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Researchers Sequence, Characterize Centipede Genome

NEW YORK (GenomeWeb) – An international team of researchers has sequenced the genome of the centipede Strigamia maritima, gaining insight into arthropod evolution.

Researchers led by Stephen Richards, an assistant professor at Baylor College of Medicine, sequenced DNA collected from various members of a population of Scottish S. maritima. As they reported in PLOS Biology today, centipedes have a fairly compact and conserved genome, though they lack some genes common in other arthropods, including olfactory, vision, and circadian rhythm-related genes.

"We have [a] good sampling of insects but this is the first time a centipede, one of the more simple arthropods — simple in terms of body plan, no wings, simple repetitive segments, etc. — has been sequenced," first author Ariel Chipman from the Hebrew University of Jerusalem said in a statement. "This is a more conservative genome, not necessarily ancient or primitive, but one that has retained ancient features more than other groups."

Centipedes and their sister herbivorous lineage millipedes make up the myriapods, a group of insects with multi-segmented trunks, though with no distinction between the thorax and abdomen. They, the researchers noted, represent one of three separate terrestrial invasions made by arthropods.

Richards, Chipman, and their colleagues collected S. maritima from a Scottish beach where they live and feed on crustaceans and insect larvae.

They sequenced genomic DNA from multiple centipede individuals and assembled it into a draft genome some 176 megabases large. The draft, they said, lacks a number of repeat sequences, which likely accounts for the difference in size from the expected 290 Mb genome size.

This assembly, the researchers reported, includes nearly 15,000 gene models.

The researchers reconstructed the evolutionary history of all of the genes in the S. maritima genome. From this, they found that about a third of its genes could be traced to duplications specific to the myriapod lineage, including genes involved in taste perception, glutamate transport, and more.

At the same time, the researchers found that S. maritima has a high level of synteny with Branchiostoma floridae and Caenorhabditis elegans.

Gene clusters, the researchers noted, can be a used to gauge how much genome rearrangement a genome has undergone. The S. maritima genome, they reported, has 113 homeobox-containing genes, more than other sequenced arthropods like Drosophila melanogaster, Tribolium castanem, and Apis mellifera. Indeed, they noted that S. maritima has a Hox cluster that houses an ortholog of each expected arthropod Hox gene, except for Hox3. They added, though, that there are two other potential Hox3 genes located elsewhere in the S. maritima genome.

This, they said, underscores the conservative nature of the S. maritima genome.

"This genome of Strigamia has proved to be particularly valuable in deducing the content of important gene families in the ancestral arthropod, this ancestor then being the starting point for the evolution of the huge diversity of arthropods that we currently see today," said the University of St. Andrews' David Ferrier.

As insects and myriapods took to the land independently, the researchers also investigated whether they relied on similar genes to adapt to these new conditions.

To do so, they searched through the S. maritima genome for copies of insect chemosensory genes. They only found two genes belonging to the chemosensory protein family and a handful from the gustatory and ionotropic receptor gene families. They didn't find any belonging to the odorant-binding protein, CheA/B, or odorant receptor gene families.

However, they observed an expansion of both the IR and GR families in the S. maritima genome. It includes, they reported, 69 IR genes and 77 GR genes, most of which appear to be exclusive to centipedes.

Based on this, the researchers concluded that centipedes adapted to land independently and relied on a novel combination of GR and IR protein families for olfaction.

"This is a nice example of parallel evolution where different group of genes expanded, providing a different solution to the same problem," Baylor's Richards, said in a statement.

Centipedes are blind and live underground, but they have also been observed avoiding open spaces and light, raising the possibility that they can still sense light.

Richards and his colleagues, thus, also hunted through the S. maritima genome for light receptor and circadian clock genes — but they weren't able to detect any.

"Strigamia live underground and have no eyes, so it is not surprising that many of the genes for light receptors are missing, but they behave as if they are hiding from the light. They must have some alternative way of detecting when they are exposed," Cambridge University's Michael Akam said. "It's curious, too, that this creature appears to have no body clock — or if it does, it must use a system very different to other animals." 

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