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Study Sees Wealth of Horizontally Acquired Genes in Water Bear Genome

NEW YORK (GenomeWeb) – The tardigrade, or water bear, genome is marked by an abundance of gene sequences obtained by horizontal gene transfer, according to a new study in the Proceedings of the National Academy of Sciences.

Researchers from the University of North Carolina at Chapel Hill, the University of Utah, and Cofactor Genomics generated a draft genome sequence from a parthenogenic tardigrade (Hypsibius dujardini) representative and used the sequence to search for clues to the microscopic animal's ability to withstand harsh, extremely dry environments.

The team's analysis indicated that more than 6,600 genes — almost one fifth of those found in the water bear genome — were obtained through horizontal gene transfer from bacteria, fungi, and other organisms. Prior to the study, the rotifer Adineta ricciae was on top of the heap when it came to genes originating from horizontal gene transfer, at just under 10 percent.

"Animals that can survive extreme stresses may be particularly prone to acquiring foreign genes — and bacterial genes might be better able to withstand stresses than animal ones," corresponding author Thomas Boothby, a postdoctoral researcher in the lab of senior author Bob Goldstein at UNC, said in a statement.

"[Horizontal gene transfer] is beginning to change the way we think about evolution and inheritance of genetic material and the stability of genomes," Boothby noted. "[I]nstead of thinking of the tree of life, we can think about the web of life and genetic material crossing from branch to branch."

Tardigrades, often called water bears, are tiny, eight-legged creatures that make up a phylum called Tardigrada. Although the animals are impervious to a range of environmental stressors such as heat, cold, radiation, pressure, and a lack of water, the team explained, not all that much is known about the genomic features that give them the wherewithal to do so.

With that in mind, the researchers used a combination of Illumina paired-end reads, long Illumina reads from Moleculo, and Pacific Biosciences data to put together a 212.3 megabase water bear draft genome, using DNA from cultures created from parthenogenic water bear individuals.

The team's analysis of this genome, sequenced to an average depth of around 126-fold coverage, pointed to the presence of some 38,145 protein-coding genes, including nearly 96 percent of the expressed sequence tags that have been described for H. dujardini in the past.

When they compared this gene repertoire with the set of genes described in a eukaryotic reference genome, the researchers found that the water bear genome housed more than 95 percent of the core genes found in a typical eukaryotic genome.

Through BLAST comparisons to known gene sequences, the team detected foreign origins for 17.5 percent of the water bear genes, including contributors to stress response-related processes. Almost 92 percent of those genes appeared to stem from horizontal gene transfer events involving bacteria, while the remaining genes coincided with coding sequences from fungi, plants, archaea, or viruses.

Taxonomic information was either missing or indeterminate for another 30 percent of the water bear genes.

Based on their findings, coupled with what is known about how water bears react to environmental stressors, the study's authors suspect tardigrades may be particularly prone to horizontal gene transfer as their cells become reanimated after a period of dormancy.

"We speculate that desiccation and associated membrane leakiness and DNA breakages might predispose these animals to take up and incorporate foreign material in their genomes," they wrote.