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Flowering Plant Phylogeny Points to Polyploidy Events

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In a paper appearing in the early, online edition of Nature yesterday, researchers from Pennsylvania State University and elsewhere brought together existing plant genome sequence information with expressed sequence tag data generated through the Ancestral Angiosperm Genome Project to come up with a phylogeny for flowering plants.

These relationships and genetic patterns point to two polyploidy events occurring much earlier than previously known, they reported. The first of these affected a shared seed plant ancestor around 320 million years ago, while the second polyploidy event occurred within the flowering plant lineage itself around 192 million years ago.

"Thanks to events such as these, where vast stretches of DNA have been duplicated and added to the genome, flowering plants have been able to evolve new and better functions," senior author Claude dePamphilis, a plant biology and molecular evolutionary genetics researcher at Pennsylvania State University, said in a statement. "They have seized on the opportunity to become so diverse, so exquisite, and so prevalent."

"It's possible that the important polyploidy events we've identified were the equivalent of two 'big bangs' for flowering plants," he added.

There are more than 300,000 known angiosperm species, researchers noted. And the diversity detected within this flowering plant group is believed to reflect gene and/or whole-genome duplications. Even so, they explained, there are still gaps in researchers' understanding about if and when such duplication events happened — and the extent to which they've influenced flowering plant features.

"Ever since Charles Darwin so famously called the rapid diversification of flowering plants in the fossil record an 'abominable mystery,'" dePamphilis said, "generations of scientists have worked to solve this puzzle."

To explore this in more detail, dePamphilis and his co-workers brought together data for seven existing angiosperm genomes, one lycophyte genome, and a single moss genome. They then incorporated new data on 12.6 million ESTs.

Using this data and a method called OrthoMCL, the team was able to define 31,433 orthogroups — sets of homologous genes stemming from an individual gene in a shared common ancestor.

Their phylogenetic analyses of these orthogroups, in turn, pointed to a pair of ancient whole-genome duplications events: a duplication between 192 and 210 million years ago that affected plants within the flowering plant group and an older duplication event in the ancestor of seed plants that happened some 319 million years ago.

When they focused in on the sorts of functions that have been acquired for some of the duplicated and retained genes, meanwhile, the researchers found evidence of such genes participating in everything from flower development to transcription factor function.

"Some of these new genes led to true innovations and have become vital parts of the genetic toolkit for the regulation of flower development," dePamphilis said in a statement. "In other words, without the genes that these polyploidy events helped to create, flowering plants as we know them today probably would not exist."

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