A large international consortium of genetic researchers has sequenced and analyzed the complete genome of Amborella trichopoda, the sole survivor of an ancient evolutionary lineage that traces back to the last common ancestor of all flowering plants.
Female flower of Amborella trichopoda. Image credit: Sangtae Kim.
The results, reported in a series of papers published in the journal Science (paper 1, paper 2 & paper 3), shed new light on the processes that paved the way for the amazing diversity of the more than 300,000 extant species 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 co-author Dr Victor Albert of the University at Buffalo.
Dr Albert and his colleagues said the genome of Amborella – a small understory tree or shrub endemic to the main island, Grande Terre, of New Caledonia in the South Pacific – 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 the apparently abrupt proliferation of new species of flowering plants in fossil records dating to the Cretaceous period. Generations of scientists have worked to solve this puzzle,” said co-author Dr Claude dePamphilis of Penn State University.
As another example of the value of the Amborella genome, co-author Dr Joshua Der at Penn State University 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.”
Dr Jim Leebens-Mack from the University of Georgia 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 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,” said co-author Dr 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.”
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The Amborella Genome and the Evolution of Flowering Plants, by Amborella Genome Project. Science 2013, vol. 342, no. 6165; doi: 10.1126/science.1241089
Rice DW et al. 2013. Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella. Science, vol. 342, no. 6165, pp. 1468-1473; doi: 10.1126/science.1246275
Chamala S et al. 2013. Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella. Science, vol. 342, no. 6165, pp. 1516-1517; doi: 10.1126/science.1241130
