Press Release

The Origin of Flowers: DNA of Storied Plant
Provides Insight into the Evolution of Flowering Plants, Study Finds

 

The newly sequenced genome of the Amborella plant addresses Darwin's
"abominable mystery" -- the question of why flowers suddenly
proliferated on Earth millions of years ago. The genome sequence sheds new
light on a major event in the history of life on Earth: the origin of flowering
plants, including all major food crop species. On 20 December 2013, a paper by
the Amborella Genome Sequencing Project
that includes a full description of the analyses performed by the project, as
well as implications for flowering plant research, will be published in the
journal Science. The paper is among three on
different research areas related to the Amborella genome that will be published in the same issue of the journal.

 

Amborella (Amborella trichopoda) is unique as the sole survivor
of an ancient evolutionary lineage that traces back to the last common ancestor
of all flowering plants. The plant is a small understory tree found only on the
main island of New Caledonia in the South Pacific. An effort to decipher the Amborella genome -- led by scientists
at Penn State University, the University at Buffalo, the University of Florida,
the University of Georgia, and the University of California-Riverside -- is
uncovering evidence for the evolutionary processes that paved the way for the
amazing diversity of the more than 300,000 flowering plant species we enjoy
today.

 

This unique heritage gives Amborella a special role in the study of flowering plants. "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 Victor Albert of the University at
Buffalo.

 

Scientists 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.

 

"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.
"Generations of scientists have worked to solve this puzzle," he
added.

 

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," stressed Doug Soltis
of the University of Florida.

 

As another example of the value of the Amborella genome, Joshua Der at Penn
State noted "We 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."

 

"This work provides the first global insight as to how
flowering plants are genetically different from all other plants on
Earth," Brad Barbazuk of the University of
Florida said, "and it provides new clues as to how seed plants are
genetically different from non-seed plants."

 

Jim Leebens-Mack from UGA noted that
"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 such as oak and
poplar." 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. Most plants show evidence of recent bursts of this mobile
DNA activity, "But Amborella is unique in that it does not seem to have acquired many new
mobile sequences in the past several million years," stated 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 utility 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 fewer
than 15 known populations of this very special 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," noted 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.

 

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The complete genome sequence of Amborella has been deposited in Genbank -- the
U.S. National Institutes of Health database of publicly available gene
sequences -- and also is available in the Amborella Genome Database (www.Amborella.org).

 

In addition to the paper about the nuclear genome sequence, two
other papers appear in this same issue: one that reports the complete
mitochondrial genome sequence of Amborella, which contains large amounts of foreign DNA resulting from
horizontal transfer (Rice et al. 2013); 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 (Chamala et al. 2013).

 

In addition to researchers at Penn State University, the
University at Buffalo, the University of Florida, the University of Georgia,
and the University of California-Riverside, the paper's authors include
scientists from other universities in the United States, Canada, Mexico, China,
Korea, Taiwan, Singapore, Germany, Italy, Denmark, France, and New Caledonia.

 

The work was funded by the National Science Foundation's Plant
Genome Research Program.

 

[ Katrina Voss / Barbara K.
Kennedy ]

 

CONTACTS

Claude dePamphilis at Penn State:  814-321-2256, cwd3@psu.edu

Victor Albert at the University of Buffalo: 716-341-5582,
vaalbert@buffalo.edu

Pamela Soltis at the University of
Florida: 352-273-1964, psoltis@flmnh.ufl.edu

Jim Leebens-Mack at the University of
Georgia: 706-583-5573, jleebensmack@plantbio.uga.edu

Barbara Kennedy (PIO): 814-863-4682, science@psu.edu

 

PHOTOS AND VIDEOS

High-resolution images and links to two videos associated with
this research are online at
http://www.science.psu.edu/news-and-events/2013-news/dePamphilis12-2013, which
is where text will be posted after the journal's news embargo lifts.

 

GRANT NUMBER: NSF Plant Genome Research Program
(0922742)