Sea spiders (Pycnogonida) have a very strange body shape. They’re tiny marine animals with super skinny trunks and legs so long that some of their organs stretch into them! Their belly is so reduced it’s barely visible. They belong to the same group as spiders and scorpions: chelicerates, named after their special claw-like mouthparts called chelicerae.
Because sea spiders look so different, researchers are exploring their genome to understand what genes create such unusual bodies and what this reveals about their evolutionary history.
Researchers from the University of Vienna and the University of Wisconsin- Madison have created the first chromosome-level genome of the sea spider Pycnogonum litorale. This breakthrough helps explain the species’ unusual body structure and offers new insights into the evolution of chelicerates—a group that includes spiders, scorpions, and horseshoe crabs.
To assemble the sea spider genome, researchers used two advanced sequencing techniques. First, they applied long-read sequencing to one individual, which captured long stretches of DNA and helped piece together tricky parts of the genome. Then, with a second individual, they studied how DNA is arranged inside the cell, figuring out which pieces sit close together.
Scientists revealed the oldest known scorpion on Earth
By combining these approaches, they successfully built 57 pseudochromosomes, covering nearly the whole genome with high precision. They also added data on gene activity across different developmental stages, giving an even deeper look into how this unique animal develops and functions.
The team mainly focused on the so-called Hox cluster, a gene family that is evolutionarily conserved across the animal kingdom. In arthropods like sea spiders, Hox genes are crucial for defining where different body segments go—head, thorax, abdomen, etc. But their role isn’t limited to creepy crawlies! Across many animal groups, Hox genes act as master regulators, guiding the overall layout during development.
In a fascinating twist, scientists discovered that Pycnogonum litorale, a sea spider, is missing a key Hox gene called abdominal-A (Abd-A), a gene normally responsible for shaping the rear end of arthropods. Its absence may explain why sea spiders have extremely reduced abdomens, a trait also seen in mites and barnacles.
This supports a broader evolutionary pattern: when certain Hox genes disappear, the body parts they control often shrink or vanish. Sea spiders now join the list of species showing this gene-body connection.
Unlike spiders and scorpions, which show signs of ancient whole-genome duplications, P. litorale has no such genetic echoes. Since sea spiders are considered the sister group to all other chelicerates, this suggests that genome duplications occurred later, in specific subgroups, not in the earliest chelicerate ancestors.
The newly completed genome of P. litorale gives scientists a powerful tool for comparing chelicerate species—like spiders, scorpions, and horseshoe crabs—and studying how their body plans evolved.
Identifying the genes behind venom production
Why sea spiders stand out:
- Their development may reflect how early arthropods grew.
- They have unique body features not seen in other species.
- They can regenerate parts of their body, which is rare and exciting for research.
With the genome and gene activity data now in hand, researchers like Georg Brenneis can explore these traits in detail at the molecular level.
Journal Reference:
- Papadopoulos, N., Kulkarni, S.S., Baranyi, C., et al. The genome of a sea spider corroborates a shared Hox cluster motif in arthropods with a reduced posterior tagma. BMC Biol 23, 196 (2025). DOI: 10.1186/s12915-025-02276-x