The genome of a sea spider corroborates a shared Hox cluster motif in arthropods with reduced posterior tagma

Background Chelicerate evolution is contentiously debated, with recent studies challenging traditional phylogenetic hypotheses and scenarios of major evolutionary events, like terrestrialization. Sea spiders (Pycnogonida) represent the uncontested marine sister group of all other chelicerates, featuring a – likely plesiomorphic – indirect development mode. Accordingly, pycnogonids hold the potential to provide crucial insight into early chelicerate genome evolution and ancestral principles of chelicerate body patterning. Leveraging this potential, however, has hitherto been hampered by the lack of high-quality genomic resources for pycnogonids. Results We employed long-read sequencing and proximity ligation data to assemble the first near chromosome-level sea spider genome for Pycnogonum litorale , complemented by developmental transcriptomes and a high-fidelity Iso-Seq dataset. The assembly has a size of 471Mb in 57 pseudochromosomes, a repeat content of 61.05%, 15,497 predicted protein-coding genes, and is highly complete (95.8% BUSCO Arthropoda score, 95.7% of conserved microRNA families present). We identified a single, intact Hox gene cluster that lacks abdominal-A/Hox9 , suggesting the loss of this Hox gene. Conclusions Our high-quality genomic and transcriptomic resources establish P. litorale as a key research organism for modern studies on chelicerate genome evolution, development, and phylogeny. The presence of a single Hox cluster in the P. litorale genome further strengthens the inference that no whole-genome duplication occurred at the base of the chelicerate tree. The lack of abdA suggests that the combination of abdA loss and posterior tagmata reduction is a common theme in arthropod evolution, as it is shared with other, distantly related arthropod taxa with a vestigial opisthosoma/abdomen.