Trees and Flowers More Akin than Dissimilar

Harvesting wood from weeds? Coaxing lumber from lobelias? Those possibilities aren't as far-fetched as you might think.

The two major kinds of plants -- woody and herbaceous -- are genetically far more similar than previously believed, according to genetic analysis conducted by forestry researchers at North Carolina State University. Comparing loblolly pines with the flowering annual Arabidopsis thaliana using DNA-sequencing technology, said Dr. Ronald R. Sederoff, Distinguished University Professor of forestry, led to a surprising finding: "The closer we looked at their genomes, the more similarities emerged."

The research also suggests that the techniques now being used to find genetic differences among plant types may exaggerate those differences, said Sederoff. "Most expressed gene-sequence analysis is limited to relatively short sequences of 500 bases or less," he said. "By looking at overlapping contiguous base sequences of 1,000 or more, we obtain a broader view that shows much more similarity between loblolly pine and Arabidopsis than we expected."

Like all plants, the towering pine and the flowering annual weed shared a common ancestor, but hundreds of millions of years ago, so their genetic differences were expected to be as diverse as their appearances. "Few genes would be expected to retain high sequence similarity for this time," the researchers say, "if they did not have essential functions. These observations suggest substantial conservation of gene sequence in seed plants."

The results are detailed in the paper "Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana" in the May 26 online issue of the Proceedings of the National Academy of Sciences (PNAS).

The two plants could hardly be more dissimilar: Arabidopsis is a small annual that lives for only weeks; the loblolly pine is a lofty tree that can live for hundreds of years. And yet, based on their analysis of more than 60,000 expressed sequence tags, Sederoff said the team found that 90 percent of the sturdy pine's genes match those of the tiny herbaceous plant.

"We wanted to know if woody and herbaceous plants evolved different genes that account for their diversity, or if they use the same genes in different ways," said Sederoff. "Our research strongly suggests the latter."

This "substantial conservation of gene sequence in seed plants," despite 300 million years of evolution and adaptation, means that herbaceous plants have the genetic potential to produce wood, and that woody plants might be engineered for other favorable characteristics.

The team's work was supported by a grant from the National Science Foundation. Matias Kirst, a graduate student in the genomics program of the Department of Genetics at NC State, is credited by Sederoff with the analytical work described in the paper. Researchers at NC State and the Center for Computational Genomics and Bioinformatics at the University of Minnesota performed the sequencing.

Sederoff, who co-directs the Forest Biotechnology Group in NC State's Department of Forestry, is a member of the National Academy of Sciences. He has specialized in the study of loblolly pines.

Sederoff and a team of molecular biologists and bioinformatics experts have been working to identify the genes used by trees to answer some basic questions: What genes do trees employ in making wood, and how do they use those genes?

Note to editors: The abstract of the loblolly/Arabidopsis paper follows.

"Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana"

Authors: Ronald Sederoff, Matias Kirst, Ross Whetten, NC State University; Arthur Johnson, Christie Baucom, Erin Ulrich, Kristy Hubbard, Rod Staggs, Charles Paule, Ernest Retzel, University of Minnesota.Date: Published in the May 26 online Proceedings of the National Academy of Sciences.

Abstract: Pinus taeda L. (loblolly pine) and Arabidopsis thaliana differ greatly in form, ecological niche, evolutionary history, and genome size. Arabidopsis is a small, herbaceous, annual dicotyledon, whereas pines are large, long-lived, coniferous forest trees. Such diverse plants might be expected to differ in a large number of functional genes. We have obtained and analyzed 59,797 expressed sequence tags (ESTs) from wood-forming tissues of loblolly pine and compared them to the gene sequences inferred from the complete sequence of the Arabidopsis genome. Approximately 50% of pine ESTs have no apparent homolog in Arabidopsis or any other angiosperm in public databases. When evaluated by using contigs containing long, high-quality sequences, we find a higher level of apparent homology between the inferred genes of these two species. For those contigs 1,100 bp or longer, about 90% have an apparent Arabidopsis homolog. Pines and Arabidopsis last shared a common ancestor approximately 300 million years ago. Few genes would be expected to retain high sequence similarity for this time if they did not have essential functions. These observations suggest substantial conservation of gene sequence in seed plants.