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Unexpected Gene Transfer Discovered in Tiny Invertebrates

NEW YORK (GenomeWeb News) – New research indicates that bdelloid rotifers — tiny animals barely visible to the human eye — are capable of remarkable genetic feats, acquiring foreign genes from many other organisms through horizontal gene transfer.
In a paper published online today in Science, researchers from Harvard University and the Woods Hole Marine Biological Laboratory showed that at least two bdelloid rotifer species can snatch up genes from bacteria, fungi, and plants and integrate them into their own genomes. While some genes get rearranged in the process, many remain intact and are expressed in the rotifers. That suggests that the creatures, which lack sexual reproduction, may have an erstwhile unrecognized strategy for sharing genetic material.
“Overall, it looks pretty random,” senior author Irina Arkhipova told GenomeWeb Daily News. “But on the other hand, there’s a certain bias towards enzymes that can digest carbohydrates that can be of use.”
There are hundreds of species of bdelloid rotifers, microscopic invertebrates found mostly in aquatic environments. The organisms are noted for their ability to survive desiccation and become reanimated when moistened. In general, their genomes house many transposable elements, particularly near telomeres.
That made Arkhipova and her team suspect that some bdelliod rotifer genes may have originated in other species. To explore that possibility, the researchers looked more closely at these transposable elements, sequencing fosmid clones from the genomic library of a bdelloid rotifer species called Adineta vaga.
They specifically honed in on DNA at the chromosome ends in the telomeric regions, Arkhipova said. Indeed, unlike gene-rich parts of the genome, the telomeric regions seemed to contain genes from a variety of other organisms. “There was a great diversity of sources,” Arkhipova said.
The researchers found at least ten protein-coding sequences that aligned with bacterial and fungal sequences in a Blast search. And half of these had no known metazoan orthologs, suggesting that the rotifer had acquired foreign genes through horizontal gene transfer — a process usually reserved for organisms engaged in phagocytic, parasitic, or endosymbiosic relationships.
“In principle, this gives them an opportunity to take advantage of the entire environmental metagenome,” lead author Eugene Gladyshev, a Harvard graduate student, said in a statement.
Not all, but most of the foreign genes were intact, Arkhipova said. Among the foreign genes found in A. vaga were various enzyme-coding genes that seemed to have originated in bacteria, fungi, and plants.
While it remains unclear if — and how — the invertebrates use these pilfered genes, Arkhipova said it appears that several of the foreign genes are correctly transcribed and spliced in the bdelloid rotifer. That’s somewhat surprising, she added, since bacterial genes aren’t expected to contain functional introns.
The researchers were also able to express one of the bacterial enzymes in Escherichia coli.
Though it is possible that the rotifers take up genes from other metazoans, Arkhipova noted that it’s much more difficult to pick out foreign metazoan genes from those originating to the rotifer.
The researchers also tested whether other bdelloid rotifers might house stolen DNA by examining the sequences near telomeres of another species, called Philodina roseola. Like A. vaga, the P. roseola genome housed stretches of foreign DNA, raising the possibility that bdelloid rotifers regularly take up DNA — perhaps in conjunction with their desiccation and re-hydration cycles.
“It may be that [horizontal gene transfer] is facilitated by membrane disruption and DNA fragmentation and repair associated with the repeated desiccation and recovery experienced in typical bdelloid habitats,” the authors wrote, “allowing DNA in ingested or other environmental material to enter bdelloid genomes.”
Although there is insufficient evidence to suggest that all bdelloid rotifers can take up genes by horizontal gene transfer, the fact both species tested share the trait is intriguing. “We may expect it that it could be shared by bdelloid rotifers,” Arkhipova said, adding that experiments need to be done on other species.
And, she said, while it’s “reasonable to expect” that there could be genetic variation between members of the same species, the experiments done for this study were done on clonal representatives with the same genetics.