All legs, no guts: Sea spider genome stuns scientists

The sea spider, those spindly marine oddities that seem composed almost entirely of legs and claws, just given up their genetic secrets.

An international effort led by the University of Vienna and the University of Wisconsin–Madison has delivered the first chromosome-level genome for Pycnogonum litorale, a species common in North Atlantic tide pools.

Stretching across 57 pseudo-chromosomes and paired with extensive developmental transcriptomes, the assembly offers an unprecedented look at how an arthropod can evolve such an extreme body plan. This includes a nearly vanishing abdomen and internal organs that spill far into its limbs.

Mapping the sea spider genome

To achieve a genome this contiguous, the team combined long-read sequencing with Hi-C proximity data. Long reads captured tens of thousands of DNA bases at a stretch. This helped bridge the repetitive regions that routinely break short-read assemblies.

Hi-C, which measures how DNA folds inside the nucleus, then provided a “scaffolding” map that placed those long contigs into chromosomal order.

“The genomes of many non-canonical laboratory organisms are challenging to assemble, and Pycnogonum is no exception,” said first author Nikolaos Papadopoulos, a zoologist at the University of Vienna.

“Only the combination of modern high-throughput data sources made a high-quality genome possible. This can now serve as a stepping stone for further research.”

Because sea spiders are not standard lab animals, researchers collected specimens by hand, often prying them from kelp during low tide. They then rushed them back to the lab for nucleic acid extraction.

The payoff is a reference genome that joins spider, scorpion, mite, and horseshoe crab assemblies on public databases. Yet it lacks the duplications that mark other arachnid genomes, making it a vital baseline for evolutionary comparisons.

Vanished gene, vanished abdomen

The analysis focused on Hox genes, key developmental regulators shared by animals from fruit flies to humans. One gene turned up missing: abdominal-A (abd-A).

In most arthropods, abd-A helps establish the rear-body segments that carry guts and reproductive organs. Sea spiders, with their virtually absent abdomens, appear to have dispensed with both the physical structure and its genetic architect.

“In arthropods, Hox genes play a central role in the correct specification of the different body segments, explained co-author Andreas Wanninger, who co-led the Vienna team. “In many other animal groups they are essential ‘master controllers’ during body plan development.”

The disappearance of abd-A mirrors patterns seen in mites and barnacles, two other arthropod groups that have independently shrunk or lost their hind segments.

Sea spiders skipped genome doubling

Spiders and scorpions carry extra copies of almost every gene, relics of an ancient whole-genome duplication that likely fueled innovations such as silk glands and complex venom cocktails.

P. litorale shows no sign of that event. Because sea spiders sit at the very base of the chelicerate lineage, the simplest explanation is that the duplication occurred later. It likely arose within the spider-scorpion branch, rather than in the common ancestor of all chelicerates.

That finding reshapes timelines for when gene families expanded and may help researchers pinpoint which duplications underlie spider-specific traits.

Tools for growth and repair

Beyond raw sequence, the consortium generated RNA profiles from embryos and juveniles, capturing when each gene flicks on and off as new body segments form.

Those developmental datasets make the sea spider a promising model for studies of ancestral arthropod development, limb regeneration, and physiological resilience in cold, nutrient-poor seas.

Georg Brenneis, an expert in arthropod development at the University of Vienna, is a senior author of the study.

“From an evolutionary developmental perspective, sea spiders are very interesting: their mode of development may be ancestral for arthropods, but at the same time they boast multiple body plan innovations unique to themselves. Beyond this, they also possess remarkable regenerative abilities.”

“Now that we have the genome and comprehensive datasets on gene activities during development, we can systematically study all of these aspects on the molecular level,” he said.

Editing limbs and trunk

With CRISPR editing becoming feasible in marine invertebrates, investigators can now ask how the remaining sea spider Hox genes choreograph eight elongated walking legs and a tubular trunk. They can also explore how the animals quickly regrow lost appendages.

Comparative physiologists might search the genome for stress-response genes that let sea spiders thrive in icy fjords, while ecological genomics teams could examine how gene flow operates across their wide geographic ranges.

Tracing ancient sea spider cousins

Without the duplication, shared sea spider genes likely existed as single copies in the last common chelicerate ancestor.

Aligning those sequences will clarify where new venom toxins arose, when silk machinery evolved, and how immune genes diversified.

The genome also lets scientists investigate regulatory DNA – enhancers, promoters, and non-coding RNAs. These elements rewired a conventional arthropod blueprint into the minimalist sea spider form.

Expanding the genomic catalog

The authors envision expanding the catalog to additional sea spider species to test whether abd-A loss is universal. They also aim to map gains and losses of other developmental genes across the group’s 1,300 known species.

Such work could uncover genetic shortcuts to extreme morphological change – insights that extend far beyond any single marine arthropod.

For now, the P. litorale genome stands as a milestone: the first high-quality reference for the world’s most enigmatic chelicerates. It’s also a reminder that even life’s strangest branches follow molecular rules that genomics can finally reveal.

The study is published in the journal BMC Biology.

Image Credit: Richard Lord/ CC BY-NC-SA 4.0

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