The sole survivor of the oldest line of flowering plants, Amborella is the last witness of the great biological success these plants have had over millions of years. The sequencing of its genome, which was just published in the journal Science, can help better understand the evolution of these plants, which has led to an incredible diversity of more than 300,000 species identified today.

The researchers also trace the history of Amborella itself, showing highly original evolutionary mechanisms in this shrub, whose so-called "mitochondrial" DNA now contains the entire genomes of other species. Lastly, in New Caledonia, where the plant is endemic, they highlight the existence of two ice age refuge areas, without which the plant would not be here today to bear witness to the past.

An open window on a common ancestor

Why did flowering plants suddenly proliferate on Earth millions of years ago? To lift part of the veil on this enigma, the researchers of the "Amborella Genome Project," coordinated by Penn State University in the United States and bringing together researchers from ten countries, focused on this New Caledonian shrub. In fact, it is the last vestige of the oldest line of flowering plants. This makes it a sort of witness to ancient times. The sequencing of its genome helped the researchers reconstruct that of the common ancestor of all flowering plants, showing that the latter saw its genome double approximately 200 million years ago. In other words, its DNA was "duplicated," which is to say completely copied, until it numbered 14,000 encoding genes. This molecular mechanism, called "duplication," is one of the engines of evolution. Among these 14,000 encoding genes, many evolved over geological time, to provide flowering plants with new functions, such as the ability of seeds to store nutrient reserves. This work shows that the doubling of the genome of their common ancestor then helped flowering plants to achieve the incredible diversity of the more than 300,000 species observed today.

The evolutionary record saved

In parallel, the IRD researchers analysed the genetic variability in Amborella populations in New Caledonia to reconstitute its evolutionary history in its natural habitat. The genomes of each Amborella population show that their common ancestor dates back at least 2 million years. The researchers also observed that the populations diminished drastically approximately 320,000 years ago. A series of other more or less important reductions then occurred. Why did the Amborella populations decline? The question remains open.

Throughout its evolution, the genetic diversity of Amborella has been structured into four geographically distinct groups on Grande Terre, to occupy a broad ecological niche. The researchers found the existence of two mountain ranges that served as refuges during the last ice ages (~21,000 years ago) and from which Amborella recolonized new territories. Without these two ice-age refuges, it would not have survived to the present, like so many New Caledonian species, and would not have been able to help researchers to explore the past of flowering plants.

Several genomes in one

Another major discovery, also published in Science: the IRD researchers contributed to finding in Amborella a highly original transfer mechanism from other plant species with so-called "mitochondrial" genomes. Mitochondrial DNA or "mtDNA," is distinct from the DNA contained in the cell nucleus. This special DNA helps trace the maternal line in the phylogenetic trees of species. Therefore, population geneticists often study it. The researchers sequenced that of Amborella, showing that it integrated the DNA of six other species, including other flowering plants that appeared after the New Caledonian shrub. Such "horizontal" transfers, also called species-to-species without passing through sexual reproduction, had already been found for isolated single genes. But this was the first time that researchers observed this mechanism on the scale of entire mitochondrial genomes! In this same study, the researchers proposed a model to explain this singular phenomenon, which is still not well understood.