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Max-Planck, WashU Researchers Sequence Genome of Dead Beetle-Scouring Nematode

NEW YORK (GenomeWeb News) – Researchers from the Max-Planck Institute for Developmental Biology and the Genome Sequencing Center at Washington University in St. Louis have sequenced the draft genome of Pristionchus pacificus — a nematode that feeds on the fungi and bacteria found on dead beetles.
The work, published online this week in Nature Genetics, suggests that the tiny worm’s genome contains an unexpectedly large and diverse set of genes — including those involved in breaking down harmful substances and surviving in harsh environments. And because P. pacificus’ lifestyle appears to be an example of pre-parasitism, the findings are expected to provide new insights into the genetics of host-parasite interactions and the evolution of parasitism.
“We found a larger number of genes than we expected,” co-author Sandra Clifton, assistant director of Washington University’s Genome Sequencing Center, said in a statement. “These include genes that help the worms live in a hostile environment, the result of living in and being exposed to the byproducts of decaying beetle carcasses, and others that also have been found in plant parasitic nematodes.”
Nematodes, tiny roundworms found in every ecosystem, represent one of the most species-rich groups in the animal kingdom. Some are free-living while others parasitize plants or animals. The best known nematode, the model organism Caenorhabditis elegans, was sequenced a decade ago. More recently, the soybean cyst nematode genome, Heterodera glycines, was sequenced in March; the root-knot nematode, Meloidogyne incognita, was sequenced in July, and the genome of the northern root-knot nematode, Meloidogyne hapla, was published earlier this week.
And as more and more nematode genomes are sequenced, researchers can use comparative genomics to begin determining which genes are associated with specific environments and lifestyle adaptations.
For this paper, researchers focused on a California strain of P. pacificus, a “necromenic” nematode that lives on an oriental beetle species in the US and Japan, feasting on the fungi, bacteria, and other miniscule creatures that colonize the beetles after they die. The worms invade beetles during their non-feeding, resting stage — which resembles the infective life stage of parasitic nematodes — and then continue developing after the beetles die.
The current draft genome — obtained by sequencing the 169 megabase genome of a California strain of P. pacificus to nine-fold coverage using whole-genome shotgun sequencing — represents roughly 84 percent of the worm’s complete genome. The researchers also sequenced three other Pristionchus genomes, including that of a Washington strain of P. pacificus, to various coverage levels, using the California strain as a reference genome.
Based on their subsequent analysis, the researchers predicted that the P. pacificus contains more than 23,500 protein-coding genes — more than the free-living nematode C. elegans, which has about 20,000 protein-coding genes, and the human parasite Brugia malayi, which has roughly 12,000 protein-coding genes.
Although a large set of genes were similar to those found in C. elegans, P. pacificus has several gene families that were larger than those in the free-living worm. For example, the researchers reported that P. pacificus has more genes coding for cytochrome p450 enzymes, glucosyltransferases, sulfotransferases, and ABC transporters. On the other hand, several gene families were also reduced relative to C. elegans, pointing to environment-specific adaptations in each organism.
The team found that P. pacificus had gene duplications in regions of the genome that could help it survive in and on the beetle. The genome also contained genes coding for detoxification and degradation enzymes that likely help the worm thrive on dead beetles.
Clues in the genome also provide support for the notion that P. pacificus might be a precursor to parasitic worms. In particular, the team found that the P. pacificus genome contains genes that are not found in C. elegans but that are similar to those found in plant parasites, including several genes coding for the enzyme cellulase, which can help break down plant and microorganism cell walls.
In the future, the team predicts that an improved understanding of the genetics behind P. pacificus’ development, behavior, and ecology will lead to a clearer view of parasitism in general.
“The really exciting questions are still to come,” senior author Ralf Sommer, director of the evolutionary biology department at the Max-Planck Institute for Developmental Biology, said in a statement. “Using the sequence data, we can test how the Pristionchus has adapted to its specific habitat. And this will undoubtedly give us new insight into the evolution of parasitism.”