Plant genes imported from unrelated species more often than previously thought, IU biologists find

Scientists have long thought gene exchange between individuals of unrelated species to be an extremely rare event among eukaryotes — the massive group of organisms that counts among its members humans, oak trees, kelp and mushrooms — throughout the group’s 2 billion year history.

But a new Indiana University Bloomington study in this week’s Nature suggests that such genetic events, called horizontal gene transfers, have happened more often than previously thought during the evolution of flowering plants. The finding hints other eukaryotes have had significant genetic influence from completely unrelated species.

“It appears horizontal gene transfer occurs for just about any gene in the plant mitochondrial genome,” said biologist and Class of 1955 Endowed Professor Jeffrey Palmer, who led the research. “There is no reason to believe that this finding would apply only to plants. We already know from past studies that other eukaryotes experience the same mechanisms of horizontal transfer for certain special pieces of DNA called transposable elements. Our results now extend this phenomenon to the thousands of ordinary genes in a genome.”

It has been common knowledge for years that horizontal gene transfer among bacteria is extremely common. Some scientists believe that as much as 25 percent of certain bacterial species’ chromosomal DNA has been acquired by way of horizontal transfer.

In eukaryotes, the rule remains that individuals get their genes from parents intergenerationally through the more familiar process called vertical transmission. But Palmer said scientists have probably underestimated the rate at which non-traditional gene transfer happens in eukaryotes.

“While our data set was small and real rates of eukaryotic horizontal gene transfer were therefore hard to predict, we can infer that even conservatively, horizontal gene transfer must have happened in flowering plants thousands of times,” Palmer said.

One of the assumptions scientists make when comparing DNA from different species is that the DNA has followed basic lines of heredity connected in the past by a common ancestor. If DNA used in these gene studies does not descend vertically, from parent to offspring, but horizontally, by jumping from another lineage, analyses might turn up confusing or misleading evolutionary relationships between species. But Palmer isn’t worried about that.

“We don’t believe horizontal gene transfer happens often enough to throw a monkey wrench into molecular genealogical studies,” he said.

While the mechanisms of horizontal gene transfer are still unknown, various explanations suggest that viruses, bacteria and fungi pack errant genetic material, or that accidental cross-species mating may play a role. However it happens, Palmer said there is no question it doeshappen. Many scientists have reported unexpectedly finding one species’ gene in another species with no reasonable explanation except horizontal gene transfer.

After encountering unique gene sequences along circular mitochondrial DNA chromosomes in three flowering plant species, Palmer and his team sought to determine the source of the anomalous genetic material. Part of the mystery was that closely related flowering plants did not possess the same gene sequences. Most of the genes the researchers examined encode parts of ribosomes, tiny assembly plants that make proteins by connecting amino acids.

Palmer’s team amassed mitochondrial gene sequence data from about 100 angiosperm species and looked for sequence similarities between them. In creating a tree of relatedness between the sequences, the scientists found that the mitochondrial genes from five flowering species — kiwi fruit, honeysuckle, birch, bloodroot and Amborella (the most primitive flowering plant in existence) — appeared far more related to unrelated species than to species more closely related to them, strongly suggesting that the four species had acquired these particular genes by way of horizontal transfer.

In the case of the bloodroot, the researchers were astonished to find a hybrid, “chimeric” mitochondrial gene. Half of this gene was captured by horizontal transfer from an unrelated plant over 100 million years distant in time, while the other half had been transmitted faithfully from parent to offspring in the lineage leading to bloodroot. “This result was so surprising, our first thought was that we’d made a mistake,” Palmer said. “Once it was confirmed we had not made an error, we understood that what we’d found was very exciting.”

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Ulfar Bergthorsson (Indiana University Bloomington), Keith Adams (now at Iowa State University) and Brendan Thomason (now at the University of Michigan School of Medicine) also contributed to the study. It was funded by a grant from the National Institutes of Health.

To speak with Palmer or Bergthorsson, contact David Bricker at 812-856-9035 or brickerd@indiana.edu.