Genome Sequence Insight Evolution Flowering Plants
December 20, 2013

Genome Sequence Gives Insight Into Evolution Of Flowering Plants

redOrbit Staff & Wire Reports - Your Universe Online

The newly-sequenced genome of the Amborella plant is shedding new light on the origin of the more than 300,000 flowering plants on the Earth today, including all major food crop species.

Amborella trichopoda, a small understory tree found only on the main island of New Caledonia in the South Pacific, is unique as the sole survivor of an ancient evolutionary lineage that traces back to the last common ancestor of all flowering plants. This heritage gives the plant a special role in the study of flowering plants, the researchers said.

"In the same way that the genome sequence of the platypus - a survivor of an ancient lineage - can help us study the evolution of all mammals, the genome sequence of Amborella can help us learn about the evolution of all flowers," said study researcher Victor Albert of the University at Buffalo.

The researchers who sequenced the Amborella genome say that it provides conclusive evidence that the ancestor of all flowering plants, including Amborella, evolved following a "genome doubling event" that occurred about 200 million years ago. Some duplicated genes were lost over time but others took on new functions, including contributions to the development of floral organs, the researchers said.

"Genome doubling may, therefore, offer an explanation to Darwin's "abominable mystery" - the apparently abrupt proliferation of new species of flowering plants in fossil records dating to the Cretaceous period," said Claude dePamphilis of Penn State University, one of the study’s researchers.

"Generations of scientists have worked to solve this puzzle.”

Comparative analyses of the Amborella genome are already providing scientists with a new perspective on the genetic origins of important traits in all flowering plants, including all major food crop species.

"Because of Amborella's pivotal phylogenetic position, it is an evolutionary reference genome that allows us to better understand genome changes in those flowering plants that evolved later, including genome evolution of our many crop plants - hence, it will be essential for crop improvement," said Doug Soltis of the University of Florida.

The researchers estimate that at least 14,000 protein-coding genes existed in the last common ancestor of all flowering plants.

“Many of these genes are unique to flowering plants, and many are known to be important for producing the flower as well as other structures and other processes specific to flowering plants,” said study researcher Joshua Der at Penn State University.


Brad Barbazuk of the University of Florida noted that another value of deciphering the Amborella genome is that it provides scientists with the first global insight as to how flowering plants differ genetically from all the other plants on Earth.

The work “provides new clues as to how seed plants are genetically different from non-seed plants” he said.

The researchers said the Amborella genome sequence facilitated reconstruction of the ancestral gene order in the 'core eudicots,' a huge group that comprises about 75 percent of all angiosperms. This group includes tomato, apple and legumes, as well as timber trees.

As an evolutionary outsider to this diverse group, the Amborella genome allowed the researchers to estimate the linear order of genes in an ancestral eudicot genome and to infer lineage-specific changes that occurred over 120 million years of evolution in the core eudicot.

At the same time, Amborella seems to have acquired some unusual genomic characteristics since it split from the rest of the flowering plant tree of life. For example, DNA sequences that can change locations or multiply within the genome (transposable elements) seem to have stabilized in the Amborella genome.

While most plants show evidence of recent bursts of this mobile DNA activity, "Amborella is unique in that it does not seem to have acquired many new mobile sequences in the past several million years," said Sue Wessler of the University of California-Riverside.

"Insertion of some transposable elements can affect the expression and function of protein-coding genes, so the cessation of mobile DNA activity may have slowed the rate of evolution of both genome structure and gene function."

In addition to its importance in retrospective studies of the evolution of flowering plants, the Amborella genome sequence offers insights into the history and conservation of Amborella populations. There are currently just 18 known populations of this very unique angiosperm in mountainous regions New Caledonia.

"Resequencing of individual Amborella plants across the species' range reveals geographic structure with conservation implications plus evidence of a recent, major genetic bottleneck," said Pam Soltis of the University of Florida.

A similar narrowing of genetic variation occurred when humans migrated from Africa to found modern-day Eurasian populations, the researchers said.

A paper about the nuclear genome sequence of the Amborella plant was published Friday in the journal Science. Two other papers appear in this same issue – one that reports the complete mitochondrial genome sequence of Amborella, and another that describes the novel assembly and validation of the nuclear genome using a combination of approaches that can be applied to other complex genomes of non-model species.