Zymogenic latency in an ∼250-million-year-old astacin metallopeptidase

The horseshoe crab Limulus polyphemus is one of few extant Limulus species, which date back to ∼250 million years ago under the conservation of a common Bauplan documented by fossil records. It possesses the only proteolytic blood-coagulation and innate immunity system outside vertebrates and is a model organism for the study of the evolution and function of peptidases. The astacins are a family of metallopeptidases that share a central ∼200-residue catalytic domain (CD), which is found in >1000 species across holozoans and, sporadically, bacteria. Here, the zymogen of an astacin from L. polyphemus was crystallized and its structure was solved. A 34-residue, mostly unstructured pro-peptide (PP) traverses, and thus blocks, the active-site cleft of the CD in the opposite direction to a substrate. A central `PP motif' (F<sup>35</sup>-E-G-D-I<sup>39</sup>) adopts a loop structure which positions Asp38 to bind the catalytic metal, replacing the solvent molecule required for catalysis in the mature enzyme according to an `aspartate-switch' mechanism. Maturation cleavage of the PP liberates the cleft and causes the rearrangement of an `activation segment'. Moreover, the mature N-terminus is repositioned to penetrate the CD moiety and is anchored to a buried `family-specific' glutamate. Overall, this mechanism of latency is reminiscent of that of the other three astacins with known zymogenic and mature structures, namely crayfish astacin, human meprin β and bacterial myroilysin, but each shows specific structural characteristics. Remarkably, myroilysin lacks the PP motif and employs a cysteine instead of the aspartate to block the catalytic metal.

Microsatellite Loci of the Atlantic Horseshoe Crab (Limulus polyphemus) Reveal Inter-Localities Genetic Diversity in the Coastal Waters of the Eastern and Northern Yucatan Peninsula

The American horseshoe crab (Limulus polyphemus) is an economically and ecologically important species, which is currently categorized as endangered in Mexico. L. polyphemus, one of four extant horseshoe crab species that constitute the class Merostomata, is distributed along the Atlantic coastline of the USA from Alabama to Maine and has another population on the coastline of Campeche, Yucatan, and Quintana Roo in the Yucatan Peninsula, Mexico. In the present study, we evaluated the genetic diversity and genetic structure of four separated localities along the coast of the Yucatan peninsula (Champoton, CH; Isla Arena, IA; Rio Lagartos, RL; and Holbox Island, HI), using nine microsatellite-type molecular markers for this species. The aim of this study is to obtain a baseline of the current level of genetic diversity, which would allow the monitoring of important changes over time. Multilocus analyses revealed moderate levels of genetic diversity (He, 0.5230 to 0.6389) and genetic structure within the whole study area (F_ST 0.025). The population from RL showed limited gene flows, differing significantly from the other sampling sites. The genetic information obtained in this study can support the implementation of management and conservation programs for this species in Mexico.

First Evidence of Glyphosate in American Horseshoe Crab from the Yucatan Peninsula in Mexico

Glyphosate is the most used herbicide in the world. Unfortunately, contamination of water bodies by this herbicide has been reported. A severe concern has been triggered given its detrimental impact on the environment and wildlife. The American horseshoe crab (Limulus polyphemus) is a benthic arthropod that inhabits the Yucatan Peninsula in Southeast Mexico. This study evaluates the glyphosate concentration in 34 recently dead specimens of L. polyphemus from four localities of the Ria Lagartos Biosphere Reserve in Yucatan, Mexico. The analysis was carried out using High-Performance Liquid Chromatography coupled with a Triple Quadrupole Mass Spectrometer. All the samples showed residues of glyphosate in the range from 0.08 to 2.38 ng g-1. These records constitute the first evidence of glyphosate bioaccumulation in this species. Although the scope might be limited, the results demonstrate a potentially prejudicial exposition of the marine biota to glyphosate-based herbicides, given its use in the region.

Differential Gene Expression Induced by Acute Exposure to Water Accommodated Fraction (WAF) and Chemically Enhanced WAF (CEWAF) of Light Crude Oil and Nokomis 3-F4 in Limulus polyphemus Larvae

In 2018 we evaluated at 48 h and 96 h, the gene expression profile of larvae of Limulus polyphemus exposed to 10% and 100% of water-accommodated fraction (WAF) of light crude oil (API 35), and 10% and 100% of a chemically enhanced WAF (CEWAF) with the dispersant Nokomis 3-F4® in a static-acute (96 h) bioassay. Alkanes and PAHs concentrations were higher in CEWAF than in WAF stock solutions. Under the proved conditions, the expression profile of genes associated to detoxification processes (glutathione S-transferase and glutathione peroxidase), stress (heat shock protein), innate immunity (tumor necrosis factor receptor-associated factor 4 traf4), cell death (apoptosis inhibitor 5) and DNA repairing (E3 ubiquitin protein ligase), showed a deregulation at 48 h followed by an upregulation at 96 h, with exception of glutathione peroxidase, heat shock protein and innate immunity that remained low in CEWAF. In conclusion, by using genes that have been proposed as biomarkers to pollutants exposure, L. polyphemus larvae showed an early activation of genes related to the immune system, antioxidant, heat shock and NER.

Development of methodology and reference intervals for the analysis of the free-ranging Atlantic horseshoe crab Limulus polyphemus hemolymph

BACKGROUND

The Atlantic horseshoe crab, Limulus polyphemus, is valuable to fishing and biomedical industries, for education in public aquaria, and of ecological importance because the eggs provide a critical food source for migratory shorebirds. While hematologic and biochemical analyses are fundamental tools for health assessment, reports are limited for the four extant species of horseshoe crabs; L polyphemus (East Coast North America), Carcinoscorpius rotundicauda (mangrove horseshoe crab Southeast Asia), Tachypleus gigas, and Tachypleus tridentatus (Southeast and East Asia).

OBJECTIVES

This prospective study measured hemolymph values to determine RIs from free-ranging horseshoe crabs during the annual breeding aggregation in Delaware Bay, USA.

METHODS

Near-shore animals were briefly manually restrained for hemolymph collection from the cardiac sinus. Hematologic samples (25 males, 25 females) were collected for hemocytometer counts using the Natt and Herrick method. A second set of 50 animals (25 males, 25 females) was sampled for biochemistry measurands, including copper concentration by spectrophotometer, osmolality by vapor pressure osmometer, and protein electrophoresis.

RESULTS

Total hemocyte counts varied widely (RI 6600-44 300/µL). Electrolytes were consistent with osmoconformers living in seawater. There was a marked difference in sexes, with females showing much lower protein, glucose, and copper levels. Eleven females had multiple outliers, and all data were excluded from RI calculations.

CONCLUSIONS

Further studies of this species outside of spawning season are needed. Expanding our knowledge of horseshoe crab health is important to decreasing morbidity and mortality in research applications and maximizing longevity and overall health in display settings.

2-PHENOXYETHANOL (2-PE) AND TRICAINE METHANESULFONATE (MS-222) IMMERSION ANESTHESIA OF AMERICAN HORSESHOE CRABS (LIMULUS POLYPHEMUS)

Despite extensive literature examining American horseshoe crab physiology, there are comparatively few publications addressing their medical care. Establishing anesthesia protocols for horseshoe crabs is integral to limiting the potential stress and pain associated with invasive procedures and for advancing euthanasia techniques. The objective of this study was to compare the effects of two immersion anesthetics, tricaine methanesulfonate (MS-222) at 1 g/L (buffered with sodium carbonate) and 2-phenoxyethanol (2-PE) at 2 mL/L, on horseshoe crabs. Twenty horseshoe crabs were assigned to one of two anesthetic treatment groups and individually anesthetized in natural seawater. Water quality, cardiac contractility, and hemolymph gas analytes were measured prior to anesthesia and at 30 min Animals were monitored via heart rate, gilling rate, and sedation score every 5 min until recovered. Transcarapacial ultrasonography was used to obtain heart rate, gilling rate, and percent fractional shortening. Light or surgical anesthesia was produced in 10/10 animals in the 2-PE group and 8/10 animals in the MS-222 group. There was no significant difference in sedation scores, induction time (median 15 min), or recovery time (median 20.5 min). Gilling rate and cardiac contractility decreased during anesthesia, whereas heart rate did not. Hemolymph pH and pO₂ were not different among treatment groups or time points. Baseline pCO₂ was higher than pCO₂ at 30 min for both groups but significantly elevated only in the MS-222 group. This is attributed to increased activity during the handling of awake animals. Invasive blood pressure obtained via cardiac catheterization in two animals was markedly decreased during surgical anesthesia. In conclusion, 2-PE and MS-222 provided effective anesthesia with clinically useful induction and recovery times. 2-PE provided a subjectively more reliable and smoother anesthesia compared to MS-222.

Histologic Findings in Captive American Horseshoe Crabs (Limulus polyphemus)

Histopathology of 61 captive American horseshoe crabs (HSCs; Limulus polyphemus) is reviewed. HSC organs evaluated histologically included body wall (chitin, epidermis, dermis, and skeletal muscle), hepatopancreas, gut, gonads, book gills, eyes, heart, brain, and coxal gland. In descending order, lesions were most frequently identified in compound eye, body wall, book gills, hepatopancreas, chitinous gut, nonchitinous gut, heart, and brain; lesions were not observed in coxal gland or gonads. Hemocytes (also called amoebocytes) surrounded infectious agents and occluded ulcers. Large hemocyte aggregates had a central eosinophilic coagulum (ie, hemocyte coagulum). Cutaneous ulceration (34/60 cases), branchitis (29/48 cases), and ophthalmitis (17/20 cases) were common lesions and consistently associated with fungi, which were invasive into subjacent tissues, and/or bacteria, which were usually superficial. Fungal culture was performed in 3 cases and isolated Fusarium spp., although fungal morphology varied and multiple fungal species may have been present. Presumptive green algae were associated with ulceration in 1 case with minimal to no inflammation. Presumptive cyanobacteria were identified within a biofilm overlying the gills in 4 of 48 cases and were not invasive. Multifocal, random hepatopancreatitis was identified in 16 of 57 cases, 10 of which were associated with bacteria. Metacercarial cysts were identified in 25 of 61 cases and associated with minimal to no inflammation. Depleted eosinophilic globules in hepatopancreatic interstitial cells were interpreted as decreased nutritional status in 12 of 57 cases.

Heavy Metals in Biota in Delaware Bay, NJ: Developing a Food Web Approach to Contaminants

Understanding the relationship between heavy metal and selenium levels in biota and their foods is important, but often difficult to determine because animals eat a variety of organisms. Yet such information is critical to managing species populations, ecological integrity, and risk to receptors (including humans) from consumption of certain prey. We examine levels of cadmium, lead, mercury, and selenium in biota from Delaware Bay (New Jersey, USA) to begin construction of a “springtime” food web that focuses on shorebirds. Horseshoe crab (Limulus polyphemus) eggs are one of the key components at the base of the food web, and crab spawning in spring provides a food resource supporting a massive stopover of shorebirds. Fish and other biota also forage on the crab eggs, and a complex food web leads directly to top-level predators such as bluefish (Pomatomus saltatrix) and striped bass (Morone saxatilis), both of which are consumed by egrets, eagles, ospreys (Pandion haliaetus), and humans. Metal levels in tissues were generally similar in algae, invertebrates, and small fish, and these were similar to those in blood of shorebirds (but not feathers). There was a significant direct relationship between the levels of metals in eggs of horseshoe crabs and mean metal levels in the blood of four species of shorebirds. Metal levels in shorebird feathers were higher than those in blood (except for selenium), reflecting sequestration of metals in feathers during their formation. Levels in feathers of laughing gulls (Leucophaeus atricilla) were similar to those in feathers of shorebirds (except for selenium). Selenium bears special mention as levels were significantly higher in the blood of all shorebird species than in other species in the food web, and were similar to levels in their feathers. Levels of metals in bluefish and striped bass were similar or higher than those found in the blood of shorebirds (except for selenium). The mean levels of cadmium, lead, and mercury in the blood and feathers of shorebirds were below any effect levels, but selenium levels in the blood and feathers of shorebirds were higher than the sublethal effect levels for birds. This is a cause for concern, and warrants further examination.

Computational biomechanical analyses demonstrate similar shell-crushing abilities in modern and ancient arthropods

The biology of the American horseshoe crab, Limulus polyphemus, is well documented-including its dietary habits, particularly the ability to crush shell with gnathobasic walking appendages-but virtually nothing is known about the feeding biomechanics of this iconic arthropod. Limulus polyphemus is also considered the archetypal functional analogue of various extinct groups with serial gnathobasic appendages, including eurypterids, trilobites and other early arthropods, especially Sidneyia inexpectans from the mid-Cambrian (508 Myr) Burgess Shale of Canada. Exceptionally preserved specimens of S. inexpectans show evidence suggestive of durophagous (shell-crushing) tendencies-including thick gnathobasic spine cuticle and shelly gut contents-but the masticatory capabilities of this fossil species have yet to be compared with modern durophagous arthropods. Here, we use advanced computational techniques, specifically a unique application of 3D finite-element analysis (FEA), to model the feeding mechanics of L. polyphemus and S. inexpectans: the first such analyses of a modern horseshoe crab and a fossil arthropod. Results show that mechanical performance of the feeding appendages in both arthropods is remarkably similar, suggesting that S. inexpectans had similar shell-crushing capabilities to L. polyphemus This biomechanical solution to processing shelly food therefore has a history extending over 500 Myr, arising soon after the first shell-bearing animals. Arrival of durophagous predators during the early phase of animal evolution undoubtedly fuelled the Cambrian 'arms race' that involved a rapid increase in diversity, disparity and abundance of biomineralized prey species.

The gnathobasic spine microstructure of recent and Silurian chelicerates and the Cambrian artiopodan Sidneyia: Functional and evolutionary implications

Gnathobasic spines are located on the protopodal segments of the appendages of various euarthropod taxa, notably chelicerates. Although they are used to crush shells and masticate soft food items, the microstructure of these spines are relatively poorly known in both extant and extinct forms. Here we compare the gnathobasic spine microstructures of the Silurian eurypterid Eurypterus tetragonophthalmus from Estonia and the Cambrian artiopodan Sidneyiainexpectans from Canada with those of the Recent xiphosuran chelicerate Limulus polyphemus to infer potential variations in functional morphology through time. The thickened fibrous exocuticle in L. polyphemus spine tips enables effective prey mastication and shell crushing, while also reducing pressure on nerve endings that fill the spine cavities. The spine cuticle of E. tetragonophthalmus has a laminate structure and lacks the fibrous layers seen in L. polyphemus spines, suggesting that E. tetragonophthalmus may not have been capable of crushing thick shells, but a durophagous habit cannot be precluded. Conversely, the cuticle of S. inexpectans spines has a similar fibrous microstructure to L. polyphemus, suggesting that S. inexpectans was a competent shell crusher. This conclusion is consistent with specimens showing preserved gut contents containing various shelly fragments. The shape and arrangement of the gnathobasic spines is similar for both L. polyphemus and S. inexpectans, with stouter spines in the posterior cephalothoracic or trunk appendages, respectively. This differentiation indicates that crushing occurs posteriorly, while the gnathobases on anterior appendages continue mastication and push food towards and into the mouth. The results of recent phylogenetic analyses that considered both modern and fossil euarthropod clades show that xiphosurans and eurypterids are united as crown-group euchelicerates, with S. inexpectans placed within more basal artiopodan clades. These relationships suggest that gnathobases with thickened fibrous exocuticle, if not homoplasious, may be plesiomorphic for chelicerates and deeper relatives within Arachnomorpha. This study shows that the gnathobasic spine microstructure best adapted for durophagy has remained remarkably constant since the Cambrian.

Metal Levels in Blood of Three Species of Shorebirds during Stopover on Delaware Bay Reflect Levels in Their Food, Horseshoe Crab Eggs

Understanding the relationship between metal level in predators and their prey is an important issue, and is usually difficult to determine because animals eat a variety of organisms. However, shorebirds that stop over during spring migration along Delaware Bay (New Jersey) stay for only 2–3 weeks, and eat mainly horseshoe crab (Limulus polyphemus) eggs. In this paper, we examine the relationship between metal levels in horseshoe crab eggs, and blood and feather levels of metals in red knot (Calidris canutus rufa; n = 30), sanderling (Calidris alba; n = 20) and semipalmated sandpiper (Calidris pusilla; n = 38) from Delaware Bay. There is a rich literature on metal levels in feathers. For all three species, the levels of arsenic, cadmium, chromium, lead and mercury in blood were highly correlated with the levels of metals in the eggs of horseshoe crab (17 pooled samples). This indicates that the levels in the blood of these shorebirds quickly reflect levels in their prey (horseshoe crab eggs), while metals in the feathers were not correlated with the levels in eggs. Semipalmated sandpipers had the lowest levels of arsenic in blood and the highest levels of arsenic in feathers, compared to the other species. At Delaware Bay, semipalmated sandpipers have a diet higher in marsh invertebrates than the other species, which may account for the differences. The levels of cadmium and chromium in blood were significantly higher in knots than other species; knots only ate horseshoe crab eggs. For all of the metals except arsenic, the ratio of levels in blood/feathers was similar among species. For arsenic, the ratio of levels in blood/feathers were significantly lower in semipalmated sandpipers than in the other species, by an order of magnitude.

Cytochrome P450 diversity in the tree of life

Sequencing in all areas of the tree of life has produced >300,000 cytochrome P450 (CYP) sequences that have been mined and collected. Nomenclature has been assigned to >41,000 CYP sequences and the majority of the remainder has been sorted by BLAST searches into clans, families and subfamilies in preparation for naming. The P450 sequence space is being systematically explored and filled in. Well-studied groups like vertebrates are covered in greater depth while new insights are being added into uncharted territories like horseshoe crab (Limulus polyphemus), tardigrades (Hypsibius dujardini), velvet worm (Euperipatoides_rowelli), and basal land plants like hornworts, liverworts and mosses. CYPs from the fungi, one of the most diverse groups, are being explored and organized as nearly 800 fungal species are now sequenced. The CYP clan structure in fungi is emerging with 805 CYP families sorting into 32 CYP clans. >3000 bacterial sequences are named, mostly from terrestrial or freshwater sources. Of 18,379 bacterial sequences downloaded from the CYPED database, all are >43% identical to named CYPs. Therefore, they fit in the 602 named P450 prokaryotic families. Diversity in this group is becoming saturated, however 25% of 3305 seawater bacterial P450s did not match known P450 families, indicating marine bacterial CYPs are not as well sampled as land/freshwater based bacterial CYPs. Future sequencing plans of the Genome 10K project, i5k and GIGA (Global Invertebrate Genomics Alliance) are expected to produce more than one million cytochrome P450 sequences by 2020. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.

Local tidal regime dictates plasticity of expression of locomotor activity rhythms of American horseshoe crabs, Limulus polyphemus

While horseshoe crabs Limulus polyphemus from regions with two daily tides express endogenous circatidal (~ 12.4 h) activity rhythms, much less is known about locomotor rhythm expression in horseshoe crabs from other tidal regimes. This study investigated whether horseshoe crabs (1) always express activity rhythms consistent with their natural tides, and (2) can alter activity rhythm expression in response to novel tide cycles. Activity rhythms of animals from environments with two daily tides (Gulf of Maine, 43°6' N/70°52' W, and Massachusetts, 41°32' N/70°40'W), one dominant daily tide (Apalachee Bay, Florida, 29°58' N/84°20' W), and microtides (Indian River Lagoon, Florida, 28°5' N/80°35' W) were recorded in 2011-2013 during three artificial tide conditions: no tides, a 12.4 h tidal cycle, and a 24.8 h tidal cycle. Interestingly, L. polyphemus from the microtidal site (n = 7) appeared "plastic" in their responses; they were able to express both bimodal and unimodal rhythms in response to different tide cycles. In contrast, the other two populations exhibited more fixed responses: regardless of the tides they were exposed to, animals from areas with one dominant daily tide (n = 18) consistently expressed unimodal rhythms, while those from areas with two daily tides (n = 28) generally expressed bimodal rhythms. Rhythms expressed by L. polyphemus thus appear to be a function of endogenous clocks, the tidal cues to which animals are exposed, and tidal cues that animals experience throughout ontogeny.

Maternal transfer of trace elements in the Atlantic horseshoe crab (Limulus polyphemus)

The maternal transfer of trace elements is a process by which offspring may accumulate trace elements from their maternal parent. Although maternal transfer has been assessed in many vertebrates, there is little understanding of this process in invertebrate species. This study investigated the maternal transfer of 13 trace elements (Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Se, and Zn) in Atlantic horseshoe crab (Limulus polyphemus) eggs and compared concentrations to those in adult leg and gill tissue. For the majority of individuals, all trace elements were transferred, with the exception of Cr, from the female to the eggs. The greatest concentrations on average transferred to egg tissue were Zn (140 µg/g), Cu (47.8 µg/g), and Fe (38.6 µg/g) for essential elements and As (10.9 µg/g) and Ag (1.23 µg/g) for nonessential elements. For elements that were maternally transferred, correlation analyses were run to assess if the concentration in the eggs were similar to that of adult tissue that is completely internalized (leg) or a boundary to the external environment (gill). Positive correlations between egg and leg tissue were found for As, Hg, Se, Mn, Pb, and Ni. Mercury, Mn, Ni, and Se were the only elements correlated between egg and gill tissue. Although, many trace elements were in low concentration in the eggs, we speculate that the higher transfer of essential elements is related to their potential benefit during early development versus nonessential trace elements, which are known to be toxic. We conclude that maternal transfer as a source of trace elements to horseshoe crabs should not be overlooked and warrants further investigation.

Environmental exposure of Atlantic horseshoe crab (Limulus polyphemus) early life stages to essential trace elements

This study investigated the accumulation Co, Cu, Fe, Mn, Ni, Se, and Zn in Atlantic horseshoe crab (Limulus polyphemus) early life stages (egg, embryo and larvae) and compared the concentrations to the concentration of each element in sediment, pore water and overlying water for 5 sites across Long Island, NY. For the majority of the sites, all essential trace elements accumulated in the embryos and larvae. However, many of the embryos and larvae at specific sites presented different concentration patterns which had no apparent relationship with the local habitat sediment and water values. Generally, Cu, Fe, and Se sequentially increased from egg stage through larval stages for the majority of sites, while Co, Mn, and Ni only did for a few sites. Zinc also showed an increase across sites from embryo to larval stage, however was the only one to show a decrease in concentration from egg to embryo stage at all sites. Interestingly, Mn at Manhasset Bay presented embryo and larval stages to be 50 fold greater than all other sites while the egg stage showed similar values to other sites; this high degree of uptake could be due to a high concentration in the overlying water. All essential trace elements can be accumulated from the environment but greater concentrations may be influenced by abiotic factors and the predominant uptake route (aqueous versus diet) at each life stage. Future laboratory experiments are required to investigate factors that influence essential trace element accumulation and loss in horseshoe crab early life stages.

Opsin Repertoire and Expression Patterns in Horseshoe Crabs: Evidence from the Genome of Limulus polyphemus (Arthropoda: Chelicerata)

Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of genes encoding Limulus opsins, the protein component of the visual pigments, are critical for understanding opsin evolution and diversification among chelicerates, where knowledge of opsins is limited, and more broadly among arthropods. In the present study, we sequenced and assembled a high quality nuclear genomic sequence of L. polyphemus and used these data to annotate the full repertoire of Limulus opsins. We conducted a detailed phylogenetic analysis of Limulus opsins, including using gene structure and synteny information to identify relationships among different opsin classes. We used our phylogeny to identify significant genomic events that shaped opsin evolution and therefore the visual system of Limulus We also describe the tissue expression patterns of the 18 opsins identified and show that transcripts encoding a number, including a peropsin, are present throughout the central nervous system. In addition to significantly extending our understanding of photosensitivity in Limulus and providing critical insight into the genomic evolution of horseshoe crab opsins, this work provides a valuable genomic resource for addressing myriad questions related to xiphosuran physiology and arthropod evolution.

Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

Background

Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of “living fossils.” As arthropods, they belong to the Ecdysozoa, an ancient super-phylum whose sequenced genomes (including insects and nematodes) have thus far shown more divergence from the ancestral pattern of eumetazoan genome organization than cnidarians, deuterostomes and lophotrochozoans. However, much of ecdysozoan diversity remains unrepresented in comparative genomic analyses.

Results

Here we apply a new strategy of combined de novo assembly and genetic mapping to examine the chromosome-scale genome organization of the Atlantic horseshoe crab, Limulus polyphemus. We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per sample. The map includes 84,307 sequence markers grouped into 1,876 distinct genetic intervals and 5,775 candidate conserved protein coding genes.

Conclusions

Comparison with other metazoan genomes shows that the L. polyphemus genome preserves ancestral bilaterian linkage groups, and that a common ancestor of modern horseshoe crabs underwent one or more ancient whole genome duplications 300 million years ago, followed by extensive chromosome fusion. These results provide a counter-example to the often noted correlation between whole genome duplication and evolutionary radiations. The new, low-cost genetic mapping method for obtaining a chromosome-scale view of non-model organism genomes that we demonstrate here does not require laboratory culture, and is potentially applicable to a broad range of other species.