Stephen Colbert's trapdoor spider genome points to a telomere code all spiders lost

UC Davis biologists have published the first reference genome for Aptostichus stephencolberti, the California trapdoor spider named after Stephen Colbert. The press release leads with the genome's size, but the paper's broader conclusion is that the repeat sequence most arthropods use to cap their chromosomes appears to have been lost in the common ancestor of all spiders.

The study appeared in the Journal of Heredity on September 8, and the university announced it on October 28. It is also the first genome for the whole family Euctenizidae, according to the authors.

A missing cap on the chromosomes

Most arthropods, from insects to many of their relatives, end their chromosomes with a short repeating DNA motif, written (TTAGG)n. These telomere repeats protect chromosome ends from wearing down each time a cell divides.

The team searched the new assembly for that motif and found none. They then widened the search to other chelicerates, the group that includes spiders, scorpions and mites. According to the paper, the repeat was present in every chelicerate group they checked except pseudoscorpions and horseshoe crabs, and absent from spiders.

"Based on the tidk search results, we conclude there has been an ancestral loss of the telomere repeat from all spiders," the authors write. They also caution that their assembly is not a telomere-to-telomere genome, and the paper does not establish what spiders use instead.

How big the genome actually is

The release describes the genome as 4.6 billion base pairs, about 50% larger than a human's. The paper gives smaller figures: a primary assembly spanning about 3.63 billion base pairs and a k-mer based size estimate of 3.87 billion. The release does not say where the 4.6 figure comes from.

Either way, most of it is repetitive. About 77% of the assembly is made of repeats, with DNA transposons the largest class. The researchers estimate 52 chromosomes, but the karyotype has not been confirmed under a microscope and no sex chromosomes were identified. The annotation lists 14,067 genes.

The DNA came from a spider collected at the Marina Dunes preserve in Monterey County in May 2020. The team used PacBio HiFi long reads and Omni-C chromosome-contact data to stitch the sequence together.

Why a comedian's spider gets a genome

Jason Bond, the paper's corresponding author, named the species in 2008 after Colbert asked on his show for a spider of his own. Bond had earlier named a trapdoor spider after Neil Young.

The species lives only in coastal dunes between the San Francisco Bay and Monterey, a habitat broken up by development. The sequencing was funded through the California Conservation Genomics Project, and the authors say the reference genome should help identify populations that need protection.

Bond's group says it is now running population-level sequencing on other Aptostichus spiders. Whether the missing telomere repeat changes how spider chromosomes age remains an open question.