Against expectation: a short sequence with high signal elucidates cone snail phylogeny

Mitogenome Characterization of Four Conus Species and Comparative Analysis

Cone snails, as a type of marine organism, have rich species diversity. Traditionally, classifications of cone snails were based mostly on radula, shell, and anatomical characters. Because of these phenotypic features' high population variability and propensity for local adaptation and convergence, identifying species can be difficult and occasionally inaccurate. In addition, mitochondrial genomes contain high phylogenetic information, so complete mitogenomes have been increasingly employed for inferring molecular phylogeny. To enrich the mitogenomic database of cone snails (Caenogastropoda: Conidae), mitogenomes of four Conus species, i.e., C. imperialis (15,505 bp), C. literatus (15,569 bp), C. virgo (15,594 bp), and C. marmoreus (15,579 bp), were characterized and compared. All 4 of these mitogenomes included 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. All the Protein Codon Genes (PCGs) of both newly sequenced mitogenomes used TAA or TAG as a terminal codon. Most PCGs used conventional start codon ATG, but an alternative initiation codon GTG was detected in a gene (NADH dehydrogenase subunit 4 (nad4)) of C. imperialis. In addition, the phylogenetic relationships were reconstructed among 20 Conus species on the basis of PCGs, COX1, and the complete mitogenome using both Bayesian Inference (BI) and Maximum Likelihood (ML). The phylogenetic results supported that C. litteratus, C. quercinus, and C. virgo were clustered together as a sister group (PP = 1, BS = 99), but they did not support the phylogenetic relation of C. imperialis and C. tribblei (PP = 0.79, BS = 50). In addition, our study established that PCGs and complete mitogenome are the two useful markers for phylogenetic inference of Conus species. These results enriched the data of the cone snail's mitochondrion in the South China Sea and provided a reliable basis for the interpretation of the phylogenetic relationship of the cone snail based on the mitochondrial genome.

Non-Peptidic Small Molecule Components from Cone Snail Venoms

Venomous molluscs (Superfamily Conoidea) comprise a substantial fraction of tropical marine biodiversity (>15,000 species). Prior characterization of cone snail venoms established that bioactive venom components used to capture prey, defend against predators and for competitive interactions were relatively small, structured peptides (10–35 amino acids), most with multiple disulfide crosslinks. These venom components (“conotoxins, conopeptides”) have been widely studied in many laboratories, leading to pharmaceutical agents and probes. In this review, we describe how it has recently become clear that to varying degrees, cone snail venoms also contain bioactive non-peptidic small molecule components. Since the initial discovery of genuanine as the first bioactive venom small molecule with an unprecedented structure, a broad set of cone snail venoms have been examined for non-peptidic bioactive components. In particular, a basal clade of cone snails (Stephanoconus) that prey on polychaetes produce genuanine and many other small molecules in their venoms, suggesting that this lineage may be a rich source of non-peptidic cone snail venom natural products. In contrast to standing dogma in the field that peptide and proteins are predominantly used for prey capture in cone snails, these small molecules also contribute to prey capture and push the molecular diversity of cone snails beyond peptides. The compounds so far characterized are active on neurons and thus may potentially serve as leads for neuronal diseases. Thus, in analogy to the incredible pharmacopeia resulting from studying venom peptides, these small molecules may provide a new resource of pharmacological agents.

Novel analgesic ω-conotoxins from the vermivorous cone snail Conus moncuri provide new insights into the evolution of conopeptides

Cone snails are a diverse group of predatory marine invertebrates that deploy remarkably complex venoms to rapidly paralyse worm, mollusc or fish prey. ω-Conotoxins are neurotoxic peptides from cone snail venoms that inhibit Ca_v2.2 voltage-gated calcium channel, demonstrating potential for pain management via intrathecal (IT) administration. Here, we isolated and characterized two novel ω-conotoxins, MoVIA and MoVIB from Conus moncuri, the first to be identified in vermivorous (worm-hunting) cone snails. MoVIA and MoVIB potently inhibited human Ca_v2.2 in fluorimetric assays and rat Ca_v2.2 in patch clamp studies, and both potently displaced radiolabeled ω-conotoxin GVIA (¹²⁵I-GVIA) from human SH-SY5Y cells and fish brain membranes (IC₅₀ 2–9 pM). Intriguingly, an arginine at position 13 in MoVIA and MoVIB replaced the functionally critical tyrosine found in piscivorous ω-conotoxins. To investigate its role, we synthesized MoVIB-[R13Y] and MVIIA-[Y13R]. Interestingly, MVIIA-[Y13R] completely lost Ca_v2.2 activity and MoVIB-[R13Y] had reduced activity, indicating that Arg at position 13 was preferred in these vermivorous ω-conotoxins whereas tyrosine 13 is preferred in piscivorous ω-conotoxins. MoVIB reversed pain behavior in a rat neuropathic pain model, confirming that vermivorous cone snails are a new source of analgesic ω-conotoxins. Given vermivorous cone snails are ancestral to piscivorous species, our findings support the repurposing of defensive venom peptides in the evolution of piscivorous Conidae.

Beyond Conus: Phylogenetic relationships of Conidae based on complete mitochondrial genomes

Understanding how the extraordinary taxonomic and ecological diversity of cone snails (Caenogastropoda: Conidae) evolved requires a statistically robust phylogenetic framework, which thus far is not available. While recent molecular phylogenies have been able to distinguish several deep lineages within the family Conidae, including the genera Profundiconus, Californiconus, Conasprella, and Conus (and within this one, several subgenera), phylogenetic relationships among these genera remain elusive. Moreover, the possibility that additional deep lineages may exist within the family is open. Here, we reconstructed with probabilistic methods a molecular phylogeny of Conidae using the newly sequenced complete or nearly complete mitochondrial (mt) genomes of the following nine species that represent all main Conidae lineages and potentially new ones: Profundiconus teramachii, Californiconus californicus, Conasprella wakayamaensis, Lilliconus sagei, Pseudolilliconus traillii, Conus (Kalloconus) venulatus, Conus (Lautoconus) ventricosus, Conus (Lautoconus) hybridus, and Conus (Eugeniconus) nobilis. To test the monophyly of the family, we also sequenced the nearly complete mt genomes of the following three species representing closely related conoidean families: Benthomangelia sp. (Mangeliidae), Tomopleura sp. (Borsoniidae), and Glyphostoma sp. (Clathurellidae). All newly sequenced conoidean mt genomes shared a relatively constant gene order with rearrangements limited to tRNA genes. The reconstructed phylogeny recovered with high statistical support the monophyly of Conidae and phylogenetic relationships within the family. The genus Profundiconus was placed as sister to the remaining genera. Within these, a clade including Californiconus and Lilliconus+Pseudolilliconus was the sister group of Conasprella to the exclusion of Conus. The phylogeny included a new lineage whose relative phylogenetic position was unknown (Lilliconus) and uncovered thus far hidden diversity within the family (Pseudolilliconus). Moreover, reconstructed phylogenetic relationships allowed inferring that the peculiar diet of Californiconus based on worms, mollusks, crustaceans and fish is derived, and reinforce the hypothesis that the ancestor of Conidae was a worm hunter. A chronogram was reconstructed under an uncorrelated relaxed molecular clock, which dated the origin of the family shortly after the Cretaceous-Tertiary boundary (about 59million years ago) and the divergence among main lineages during the Paleocene and the Eocene (56-30million years ago).

Insights into the origins of fish hunting in venomous cone snails from studies of Conus tessulatus

Prey shifts in carnivorous predators are events that can initiate the accelerated generation of new biodiversity. However, it is seldom possible to reconstruct how the change in prey preference occurred. Here we describe an evolutionary "smoking gun" that illuminates the transition from worm hunting to fish hunting among marine cone snails, resulting in the adaptive radiation of fish-hunting lineages comprising ∼100 piscivorous Conus species. This smoking gun is δ-conotoxin TsVIA, a peptide from the venom of Conus tessulatus that delays inactivation of vertebrate voltage-gated sodium channels. C. tessulatus is a species in a worm-hunting clade, which is phylogenetically closely related to the fish-hunting cone snail specialists. The discovery of a δ-conotoxin that potently acts on vertebrate sodium channels in the venom of a worm-hunting cone snail suggests that a closely related ancestral toxin enabled the transition from worm hunting to fish hunting, as δ-conotoxins are highly conserved among fish hunters and critical to their mechanism of prey capture; this peptide, δ-conotoxin TsVIA, has striking sequence similarity to these δ-conotoxins from piscivorous cone snail venoms. Calcium-imaging studies on dissociated dorsal root ganglion (DRG) neurons revealed the peptide's putative molecular target (voltage-gated sodium channels) and mechanism of action (inhibition of channel inactivation). The results were confirmed by electrophysiology. This work demonstrates how elucidating the specific interactions between toxins and receptors from phylogenetically well-defined lineages can uncover molecular mechanisms that underlie significant evolutionary transitions.

One, four or 100 genera? A new classification of the cone snails

We present a new classification for the genus Conus sensu lato (family Conidae), based on molecular phylogenetic analyses of 329 species. This classification departs from both the traditional classification in only one genus and from a recently proposed shell- and radula-based classification scheme that separates members of this group into five families and 115 genera. Roughly 140 genus-group names are available for Recent cone snails. We propose to place all cone snails within a single family (Conidae) containing four genera-Conus, Conasprella, Profundiconus and Californiconus (with Conus alone encompassing about 85% of known species)-based on the clear separation of cone snails into four distinct and well-supported groups/lineages in molecular phylogenetic analyses. Within Conus and Conasprella, we recognize 57 and 11 subgenera, respectively, that represent well-supported subgroupings within these genera, which we interpret as evidence of intrageneric distinctiveness. We allocate the 803 Recent species of Conidae listed as valid in the World Register of Marine Species into these four genera and 71 subgenera, with an estimate of the confidence for placement of species in these taxonomic categories based on whether molecular or radula and/or shell data were used in these determinations. Our proposed classification effectively departs from previous schemes by (1) limiting the number of accepted genera, (2) retaining the majority of species within the genus Conus and (3) assigning members of these genera to species groups/subgenera to enable the effective communication of these groups, all of which we hope will encourage acceptance of this scheme.

Molecular phylogeny and evolution of the cone snails (Gastropoda, Conoidea)

We present a large-scale molecular phylogeny that includes 320 of the 761 recognized valid species of the cone snails (Conus), one of the most diverse groups of marine molluscs, based on three mitochondrial genes (COI, 16S rDNA and 12S rDNA). This is the first phylogeny of the taxon to employ concatenated sequences of several genes, and it includes more than twice as many species as the last published molecular phylogeny of the entire group nearly a decade ago. Most of the numerous molecular phylogenies published during the last 15years are limited to rather small fractions of its species diversity. Bayesian and maximum likelihood analyses are mostly congruent and confirm the presence of three previously reported highly divergent lineages among cone snails, and one identified here using molecular data. About 85% of the species cluster in the single Large Major Clade; the others are divided between the Small Major Clade (∼12%), the Conus californicus lineage (one species), and a newly defined clade (∼3%). We also define several subclades within the Large and Small major clades, but most of their relationships remain poorly supported. To illustrate the usefulness of molecular phylogenies in addressing specific evolutionary questions, we analyse the evolution of the diet, the biogeography and the toxins of cone snails. All cone snails whose feeding biology is known inject venom into large prey animals and swallow them whole. Predation on polychaete worms is inferred as the ancestral state, and diet shifts to molluscs and fishes occurred rarely. The ancestor of cone snails probably originated from the Indo-Pacific; rather few colonisations of other biogeographic provinces have probably occurred. A new classification of the Conidae, based on the molecular phylogeny, is published in an accompanying paper.

Biodiversity of cone snails and other venomous marine gastropods: evolutionary success through neuropharmacology

Venomous marine snails (superfamily Conoidea) are a remarkably biodiverse marine invertebrate lineage (featuring more than 10,000 species). Conoideans use complex venoms (up to 100 different components for each species) to capture prey and for other biotic interactions. Molecular phylogeny and venom peptide characterization provide an unusual multidisciplinary view of conoidean biodiversity at several taxonomic levels. Venom peptides diverge between species at an unprecedented rate through hypermutation within gene families. Clade divergence within a genus occurs without recruiting new gene families when a saltatory event, such as colonization of new prey types (e.g., fish), leads to a new radiation. Divergence between genera in the same family involves substantial divergence in gene families. In the superfamily Conoidea, the family groups recruited distinct sets of different venom gene superfamilies. The associated morphological, behavioral, and prey-preference changes that accompany these molecular changes are unknown for most conoidean lineages, except for one genus, Conus, for which many associated phenotypic changes have been documented.

Molecular phylogeny, classification and evolution of conopeptides

Conopeptides are toxins expressed in the venom duct of cone snails (Conoidea, Conus). These are mostly well-structured peptides and mini-proteins with high potency and selectivity for a broad range of cellular targets. In view of these properties, they are widely used as pharmacological tools and many are candidates for innovative drugs. The conopeptides are primarily classified into superfamilies according to their peptide signal sequence, a classification that is thought to reflect the evolution of the multigenic system. However, this hypothesis has never been thoroughly tested. Here we present a phylogenetic analysis of 1,364 conopeptide signal sequences extracted from GenBank. The results validate the current conopeptide superfamily classification, but also reveal several important new features. The so-called "cysteine-poor" conopeptides are revealed to be closely related to "cysteine-rich" conopeptides; with some of them sharing very similar signal sequences, suggesting that a distinction based on cysteine content and configuration is not phylogenetically relevant and does not reflect the evolutionary history of conopeptides. A given cysteine pattern or pharmacological activity can be found across different superfamilies. Furthermore, a few conopeptides from GenBank do not cluster in any of the known superfamilies, and could represent yet-undefined superfamilies. A clear phylogenetically based classification should help to disentangle the diversity of conopeptides, and could also serve as a rationale to understand the evolution of the toxins in the numerous other species of conoideans and venomous animals at large.

A very short, functionally constrained sequence diagnoses cone snails in several Conasprella clades

The traditional taxonomy of ca. 700 cone snails assigns all species to a single genus, Conus Linnaeus 1758. However, an increasing body of evidence suggests that some belong to a phylogenetically distinct clade that is sometimes referred to as Conasprella. Previous work (Kraus et al., 2011) showed that a short (259 bp) conserved intronic sequence (CIS) of the γ-glutamyl carboxylase gene (intron 9) can be used to delineate deep phylogenetic relationships among some groups of Conus. The work described here uses intron 9 (338 bp) to resolve problematic relationships among the conasprellans and to distinguish them from Conus proper. Synapomorphic mutations at just 39 sites can resolve several groups within Conasprella because the informative region of intron 9 is so well conserved that the phylogenetic signal is not obscured by homoplasies at conflicting sites. Intron 9 also unambiguously distinguishes Conasprella as a whole from Conus because the conserved regions that are so well conserved within each group are not alignable and clearly not homologous between them. This pattern suggests that expression of the γ-glutamyl carboxylase gene may have undergone a functionally significant change in Conus or Conasprella shortly after they diverged.

Natural products and ion channel pharmacology

An accelerated rate of natural-product discovery is critical for the future of ion channel pharmacology. For the full potential of natural products to be realized, an interdisciplinary initiative is required that combines chemical ecology and ion channel physiology. A prime source of future drug leads targeted to ion channels is the vast assortment of compounds that mediate biotic interactions in the marine environment. Many animals have evolved a chemical strategy to change the behavior of their prey, predators or competitors, which appears to require a large set of ion channel-targeted compounds acting in concert. Some of these compounds (e.g., ziconotide [Prialt(®)]) have already found important biomedical applications. The elucidation of molecular mechanisms mediating biotic interactions should yield a rich stream of potent and selective natural products for the drug pipeline.