetic variations between several parts of a single individual, a first in the field of plant biology. The researchers took and analyzed samples from 26 branches of the tree. The respective genomes of two of them, at the extremities of the oak, almost 40 metres away from each other, have been fully sequenced.

The scientists began by determining the sequence of nucleotides (the building blocks of DNA, made up of the letters ACGT) and then compared them, finding just 17 differences (inversions of the letters) among the tree's 750 million nucleotides. The origin and spread of these 17 mutations in the tree were traced back by analyzing the 24 other samples.

"We were expecting a figure 10 to 100 times higher," comments Philippe Reymond, professor in the Department of Plant Molecular Biology at UNIL and the project's coordinator. "The result, published in the journal Nature Plants in early December 2017, was so surprising that we had to carry out an extensive amount of bioinformatics work to persuade our colleagues that we hadn't made a mistake in our analyses."

A cunning plan to avoid the effects of time

When a cell divides to reproduce itself, it makes a complete copy of its DNA. However, mistakes can occur during the operation and might introduce mutations. These can also be introduced by external factors, such as UV radiation.

"Our initial assumption was therefore that a tree as large and old as this one would have accumulated numerous mutations," explains Philippe Reymond.

"As our German-speaking colleagues predicted (see Box 2), the Napoleon oak appears to have developed a defence mechanism to prevent its stem cells from dividing too frequently. This protects it from an accumulation of harmful genetic mutations," explains Philippe Reymond. "Moreover, the apical meristem is covered in multiple layers of leaves (giving the bud its conical appearance), which protects it from UV rays."

According to Philippe Reymond, the same mechanism might also be seen in other plant species, in particular those that live for a long time. "Some scientific studies on the number of mutations in plants could be re-examined in light of these results and the recent development of bioinformatics."

Participative science project

The "Napoleome" project was mainly funded by the Rectorate at UNIL and supported by the "Agora" programme of the Swiss National Science Foundation (SNSF), which promotes projects aimed at communicating with the general public. Numerous meetings and workshops were organized by the Science-Society Interface at UNIL to help people understand the various current issues in genomics.

Adapted from UNIL press release (in French)

Reference

Schmid-Siegert E et al. Low number of fixed somatic mutations in a long-lived oak tree, Nature Plants 2017. https://doi.org/10.1038/s41477-017-0066-9

Links

The Napoleome project

News coverage in Le Temps (in French), including an interview of SIB's Group Leader Ioannis Xenarios

News piece in Nature: Ancient oak's youthful genome surprises biologists