The newly sequenced genome of the Amborella plant addresses Darwin's "abominable（讨厌的） 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（下层植被） 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（鸭嘴兽） -- 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（被子植物）. 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（双子叶植物）.