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Recent molecular phylogenetic investigations strongly supported the placement of the shell-less, worm-shaped aplacophoran molluscs (Solenogastres and Caudofoveata) and chitons (Polyplacophora) in a clade called Aculifera, which is the sister taxon of all other molluscs. Thus, understanding the evolutionary history of aculiferan molluscs is important for understanding early molluscan evolution. In particular, fundamental questions about evolutionary relationships within Aplacophora have long been unanswered. Here, we supplemented the paucity of available data with transcriptomes from 25 aculiferans and conducted phylogenomic analyses on datasets with up to 525 genes and 75 914 amino acid positions. Our results indicate that aplacophoran taxonomy requires revision as several traditionally recognized groups are non-monophyletic. Most notably, Cavibelonia, the solenogaster taxon defined by hollow sclerites, is polyphyletic, suggesting parallel evolution of hollow sclerites in multiple lineages. Moreover, we describe Apodomenia enigmatica sp. nov. , a bizarre new species that appears to be a morphological intermediate between Solenogastres and Caudofoveata. This animal is not a missing link, however; molecular and morphological studies show that it is a derived solenogaster that lacks a foot, mantle cavity and radula. Taken together, these results shed light on the evolutionary history of Aplacophora and reveal a surprising degree of morphological plasticity within the group.

Caudofoveata are molluscs that protect their vermiform body with a scleritome, a mosaic of unconnected blade/lanceolate-shaped aragonite sclerites. For the species Falcidens gutturosus and Scutopus ventrolineatus we studied the crystallographic constitution and crystal orientation texture of the sclerites and the scleritome with electron-backscatter-diffraction (EBSD), laser-confocal-microscopy (LCM) and field-emission electron microscopy (FE-SEM) imaging. Each sclerite is an aragonite single crystal that is completely enveloped by an organic sheath. Adjacent sclerites overlap laterally and vertically are, however, not connected to each other. Sclerites are thickened in their central portion, relative to their periphery. Thickening increases also from sclerite tip towards its base. Accordingly, cross-sections through a sclerite are straight at its tip, curved and bent towards the sclerite base. Irrespective of curved sclerite morphologies, the aragonite lattice within the sclerite is coherent. Sclerite aragonite is not twinned. For each sclerite the crystallographic c-axis is parallel to the morphological long axis of the sclerite, the a-axis is perpendicular to its width and the b-axis is within the width of the sclerite. The single-crystalinity of the sclerites and their mode of organization in the scleritome is outstanding. Sclerite and aragonite arrangement in the scleritome is not given by a specific crystal growth mode, it is inherent to the secreting cells. We discuss that morphological characteristics of the sclerites and crystallographic preferred orientation (texture) of sclerite aragonite is not the result of competitive growth selection. It is generated by the templating effect of the organic substance of the secreting cells and associated extracellular biopolymers.

Protein domains are independent structural and functional modules that can rearrange to create new proteins. While the evolution of multidomain proteins through the shuffling of different preexisting domains has been well documented, the evolution of domain repeat proteins and the origin of new domains are less understood. Metallothioneins (MTs) provide a good case study considering that they consist of metal-binding domain repeats, some of them with a likely de novo origin. In mollusks, for instance, most MTs are bidomain proteins that arose by lineage-specific rearrangements between six putative domains: α, β1, β2, β3, γ and δ. Some domains have been characterized in bivalves and gastropods, but nothing is known about the MTs and their domains of other Mollusca classes. To fill this gap, we investigated the metal-binding features of NpoMT1 of Nautilus pompilius (Cephalopoda class) and FcaMT1 of Falcidens caudatus (Caudofoveata class). Interestingly, whereas NpoMT1 consists of α and β1 domains and has a prototypical Cd2+ preference, FcaMT1 has a singular preference for Zn2+ ions and a distinct domain composition, including a new Caudofoveata-specific δ domain. Overall, our results suggest that the modular architecture of MTs has contributed to MT evolution during mollusk diversification, and exemplify how modularity increases MT evolvability.

The worm-shaped, shell-less Caudofoveata is one of the least known groups of molluscs. As early-branching molluscs, the lack of high-quality genomes hinders our understanding of their evolution and ecology. Here, we report a high-quality chromosome-scale genome of Chaetoderma sp. combining PacBio, Illumina, and high-resolution chromosome conformation capture sequencing. The final assembly has a size of 2.45 Gb, with a scaffold N50 length of 141.46 Mb, and is anchored to 17 chromosomes. Gene annotations showed a high level of accuracy and completeness, with 23,675 predicted protein-coding genes and 94.44% of the metazoan conserved genes by BUSCO assessment. We further present 16S rRNA gene amplicon sequencing of the gut microbiota in Chaetoderma sp., which was dominated by the chemoautotrophic bacteria (phylum Gammaproteobacteria). This chromosome-level genome assembly presents the first genome for the Caudofoveata, which constitutes an important resource for studies ranging from molluscan evolution, symposium, to deep-sea adaptation.

The mollusc fauna of the Mediterranean Sea is still considered as the best-known marine mollusc fauna in the world. The previous modern checklists of marine Mollusca were produced by joint teams of amateurs and professionals. During the last years the Italian Society of Malacology (Società Italiana di Malacologia – S.I.M.) maintained an updated version of the Mediterranean checklist, that served as the backbone for the development of the new Italian checklist. According to the current version (updated on April 1st, 2021), 1,777 recognised species of marine molluscs are present in the Italian Economic Exclusive Zone, including also the Tyrrhenian coasts of Corsica and the continental shelf of the Maltese archipelago. The new checklist shows an increase of 17% of the species reported in the 1995 Checklist. This is largely (yet not solely) due to the new wave of studies based on Integrative Taxonomy approaches. A total of 135 species (7.6%) are strictly endemic to the Italian waters; 44 species (2.5%) are alien and correspond to the 28% of the Mediterranean alien marine molluscs. All eight extant molluscan classes are represented. The families represented in the Italian fauna are 307, an increase of 14.6% from the first checklist, partly due to new records and partly to new phylogenetic systematics. Compared with the whole Mediterranean mal-acofauna, the Italian component represents 71% in species and 61% in families, which makes it a very remarkable part of the Mediterranean fauna.

Caudofoveata is a class of worm-like molluscs (aplacophorans) that typically have an infaunal lifestyle, burrowing in soft bottoms in a wide range of marine habitats from shallow to deep waters. Here, we describe a very large new species of caudofoveate from South China Sea methane seeps growing up to 154 mm in length: Chaetoderma shenloong sp. nov. It is the first caudofoveate to be named from a chemosynthetic ecosystem and the first aplacophoran mollusc associated with seeps. Our new species stands out from other Pacific Chaetoderma species by its large size, a wide body relative to its length, a barely sclerotised radula, and the presence of isosceles-triangular sclerites. Phylogenetic reconstruction using the mitochondrial cytochrome c oxidase subunit I (COI) gene placed it within a paraphyletic clade comprising Chaetodermatidae and Limifossoridae, in line with a previous phylogenetic analysis. This also revealed that C. shenloong sp. nov. is conspecific with a Chaetoderma sp. whose whole genome was recently sequenced and assembled but remained undescribed until now. The most closely related species with an available COI sequence was C. felderi , the largest caudofoveate species recorded. Our discovery suggests caudofoveates may be present in other seeps globally but so far neglected; a potential example is C. felderi from the Gulf of Mexico, where seeps are abundant but whose exact habitat remains unclear.

Background With more than 100000 living species, mollusks are the second most diverse metazoan phylum. The current taxonomic classification of mollusks recognizes eight classes (Neomeniomorpha, Chaetodermomorpha, Polyplacophora, Monoplacophora, Cephalopoda, Gastropoda, Bivalvia, and Scaphopoda) that exhibit very distinct body plans. In the past, phylogenetic relationships among mollusk classes have been contentious due to the lack of indisputable morphological synapomorphies. Fortunately, recent phylogenetic analyses based on multi-gene data sets are rendering promising results. In this regard, mitochondrial genomes have been widely used to reconstruct deep phylogenies. For mollusks, complete mitochondrial genomes are mostly available for gastropods, bivalves, and cephalopods, whereas other less-diverse lineages have few or none reported. Results The complete DNA sequence (14662 bp) of the mitochondrial genome of the chaetodermomorph Scutopus ventrolineatus Salvini-Plawen, 1968 was determined. Compared with other mollusks, the relative position of protein-coding genes in the mitochondrial genome of S. ventrolineatus is very similar to those reported for Polyplacophora, Cephalopoda and early-diverging lineages of Bivalvia and Gastropoda (Vetigastropoda and Neritimorpha; but not Patellogastropoda). The reconstructed phylogenetic tree based on combined mitochondrial and nuclear sequence data recovered monophyletic Aplacophora, Aculifera, and Conchifera. Within the latter, Cephalopoda was the sister group of Gastropoda and Bivalvia + Scaphopoda. Conclusions Phylogenetic analyses of mitochondrial sequences showed strong among-lineage rate heterogeneity that produced long-branch attraction biases. Removal of long branches (namely those of bivalves and patellogastropods) ameliorated but not fully resolved the problem. Best results in terms of statistical support were achieved when mitochondrial and nuclear sequence data were concatenated.

We present the first DNA taxonomy publication on abyssal Mollusca from the Clarion-Clipperton Zone (CCZ), central Pacific ocean, using material collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruise 'AB01' to the UK Seabed Resources Ltd (UKSRL) polymetallic-nodule exploration area 'UK-1' in the eastern CCZ. This is the third paper in a series to provide regional taxonomic data for a region that is undergoing intense deep-sea mineral exploration for high-grade polymetallic nodules. Taxonomic data are presented for 21 species from 42 records identified by a combination of morphological and genetic data, including molecular phylogenetic analyses. These included 3 heterodont bivalves, 5 protobranch bivalves, 4 pteriomorph bivalves, 1 caudofoveate, 1 monoplacophoran, 1 polyplacophoran, 4 scaphopods and 2 solenogastres. Gastropoda were recovered but will be the subject of a future study. Seven taxa matched published morphological descriptions for species with deep Pacific type localities, and our sequences provide the first genetic data for these taxa. One taxon morphologically matched a known cosmopolitan species but with a type locality in a different ocean basin and was assigned the open nomenclature ' ' as a precautionary approach in taxon assignments to avoid over-estimating species ranges. One taxon is here described as a new species, sp. n. For the remaining 12 taxa, we have determined them to be potentially new species, for which we make the raw data, imagery and vouchers available for future taxonomic study. The Clarion-Clipperton Zone is a region undergoing intense exploration for potential deep-sea mineral extraction. We present these data to facilitate future taxonomic and environmental impact study by making both data and voucher materials available through curated and accessible biological collections.

Caudofoveates are benthic organisms that reside in the deep waters of continental slopes in the world. They are considered to be a group that is of phylogenetic and ecological importance for the phylum Mollusca. However, they remain poorly studied. In this work, we revealed the structure of the spicules of Caudofoveatan mollusks Falcidens sp. The spicules presented a hierarchical organization pattern across different length scales. Various imaging and analytical methods related to light and electron microscopy were employed to characterize the samples. The primary imaging methods utilized included: low voltage field emission scanning electron microscopy (FEG-SEM), focused ion beam-scanning electron microscopy (FIB-SEM), high-resolution transmission electron microscopy (HRTEM), atomic force microscopy (AFM), and electron diffraction. In addition, we performed a physicochemical analysis by electron energy loss spectroscopy (EELS) and energy dispersive X-ray spectroscopy (EDS). A crucial factor for successfully obtaining the results was the preparation of lamellae from the spicules without damaging the original structures, achieved using FIB-SEM. This allowed us to obtain diffraction patterns of significant areas of well-preserved sections (lamellae) of the spicules in specific directions and demonstrate for the first time that the bulk of these structures is organized as a single crystal of calcium carbonate aragonite. On the other hand, AFM imaging of the spicules’ dorsal surface revealed a wavy appearance, composed of myriads of small, pointed crystallites oriented along the spicules’ longer axis (i.e., the c-axis of the aragonite). The organization pattern of these small crystallites, the possible presence of twins, the relationship between confinement conditions and accessory ions in the preference for mineral polymorphs, and the single crystalline appearance of the entire spicule, along with the observation of growth lines, provide support for further studies employing Caudofoveata spicules as a model for biomineralization studies.

Aplacophorans are common inhabitants of the deep-sea, where many places remain unexplored regarding their biodiversity. Filling a gap in knowledge about these animals from the South Atlantic, Scutopus variabilis sp. nov. (Caudofoveata, Limifossoridae) is described; further, species distribution modelling (SDM) was performed to elucidate the distribution patterns of Atlantic species of Scutopus . The type materials of S. megaradulatus Salvini-Plawen (1972) and S. chilensis Salvini-Plawen (1972) , were examined and a search was performed for specimens of Scutopus held in museum collections. Scutopus variabilis sp. nov. has a slender and highly variable body form and a very distinct suture line is present midventrally. Two dominant types of trunk sclerites were observed by Scanning Electron Microscopy (SEM): one elongated with lateral margins slightly concave in medial portion, and another longer, with narrower base; its radula bears up to eight rows of heavily sclerotized teeth bearing 12–16 small denticles. The species occurs in a wide bathymetric range (40–1300 m), being more abundant at the edge between the continental shelf and upper slope. Outside the areas from where these samples were obtained, suitable areas for S. variabilis sp. nov. were found in the Southern Caribbean Sea (from where S. megaradulatus is recorded) and in the Brazilian Northern coast; the Gulf of Mexico and the Brazilian Northeastern coasts were found as unsuitable. Species of Scutopus appear to exhibit different patterns of geographical distribution: the European S. ventrolineatus Salvini-Plawen (1968) and S. robustus Salvini-Plawen (1970) are known as widely distributed, while non-European representants, the American S. megaradulatus , S. chilensis and S. variabilis sp. nov., and the Japanese S. schanderi Saito and Salvini-Plawen (2014) and S. hamatamii Saito and Salvini-Plawen (2014) have more restricted distributions. However, clear and definite patterns of distribution of some of these species are probably blurred by sampling bias, for the European area is better studied. In the Atlantic, the SDM showed that species of Scutopus occur in a way that overlapping is minimized. Great sampling efforts combined with detailed descriptions based on SEM have revealed an interesting, abundant and up to now undescribed Brazilian deep-sea malacofauna.