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Researchers Find Evidence for Horizontal Gene Transfer in Mammals, Reptiles

NEW YORK (GenomeWeb News) – New research suggests that some mammal and reptile genomes been shaped, in part, by horizontal gene transfer.
 
While horizontal gene transfer is typically associated with prokaryotic genomes, researchers from the University of Texas at Arlington have found evidence that it has occurred during eukaryotic evolution as well. The work, scheduled to appear online this week in the Proceedings of the National Academy of Sciences, indicates that a flurry of horizontal gene transfer events occurred 15 million to 46 million years ago, plopping mobile genetic elements called transposons into at least seven tetrapod lineages.
 
And as more genome sequences become available, researchers say, it should be possible to understand even more about the mode, frequency, and consequences of these horizontal gene transfer events.
 
Lateral or horizontal gene transfer occurs when stretches of DNA from one organism become incorporated into the genome of another, unrelated organism. For instance, viral phages or bacterial plasmids can hop from one organism to another, carting bits of DNA between genomes.
 
But horizontal gene transfer is less well characterized in eukaryotes, though there are some examples. For instance, there is evidence of horizontal gene transfer in some insects. And mammals may also acquire sequence from retroviruses, senior author Cédric Feschotte, a biologist at the University of Texas at Arlington, told GenomeWeb Daily News. When these retroviruses infect germ line cells, they can be passed along to the next generation, he explained.
 
But Feschotte and his team uncovered a new type of horizontal gene transfer in mammals and other higher eukaryotes when they started comparing sequences from the genome of the bushbaby, a primate species, with those from other animals.
 
The team used Blast to compare a bushbaby sequence resembling a group of hobo/Activator/Tam3 or hAT superfamily transposons to the genomes of other animals. As it turned out, they found nearly identical sequences in seven other species: the rat, mouse, little brown bat, tenrec, opposum, green anole lizard, and African clawed frog. The sequence was missing from the genomes of 19 other mammalian species for which draft assemblies were available.
 
But, evolutionarily, the sequence showed a strange pattern, popping up here and there on vastly different branches of the tetrapod tree. And despite the fact that it is usually non-coding, the sequence appeared to remain nearly identical — though duplicated to varying degrees — across a broad range of species.
 
Based on this patchy taxonomic distribution and high level of conservation, the team concluded that the sequences could not have been acquired vertically, especially since the sequences appear to be under neutral evolutionary pressure.
 
“The only way to explain this sequence similarity is that they arrived [in the genome] more recently,” Feschotte said, noting that the species represented span more than 350 million years of evolution whereas the sequences they found appear to have been evolving over a much, much shorter time frame.
 
Because the sequence seems to have appeared out of nowhere, the researchers dubbed them “Space Invaders” or SPIN elements. Overall, the team found 96 percent sequence identity between SPIN elements in any two of the species in which they were detected.
 
“[T]he only plausible scenario is that active and nearly identical SPIN elements were introduced horizontally, and relatively recently, into several tetrapod species and subsequently spawned different waves of SPIN amplification along these species lineages,” the authors argued.
 
Although hAT transposons are widespread in eukaryotic genomes, Feschotte explained, they usually move within rather than between genomes. “Normally, [transposons] have no way to get out of the cell,” he said. “This is unusual or unexpected to find horizontal movement of this type of elements.”
 
More research is necessary to determine how SPIN elements entered tetrapod genomes. But the team has a few ideas. For instance, Feschotte suspects transposons may have been shuttled out of their original host genome by viruses that went on to infect other organisms. Consistent with that notion, Feschotte said, others have found some DNA viruses containing transposon sequences.
 
Regardless of how it occurred, Feschotte said that it’s clear that the introduction and subsequent duplication of these transposons has helped to shape the genomes of some tetrapod species. For example, he said, the tenrec genome contains nearly 100,000 copies of the SPIN sequence, which likely influenced the genome as a whole. Meanwhile, in mice and rats, the transposon has helped to give rise to a functional gene.
 
“This introduction was evolutionarily consequential for these species,” Feschotte said. “There’s no doubt about it.”
 
At the moment, the team’s understanding of these transfer events is biased toward the genomes available, Feschotte conceded. But as more and more genome sequences become available in the future, it will be possible to gain deeper insights into this process.
 
For now, though, Feschotte credits the existing genome sequences for helping to improve researchers understanding of genome evolution. “It is really because we had all these genomes available that we could see this,” he said. “I think we’re going to get a clearer picture of how prevalent this is as we look at other species.”

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