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Transcript Sequencing Study Highlights Use of Foreign Genes by Asexual Invertebrate

NEW YORK (GenomeWeb News) – An asexual invertebrate species that can survive harsh environmental conditions seems to owe at least some of its biochemical prowess to genes acquired from other organisms, such as bacteria and fungi, according to a new study.

Researchers from the University of Cambridge and elsewhere used transcriptome sequencing to look at the extent to which foreign genes obtained by horizontal gene transfer are used by the bdelloid rotifer Adineta ricciae, a tiny, stress and desiccation-resistant invertebrate that reproduces asexually.

The findings, appearing online last night in PLOS Genetics, indicate that genes nabbed from other creatures through horizontal gene transfer — particularly those coding for enzymes — account for a significant proportion of the bdelloid rotifers' expressed transcripts.

"We were thrilled when we discovered that nearly 10 percent of bdelloids' active genes are foreign, adding to the weirdness of an already odd little creature," co-corresponding author Alan Tunnacliffe, a chemical engineering and biotechnology researcher at the University of Cambridge, said in a statement.

"We don't know how the gene transfer occurs, but it almost certainly involves ingesting DNA in organic debris, which their environments are full of," he added.

Although they occur in a range of aqueous environments, bdelloid rotifers are known for their ability to survive extremely dry conditions, potentially damaging radiation, and other harsh environmental stresses, Tunnacliffe and his co-authors said.

Because the animals have apparently been reproducing asexually for more than tens of millions of years, researchers suspect that some of the sequences that help the bdelloid rotifer adapt and accomplish its impressive range of metabolic and biochemical abilities can be traced back to horizontal gene transfer.

Past research on A. ricciae and another bdelloid rotifer species support that idea, they added. In particular, foreign sequences — including some expressed during desiccation stress — have been found in some telomeric regions of bdelloid rotifer genomes. But the degree to which horizontal gene transfer bolsters bdelloid rotifer biology is poorly understood.

To explore that in more detail, authors of the current study used Illumina paired-end sequencing to assess pooled complementary DNA prepared using RNA from hydrated or dried-out bdelloid rotifers grown in the lab.

By cross-referencing the more than 61,200 transcript sequences generated from the well-watered or desiccated bdelloids with protein database sequences, researchers came up with a list of bdelloid rotifer transcripts suspected to stem from foreign genes.

All told, 28,922 expressed bdelloid rotifer transcripts corresponded to sequences in the database. Of these, around 10 percent most closely matched sequences from other organisms such as fungi, bacteria, archaea, protists, plants, or algae.

"After allowing for sources of error," the study's authors wrote, "the rate of [horizontal gene transfer] is at least 8 percent to 9 percent, a level significantly higher than other invertebrates."

This sequence grabbing seems to help the bdelloid rotifer perform processes it could not otherwise, the researchers said, including some biochemical feats typically associated with microorganisms, such as toxic compound degradation.

Some 80 percent of transcripts from genes that the bdelloid rotifer has apparently snatched up by horizontal gene transfer correspond to enzyme coding sequences, the team noted. And more than one-third of all the known enzymes expressed in the gene-scavenging invertebrate could be traced back to foreign genes.

"Bdelloid rotifers … express horizontally acquired genes on a scale unprecedented in animals," Tunnacliffe and co-authors wrote, "and foreign genes make a profound contribution to their metabolism."

That does not appear to be the case for another rotifer species called Brachionus plicatilis, which has both sexual and asexual life stages.

The team's analyses indicate that B. plicatilis is far less likely to use genes obtained by horizontal gene transfer, as is the nematode worm Caenorhabditis elegans. In both organisms, less than 1.8 percent of expressed transcripts seemed to stem from foreign genes. For the fruit fly, that proportion was even lower at 0.6 percent.

Together, the researchers' results hint that the adoption and use of genes from other organisms could help augment the genetic diversity and functional wherewithal of the asexual bdelloid rotifer.

"This represents a potential mechanism for ancient asexuals to adapt rapidly to changing environments, and thereby persist over long evolutionary time periods in the absence of sex," the study's authors wrote.

"Uptake and expression of genes from other organisms is a means of diversifying functional capability, particularly biochemical capability," they added, "and the potential to replace defective genes with foreign counterparts could protect against loss of function through mutation."