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Genome Duplication May Have Helped Plants Survive Mass Extinction

NEW YORK (GenomeWeb News) – Relatively recent genome duplications may have helped many plants survive a mass extinction that wiped out a slew of animals and about 60 percent of plant species.

A team of Belgian researchers used bioinformatics to estimate when the most recent spate of plant genome duplications occurred. The research, scheduled to appear online this week in the Proceedings of the National Academy of Sciences, suggests plant polyploidization events roughly coincided with the Cretaceous-Tertiary extinction period and may have offered a survival advantage for some plants.

"Due to advantages such as altered gene expression leading to hybrid vigor and an increased set of genes and alleles available for selection, polyploid plants might have been better able to adapt to the drastically changed environment 65 million years ago," senior author Yves Van de Peer, a bioinformatics and evolutionary genomics researcher affiliated with Ghent University and the Flanders Institute for Biotechnology, and his colleagues wrote.

Several plant species have genomes that have gone through between one and several whole genome duplications. For instance, the model organism Arabidopsis thaliana appears to have undergone three or four complete genome duplications, while the poplar genome probably doubled twice. And many other plants are in the same boat.

Previous research suggests flowering plants experienced ancient genome duplications. But a more recent round of plant genome duplications seems to have occurred sometime between 40 million and 80 million years ago.

In an effort to tweak their understanding of this most recent round of plant genome duplications, Van de Peer and his colleagues used a combination of published research, fossil data, molecular clock calibration, and phylogenetics to estimate when these recent duplication events occurred.

By looking at synonymous substitution rates for various monocot and eudicot species such as A. thaliana, legumes, and rice whose genomes contain evidence of large-scale duplications, the team developed molecular clock rate estimates. They also applied methods such as penalized likelihood phylogenetic tree inferences to assess divergence rates of paralogous genes within phylogenetic trees containing whole genome duplicated plants.

Their results suggest the most recent round of plant genome duplications occurred between 60 million and 70 million years ago, roughly coinciding with the Cretaceous-Tertiary mass extinction event, which occurred about 65 million years ago. That mass extinction is believed to have been caused by one or more catastrophic events such as a comet striking the Earth or a flurry of volcanic activity led to wildfires, smoke, and dust that choked off sunlight from reaching the Earth.

"We show that the independent [whole genome duplications] are not randomly distributed in time but instead cluster around the Cretaceous-Tertiary (KT) boundary," Van de Peer and his co-authors wrote. "To explain this pattern, we argue that polyploidy may have increased the survival chances and recolonization capacity of plant lineages during and/or after the KT mass extinction."

Based on these results, the team argued that genome duplications may have offered plants a means for surviving harsh conditions that eliminated many other species. For instance, the researchers noted that genome duplication may lead to enhanced plant diversification, through processes such as new gene evolution or sub-functionalization of duplicated genes, changes to gene expression, or epigenetic changes.

"In a drastically changed environment such as on Earth after the cataclysmic events that occurred [about 65 million years ago], where many plants became extinct, it is likely that competition was seriously reduced and new niches suddenly became available for occupation, and therefore invasive species with double genomes might have spread rapidly," the researchers explained.

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