Sea Spider Genome Unlocks Secrets of Extreme Body Plan

Marine sea spiders, those strange, spindly creatures seemingly made of legs, have revealed their genetic make-up. Now, how these arthropods evolved such unique anatomies might be understood.

Mapping the Genes

An international team of scientists, including researchers from the University of Vienna and the University of Wisconsin–Madison, has successfully mapped the first chromosome-level genome of Pycnogonum litorale. The species is commonly found in North Atlantic tide pools.

The comprehensive assembly, encompassing 57 pseudo-chromosomes and paired with extensive developmental transcriptomes, offers a detailed look at the animal’s evolution. Scientists are hoping to understand the extreme body plan, including its reduced abdomen and internal organs extending into its legs.

Decoding the Data

The team used long-read sequencing combined with Hi-C proximity data to assemble the genome. Long reads, which captured tens of thousands of DNA bases, helped connect repetitive regions that typically disrupt short-read assemblies. Hi-C data then mapped how DNA folds inside the nucleus, creating a “scaffolding” map for chromosomal order.

“The genomes of many non-canonical laboratory organisms are challenging to assemble, and Pycnogonum is no exception,” stated **Nikolaos Papadopoulos**, a zoologist at the University of Vienna. He added that only a combination of high-throughput data sources made a high-quality genome achievable, which can serve as a foundation for future research.

Evolutionary Insights

The reference genome joins other arachnid genomes on public databases, including those of spiders, scorpions, mites, and horseshoe crabs. Intriguingly, the sea spider genome lacks the duplications found in other arachnids, making it a valuable baseline for comparative evolutionary studies. Approximately 90% of human genes have a corresponding gene in the sea spider, highlighting their potential for broad biological research (National Human Genome Research Institute).

The Missing Gene

Focusing on Hox genes, the analysis revealed a missing gene: abdominal-A (abd-A). These genes regulate development, and abd-A usually establishes rear-body segments housing guts and reproductive organs in most arthropods. Sea spiders, with their nearly absent abdomens, seem to have evolved without both the structure and its genetic architect.

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

The absence of abd-A echoes patterns observed in mites and barnacles, other arthropod groups that have independently reduced or lost their hind segments.

Skipped Genome Doubling

Unlike spiders and scorpions, P. litorale shows no evidence of an ancient whole-genome duplication. Given the sea spider’s position at the base of the chelicerate lineage, scientists believe the duplication occurred later, within the spider-scorpion branch.

This finding changes the timeline for gene family expansion and could help researchers identify the duplications underlying spider-specific traits. The team also generated RNA profiles from embryos and juveniles, capturing gene activity during body segment formation.

**Georg Brenneis**, an expert in arthropod development at the University of Vienna, noted that sea spiders have a unique development mode. He said that the genome and datasets on gene activities now allow for systematic study on the molecular level.

Future Research

With CRISPR editing becoming more accessible in marine invertebrates, researchers can investigate how the remaining sea spider Hox genes orchestrate limb and trunk development. Comparative physiologists can also search for stress-response genes that enable sea spiders to thrive in cold waters. Ecological genomics teams could study gene flow across their geographic ranges.

Without the duplication, shared sea spider genes likely existed as single copies in the last common chelicerate ancestor. Aligning these sequences may clarify the origins of venom toxins, silk machinery, and immune gene diversification.

The genome also enables scientists to explore regulatory DNA, which rewired the arthropod blueprint into the minimalist sea spider form.

Expanding the Catalog

The researchers aim to expand the genomic catalog to include additional sea spider species to determine if abd-A loss is universal. They also plan to map developmental gene gains and losses across the group’s 1,300 known species.

Ultimately, this work could reveal genetic pathways to extreme morphological change. The P. litorale genome represents a significant step forward, offering a high-quality reference for these enigmatic creatures, and a reminder that even the strangest life forms follow molecular rules that genomics can uncover.

The study appears in the journal BMC Biology.