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Abstract Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species. 

Abstract The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily “short” timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.