UA Scientists Help Decipher Origin of Flowers

Researchers have deciphered the DNA of the earliest ancestor of flowering plants, providing long-awaited insight into their evolution.
Dec. 21, 2013
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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.
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. 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, was published last month in the journal Science. The paper is among three on different research areas related to the Amborella genome 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.
"Amborella represents the earliest diverging lineage of flowering plants, which means it is more distantly related to all of the other flowering plants on the planet," said Eric Lyons, an assistant professor in the University of Arizona School of Plant Sciences and a member of the iPlant Collaborative, who contributed to the project. "In other words, Amborella is the earliest ancestor of flowering plants."
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."
"Our lab played a key role in getting the project started with the development of genetic libraries for Amborella," said Rod Wing, a UA professor of plant sciences and director of the Arizona Genomics Institute who is also affiliated with BIO5. "The initial funded project was to build a physical map of the Amborella genome that could serve as a basis to decipher the DNA sequence. The project ultimately took a slightly different direction but still used our sequences to assemble the pieces of genetic information."
Wing said he was thrilled to be part of the project both for its evolutionary and technical aspects. His lab group co-authored the main publication on the Amborella genome as well as the genome assembly and validation papers, which were published in the same issue of Science. 
"Amborella is really exciting because not only is this plant a living fossil, but its genome structure also shows a similar structure of being ancient – a living genome fossil, if you will," Lyons said. "Every time genome duplication occurs, genes are lost quickly, because the plant doesn't need all of them. Some acquire new functions, but many are lost. With each cycle of gene duplication and gene loss these changes become harder and harder to detect. It starts to look scrambled really quickly."
Under the umbrella of the iPlant Collaborative, Lyons is part of a team designing the algorithms to allow these discoveries to happen anywhere in the world. Thanks to the iPlant cyberinfrastructure, not only were the researchers able to see the evidence of those events, but also perform all the necessary analyses rapidly. 
"The iPlant infrastructure provides all the heavy-lifting power computing in the background, which means we can now make these discoveries sitting in front of our laptops at home," Lyons said. "You can get up, make a cup of coffee, and by the time you're done with it, the calculations will be ready. That is what iPlant does."
The iPlant Collaborative is based at the UA’s BIO5 Institute.
Comparative analyses of the Amborella genome already are 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, Josh Der at Penn State said: "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.