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Transcriptome Analysis Reveals Whole-Genome Duplications in Conifer Lineage

Conifer trees.

NEW YORK (GenomeWeb) – A new study in Science Advances suggests at least two whole-genome duplications have occurred in the coniferous tree lineage, arguing against the notion that polyploidy is particular to the evolution of flowering plants.

Researchers from the US and Canada did transcriptome sequencing on leaf samples from three plants: the long stem adderstongue fern Ophioglossum petiolatum; the melinjo tree Gnetum gnemon; and a shrub plant called Ephedra frustillata. When these sequences were folded into a phylogenetic analysis of two-dozen vascular plants and three outgroup plants, they found three historical duplications involving the ancestors of gymnosperms — conifers and other plants with 'naked' seeds.

Using a new computational approach, the team narrowed in on the timing of these events, placing two of the whole-genome duplications into the lineage leading to the conifer clade. The analysis placed a third duplication event in the ancestors of seed plants after their divergence from the lineage leading to ferns.

"Contrary to previous genomic research that reported an absence of polyploidy in the ancestry of contemporary gymnosperms, our analyses indicate that polyploidy has contributed to the evolution of conifers and other gymnosperms," senior author Michael Barker, an ecology and evolutionary biology researcher at the University of Arizona, and his colleagues wrote.

"As in flowering plants, the evolution of the large genome sizes of gymnosperms involved both polyploidy and repetitive element activity," they explained.

Whole-genome duplications are well documented in the shared ancestors of the gymnosperm and angiosperm plants, the team noted. And further duplication events have been linked to the evolution and diversification of the angiosperm, or flowering, plants in the more than 300 million years since the angiosperm-gymnosperm split.

Studies on plants such as the Norway spruce have found little or no evidence for whole-genome duplications specific to gymnosperms, on the other hand, though the study's authors suspected such events may have made unappreciated contributions to gymnosperm genomes.

With that in mind, they used Roche 454 sequencing to produce transcriptome sequences for RNA extracted from flash frozen O. petiolatum, G. gnemon, and E. frustillata leaves collected at the University of British Columbia's Botanical Gardens and Greenhouse.

For its analysis, the team also tapped into available GenBank sequences for 22 gymnosperm or vascular plant species as well as sequences from a moss and an angiosperm shrub represented in the Phytozome database.

The researchers then used a bioinformatics-based approach to find and assign ages to gene paralogs produced through duplications. While that analysis pointed primarily to a whole-genome duplication event in ancestral seed plants, there were hints of subsequent duplications in the gymnosperms.

With the help of an algorithm called Multi-tAxon Paleopolyploidy Search, or MAPS, the team verified a duplication event in the ancestors of angiosperm and gymnosperm plants that occurred after the split from ferns. And it uncovered signs of two more whole-genome duplications in the ancestors of conifer plants from the Pinaceae family and in the lineage leading to conifers from the Taxaceae and Cupressaceae families.

"Examining further data sets to more precisely pinpoint these [whole-genome duplications] in the conifer phylogeny," the study's authors concluded, "and to explore the effects of duplication on specific gene families will be critical to further answer how polyploidy has contributed to conifer evolution."