Insights into the genome of the 'Loco' Concholepas concholepas (Gastropoda: Muricidae) from low-coverage short-read sequencing: genome size, ploidy, transposable elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Muricidae.

BACKGROUND: The Peruvian 'chanque' or Chilean 'loco' Concholepas concholepas is an economically, ecologically, and culturally important muricid gastropod heavily exploited by artisanal fisheries in the temperate southeastern Pacific Ocean. In this study, we have profited from a set of bioinformatics tools to recover important biological information of C. concholepas from low-coverage short-read NGS datasets. Specifically, we calculated the size of the nuclear genome, ploidy, and estimated transposable elements content using an in silico k-mer approach, we discovered, annotated, and quantified those transposable elements, we assembled and annotated the 45S rDNA RNA operon and mitochondrial genome, and we confirmed the phylogenetic position of C. concholepas within the muricid subfamily Rapaninae based on translated protein coding genes. RESULTS: Using a k-mer approach, the haploid genome size estimated for the predicted diploid genome of C. concholepas varied between 1.83 Gbp (with kmer = 24) and 2.32 Gbp (with kmer = 36). Between half and two thirds of the nuclear genome of C. concholepas was composed of transposable elements. The most common transposable elements were classified as Long Interspersed Nuclear Elements and Short Interspersed Nuclear Elements, which were more abundant than DNA transposons, simple repeats, and Long Terminal Repeats. Less abundant repeat elements included Helitron mobile elements, 45S rRNA DNA, and Satellite DNA, among a few others.The 45S rRNA DNA operon of C. concholepas that encodes for the ssrRNA, 5.8S rRNA, and lsrRNA genes was assembled into a single contig 8,090 bp long. The assembled mitochondrial genome of C. concholepas is 15,449 bp long and encodes 13 protein coding genes, two ribosomal genes, and 22 transfer RNAs. CONCLUSION: The information gained by this study will inform the assembly of a high quality nuclear genome for C. concholepas and will support bioprospecting and biomonitoring using environmental DNA to advance development of conservation and management plans in this overexploited marine snail.

Phylogenomic analyses shed light on the relationships of chiton superfamilies and shell-eye evolution.

Mollusca is the second-largest animal phylum with over 100,000 extant species representing eight classes. Across 1000 extant species in the class Polyplacophora, chitons have a relatively constrained morphology but with some notable deviations. Several genera possess "shell eyes", i.e., true eyes with a lens and retina that are embedded within the dorsal shells. The phylogeny of the major chiton clades is mostly well established, in a set of superfamily-level and higher level taxa supported by various approaches, including morphological studies, multiple gene markers, mitogenome-phylogeny, and phylotranscriptomic approaches. However, one critical lineage has remained unclear, namely Schizochiton which was controversially suggested as being the potential independent origin of chiton shell eyes. Here, with the draft genome sequencing of Schizochiton incisus (superfamily Schizochitonoidea) plus assemblies of transcriptome data from other polyplacophorans, we present phylogenetic reconstructions using both mitochondrial genomes and phylogenomic approaches with multiple methods. We found that phylogenetic trees from mitogenomic data are inconsistent, reflecting larger scale confounding factors in molluscan mitogenomes. However, a consistent and robust topology was generated with protein-coding genes using different models and methods. Our results support Schizochitonoidea as the sister group to other Chitonoidea in Chitonina, in agreement with the established classification. Combined with evidence from fossils, our phylogenetic results suggest that the earliest origin of shell eyes is in Schizochitonoidea, and that these structures were also gained secondarily in other genera in Chitonoidea. Our results have generated a holistic review of the internal relationship within Polyplacophora, and a better understanding of the evolution of Polyplacophora.

Clarification of the taxonomic status of Acanthochitonadiscrepans (Brown, 1827) with new data for the North-East Atlantic Acanthochitona (Polyplacophora, Acanthochitonidae).

Background: The genus Acanthochitona can be easily distinguished from other chitons by having eighteen tufts of bristles on the dorsal side of the densely spiculose girdle. In the North-East Atlantic, five species of this genus have been recognised so far: A.crinita (Pennant, 1777), A.discrepans (Brown, 1827), A.fascicularis (Linnaeus, 1767), A.oblonga Leloup, 1968 and A.pilosa Schmidt-Petersen, Schwabe et Haszprunar, 2015. The nomenclature of A.crinita, A.discrepans and A.fascicularis was confused for a very long time until Kaas (1985) designated type specimens for them and provided a brief key. However, his work lacked detailed descriptions of the three species and some authors doubted that A.discrepans constitutes a separate species. Subsequently, the taxonomic status of A.discrepans has remained unclear. New information: Here, we implemented an integrative approach which combined morphology and molecular evidence to show that Acanthochitonadiscrepans is, indeed, a valid species and we present re-descriptions for A.crinita, A.discrepans and A.fascicularis.

The lost vent gastropod species of Lothar A. Beck.

Deep-sea hydrothermal vents host many endemic species adapted to these chemosynthesis-based ecosystems. The exploration of vent fields including those in the tropical Pacific is currently accelerating, due to the development of deep-sea mining for valuable minerals. Molecular evidence has shown that many vent endemic gastropod lineages include sibling species pairs in adjacent oceanic basins. While the fauna of the Manus Basin is relatively well described, many lineages in adjacent regions in North Fiji or Lau Basins are recognised as separate species, but unnamed. Valuable material from this fauna was studied by Lothar A. Beck in the 1990s, who fully drafted descriptions for these species, but did not publish them. Beck's manuscript names, prior to the present study, represented real species but nomina nuda without taxonomic validity. Here we present the descriptions of seven new species and one new genus, extracted from Beck's unpublished manuscript that was rediscovered after his death in 2020. The publication of these descriptions makes them taxonomically available and respects the scientific contributions of Beck. Providing valid descriptions of these species is critically important now to enable the recognition of species that may require conservation in the face of future environmental destruction. Symmetriapelta Beck, gen. nov. is described as new genus. Bathyacmaea nadinae Beck, sp. nov., Pyropelta ovalis Beck, sp. nov., Pseudorimula leisei Beck, sp. nov., Lepetodrilus fijiensis Beck, sp. nov., Shinkailepas conspira Beck, sp. nov., Symmetromphalus mcleani Beck, sp. nov. and Symmetriapelta wareni Beck, sp. nov. are introduced as new species.

Why is there no service to support taxonomy?

Increasing complexity and specialisation of modern sciences has led to increasingly collaborative publications, as well as the involvement of commercial services. Modern integrative taxonomy likewise depends on many lines of evidence and is increasingly complex, but the trend of collaboration lags and various attempts at 'turbo taxonomy' have been unsatisfactory. We are developing a taxonomic service in the Senckenberg Ocean Species Alliance to provide fundamental data for new species descriptions. This will also function as a hub to connect a global network of taxonomists, assembling an alliance of scientists working on potential new species to tackle both the extinction and inclusion crises we face today. The current rate of new species descriptions is simply too slow; the discipline is often dismissed as old fashioned, and there is a crisis level need for taxonomic descriptions to come to grips with the scale of Anthropocene biodiversity loss. Here, we envision how the process of describing and naming species would benefit from a service supporting the acquisition of descriptive data. Also see the video abstract here: https://youtu.be/E8q3KJor_F8.

Complex sublinear burrows in the deep sea may be constructed by amphipods.

Trails, burrows, and other "life traces" in sediment provide important evidence for understanding ecology-both of the maker and of other users-and behavioral information often lacking in inaccessible ecosystems, such as the deep sea or those that are already extinct. Here, we report novel sublinear rows of openings in the abyssal plains of the North Pacific, and the first plausible hypothesis for a maker of these constructions. Enigmatic serial burrows have now been recorded in the Pacific and Atlantic deep sea. Based on image and specimen evidence, we propose that these Bering Sea excavations represent amphipod burrows, while the maker of the previously known Mid-Atlantic Ridge constructions remains undetermined. We propose that maerid amphipods could create the Pacific burrows by eating-digging horizontally below the surface along a nutrient-rich layer in the sediment, making the serial openings above them as they go, for conveniently removing excavated sediment as the excavation progresses. These striking structures contribute to local biodiversity, and their maker could be considered a deep-sea ecosystem engineer.

Assessing the extinction risk of insular, understudied marine species.

Hydrothermal vents are rare deep-sea oases that house faunal assemblages with a similar density of life as coral reefs. Only approximately 600 of these hotspots are known worldwide, most only one-third of a football field in size. With advancing development of the deep-sea mining industry, there is an urgent need to protect these unique, insular ecosystems and their specialist endemic faunas. We applied the IUCN (International Union for the Conservation of Nature) Red List criteria to assess the extinction risk of vent-endemic molluscs with varying exposure to potential deep-sea mining. We assessed 31 species from three key areas under different regulatory frameworks in the Indian, West Pacific, and Southern Oceans. Three vent mollusc species were also examined as case studies of different threat contexts (protected or not from potential mining) to explore the interaction of local regulatory frameworks and IUCN Red List category assignment. We found that these assessments were robust even when there was some uncertainty in the total range of individual species, allowing assessment of species that have only recently been named and described. For vent-endemic species, regulatory changes to area-based management can have a greater impact on IUCN Red List assessment outcomes than incorporating additional data about species distributions. Our approach revealed the most useful IUCN Red List criteria for vent-endemic species: criteria B and D2. This approach, combining regulatory framework and distribution, has the potential to rapidly gauge assessment outcomes for species in insular systems worldwide.

Evaluación del Riesgo de Extinción de Especies Marinas Insulares Poco Estudiadas Resumen Los respiraderos hidrotermales son oasis poco comunes en las profundidades del mar en donde se encuentran conjuntos de fauna con una densidad similar a la de los arrecifes de coral. A nivel mundial, sólo se conocen aproximadamente 600 de estos puntos calientes, la mayoría solamente del tamaño de un tercio de una cancha de fútbol. Conforme avanza el desarrollo de la industria minera en mares profundos, también hay una urgente necesidad por proteger estos ecosistemas únicos e insulares y a su fauna endémica especialista. Aplicamos el criterio de la Lista Roja de la UICN (Unión Internacional para la Conservación de la Naturaleza) para evaluar el riesgo de extinción que tienen los moluscos endémicos de los respiraderos ante una exposición variable a la potencial minería de mar profundo. Evaluamos 31 especies de tres áreas importantes bajo diferentes marcos regulatorios en los océanos Índico, Pacífico Occidental y del Sur. Analizamos tres especies de moluscos de los respiraderos como estudios de caso para diferentes contextos de amenazas (protegidas o no de la minería potencial) para explorar la interacción de los marcos regulatorios locales y la clasificación categórica dentro de la Lista Roja de la UICN. Descubrimos que estos análisis eran sólidos incluso cuando existía algo de incertidumbre en cuanto a la extensión total de la especie individual, lo que permite la valoración de especies que han sido descritas y nombradas recientemente. Para las especies endémicas de las chimeneas, los cambios regulatorios a un manejo basado en el área pueden tener un mayor impacto sobre los resultados de evaluación de la Lista Roja de la UICN que la incorporación de datos adicionales sobre la distribución de las especies. Nuestra estrategia reveló los criterios más útiles de la Lista Roja de la UICN para las especies endémicas de las chimeneas: los criterios B y D2. Esta estrategia, que combina un marco regulatorio con la distribución, tiene el potencial para medir rápidamente los resultados de las evaluaciones para las especies que se encuentran en sistemas insulares en todo el mundo.

Molecular analysis of Lepidopleuruscajetanus (Poli, 1791) (Polyplacophora, Leptochitonidae) from the Mediterranean and near Atlantic.

In the present paper we used a molecular data set (including mitochondrial partial 16S rRNA and COI gene sequences) to examine the genetic structure of Lepidopleuruscajetanus (Poli, 1791) (Polyplacophora, Leptochitonidae) - a distinctive shallow water chiton and member of the basal branching Lepidopleurida, which is widespread in and adjacent to the Mediterranean. The analyses of the two mt-standard marker fragments resolved two main discrete clusters reported as L.cajetanus s.s. and L.aff.cajetanus, respectively. Lepidopleuruscajetanus s.s. is widespread throughout the area under study, while the second distinct lineage apparently co-occurs on the eastern Spanish mainland coast of the Balearic Sea. This result is discussed comparing our data with those reported, in 2014, by Fernández and colleagues who described L.cajetanus as exhibiting "a 'chaotic patchiness' pattern defined by a high genetic variability with locality-exclusive haplotypes, high genetic divergence, and a lack of geographic structure". Although genetic data alone are not sufficient to draw any definitive conclusions, nevertheless we believe that present results shed new light on L.cajetanus which apparently shows more geographically patterned genetic structure than supposed so far.

Unlocking the potential of marine biodiscovery.

The tremendous diversity of life in the ocean has proven to be a rich source of inspiration for drug discovery, with success rates for marine natural products up to 4 times higher than other naturally derived compounds. Yet the marine biodiscovery pipeline is characterized by chronic underfunding, bottlenecks and, ultimately, untapped potential. For instance, a lack of taxonomic capacity means that, on average, 20 years pass between the discovery of new organisms and the formal publication of scientific names, a prerequisite to proceed with detecting and isolating promising bioactive metabolites. The need for "edge" research that can spur novel lines of discovery and lengthy high-risk drug discovery processes, are poorly matched with research grant cycles. Here we propose five concrete pathways to broaden the biodiscovery pipeline and open the social and economic potential of the ocean genome for global benefit: (1) investing in fundamental research, even when the links to industry are not immediately apparent; (2) cultivating equitable collaborations between academia and industry that share both risks and benefits for these foundational research stages; (3) providing new opportunities for early-career researchers and under-represented groups to engage in high-risk research without risking their careers; (4) sharing data with global networks; and (5) protecting genetic diversity at its source through strong conservation efforts. The treasures of the ocean have provided fundamental breakthroughs in human health and still remain under-utilised for human benefit, yet that potential may be lost if we allow the biodiscovery pipeline to become blocked in a search for quick-fix solutions.

Seagrass-driven changes in carbonate chemistry enhance oyster shell growth.

Quantifying the strength of non-trophic interactions exerted by foundation species is critical to understanding how natural communities respond to environmental stress. In the case of ocean acidification (OA), submerged marine macrophytes, such as seagrasses, may create local areas of elevated pH due to their capacity to sequester dissolved inorganic carbon through photosynthesis. However, although seagrasses may increase seawater pH during the day, they can also decrease pH at night due to respiration. Therefore, it remains unclear how consequences of such diel fluctuations may unfold for organisms vulnerable to OA. We established mesocosms containing different levels of seagrass biomass (Zostera marina) to create a gradient of carbonate chemistry conditions and explored consequences for growth of juvenile and adult oysters (Crassostrea gigas), a non-native species widely used in aquaculture that can co-occur, and is often grown, in proximity to seagrass beds. In particular, we investigated whether increased diel fluctuations in pH due to seagrass metabolism affected oyster growth. Seagrasses increased daytime pH up to 0.4 units but had little effect on nighttime pH (reductions less than 0.02 units). Thus, both the average pH and the amplitude of diel pH fluctuations increased with greater seagrass biomass. The highest seagrass biomass increased oyster shell growth rate (mm day-1) up to 40%. Oyster somatic tissue weight and oyster condition index exhibited a different pattern, peaking at intermediate levels of seagrass biomass. This work demonstrates the ability of seagrasses to facilitate oyster calcification and illustrates how non-trophic metabolic interactions can modulate effects of environmental change.

Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes.

Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations. Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) has also brought about a large variety of assemblers. Although these have been extensively tested on model species such as Homo sapiens and Drosophila melanogaster, such benchmarking has not been done in Mollusca, which lacks widely adopted model species. Molluscan genomes are notoriously rich in repeats and are often highly heterozygous, making their assembly challenging. Here, we benchmarked 10 assemblers based on ONT raw reads from two published molluscan genomes of differing properties, the gastropod Chrysomallon squamiferum (356.6 Mb, 1.59% heterozygosity) and the bivalve Mytilus coruscus (1593 Mb, 1.94% heterozygosity). By optimizing the assembly pipeline, we greatly improved both genomes from previously published versions. Our results suggested that 40-50X of ONT reads are sufficient for high-quality genomes, with Flye being the recommended assembler for compact and less heterozygous genomes exemplified by C. squamiferum, while NextDenovo excelled for more repetitive and heterozygous molluscan genomes exemplified by M. coruscus. A phylogenomic analysis using the two updated genomes with 32 other published high-quality lophotrochozoan genomes resulted in maximum support across all nodes, and we show that improved genome quality also leads to more complete matrices for phylogenomic inferences. Our benchmarking will ensure efficiency in future assemblies for molluscs and perhaps also for other marine phyla with few genomes available. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Molluscan phylogenomics requires strategically selected genomes.

The extraordinary diversity in molluscan body plans, and the genomic mechanisms that enable it, remains one of the great questions of evolution. The eight distinct living taxonomic classes of molluscs are each unambiguously monophyletic; however, significant controversy remains about the phylogenetic relationships among those eight branches. Molluscs are the second-largest animal phylum, with over 100 000 living species with broad biological, economic and medical interest. To date, only around 53 genome assemblies have been accessioned to NCBI GenBank covering only four of the eight living molluscan classes. Furthermore, the molluscan taxa where partial or whole-genome assemblies are available are often aberrantly fast evolving or recently derived lineages. Characteristic adaptations provide interesting targets for whole-genome projects, in animals like the scaly-foot snail or octopus, but without basal-branching lineages for comparison, the context of recently derived features cannot be assessed. The currently available genomes also create a non-optimal set of taxa for resolving deeper phylogenetic branches: they are a small sample representing a large group, and those that are available come primarily from a rarefied pool. Thoughtful selection of taxa for future projects should focus on the blank areas of the molluscan tree, which are ripe with opportunities to delve into peculiarities of genome evolution, and reveal the biology and evolutionary history of molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Continuous and Regular Expansion of a Distributed Visual System in the Eyed Chiton Tonicia lebruni.

AbstractChitons have a distinctive armature of eight articulating dorsal shells. In all living species, the shell valves are covered by a dense array of sensory pores called aesthetes; but in some taxa, a subset of these are elaborated into lensed eyes, which are capable of spatial vision. We collected a complete ontogenetic series of the eyed chiton Tonicia lebruni de Rochebrune, 1884 to examine the growth of this visual network and found that it expands continuously as eyes are added at the margin during shell growth. Our dataset ranged from a 2.58-mm juvenile with only 16 eyes to adults of 25-31 mm with up to 557 eyes each. This allowed us to investigate the organization (and potential constraints therein) of these sensory structures and their development. Chiton eyes are constrained to a narrowly defined region of the shell, and data from T. lebruni indicate that they are arranged roughly bilaterally symmetrically. We found deviations from symmetry of up to 10%, similar to irregularity reported in some other animals with multiplied eyes. Distances separating successive eyes indicate that, while shell growth slows during the life of an individual chiton, eyes are generated at regular time intervals. Although we could not identify a specific eye-producing tissue or organ, we propose that the generation of new eyes is controlled by a clock-like mechanism with a stable periodicity. The apparent regularity and organization of the chiton visual system are far greater than previously appreciated. This does not imply the integration of shell eyes to form composite images, but symmetry and regular organization could be equally beneficial to a highly duplicated system by ensuring even and comprehensive sampling of the total field of view.

High Abundances of Microplastic Pollution in Deep-Sea Sediments: Evidence from Antarctica and the Southern Ocean.

Plastic pollution in Antarctica and the Southern Ocean has been recorded in scientific literature since the 1980s; however, the presence of microplastic particles (<5 mm) is less understood. Here, we aimed to determine whether microplastic accumulation would vary among Antarctic and Southern Ocean regions through studying 30 deep-sea sediment cores. Additionally, we aimed to highlight whether microplastic accumulation was related to sample depth or the sediment characteristics within each core. Sediment cores were digested and separated using a high-density sodium polytungstate solution (SPT) and microplastic particles were identified using micro-Fourier-transform infrared spectroscopy (µFTIR). Microplastic pollution was found in 93% of the sediment cores (28/30). The mean (±SE) microplastics per gram of sediment was 1.30 ± 0.51, 1.09 ± 0.22, and 1.04 ± 0.39 MP/g, for the Antarctic Peninsula, South Sandwich Islands, and South Georgia, respectively. Microplastic fragment accumulation correlated significantly with the percentage of clay within cores, suggesting that microplastics have similar dispersion behavior to low density sediments. Although no difference in microplastic abundance was found among regions, the values were much higher in comparison to less remote ecosystems, suggesting that the Antarctic and Southern Ocean deep-sea accumulates higher numbers of microplastic pollution than previously expected.

The Scaly-foot Snail genome and implications for the origins of biomineralised armour.

The Scaly-foot Snail, Chrysomallon squamiferum, presents a combination of biomineralised features, reminiscent of enigmatic early fossil taxa with complex shells and sclerites such as sachtids, but in a recently-diverged living species which even has iron-infused hard parts. Thus the Scaly-foot Snail is an ideal model to study the genomic mechanisms underlying the evolutionary diversification of biomineralised armour. Here, we present a high-quality whole-genome assembly and tissue-specific transcriptomic data, and show that scale and shell formation in the Scaly-foot Snail employ independent subsets of 25 highly-expressed transcription factors. Comparisons with other lophotrochozoan genomes imply that this biomineralisation toolkit is ancient, though expression patterns differ across major lineages. We suggest that the ability of lophotrochozoan lineages to generate a wide range of hard parts, exemplified by the remarkable morphological disparity in Mollusca, draws on a capacity for dynamic modification of the expression and positioning of toolkit elements across the genome.

Environmental and ecological factors mediate taxonomic composition and body size of polyplacophoran assemblages along the Peruvian Province.

Intertidal communities' composition and diversity usually exhibit strong changes in relation to environmental gradients at different biogeographical scales. This study represents the first comprehensive diversity and composition description of polyplacophoran assemblages along the Peruvian Province (SE Pacific, 12°S-39°S), as a model system for ecological latitudinal gradients. A total of 4,775 chitons from 21 species were collected on twelve localities along the Peruvian Province. This sampling allowed us to quantitatively estimate the relative abundance of the species in this assemblage, and to test whether chitons conform to elementary predictions of major biogeographic patterns such as a latitudinal diversity gradient. We found that the species composition supported the division of the province into three ecoregional faunal groups (i.e. Humboldtian, Central Chile, and Araucanian). Though chiton diversity did not follow a clear latitudinal gradient, changes in species composition were dominated by smaller scale variability in salinity and temperature. Body size significantly differed by ecoregions and species, indicating latitudinal size-structure assamblages. In some localities body size ratios differed from a random assemblage, evidencing competition at local scale. Changes in composition between ecoregions influence body size structure, and their overlapping produce vertical size segregation, suggesting that competition coupled with environmental conditions structure these assemblages.

Why do chitons curl into a ball?

Many animals with external armour, such as hedgehogs, isopods and trilobites, curl into a protective ball when disturbed. However, in situations where predators would engulf an exposed animal whole, regardless of position, conglobation may provide limited added defence and the benefits were previously unclear. We show that polyplacophoran molluscs (chitons) are three times less likely to spend time curled into a ball in the presence of a predator. When the cue of a potential predator is present, animals instead spend significantly more time in active, high risk, high reward behaviours such as arching, balancing on the head and tail ends of their girdle and pushing the soft foot up into an exposed position. Arching increases vulnerability, but also can increase the likelihood of rapidly encountering new substratum that would allow the animal to right itself. In some other animals, the ability to roll into a ball is associated with rolling away from danger. Curling into a ball would improve mobility, to be rolled on to a safer position, but reattachment is the higher priority for chitons in the face of danger.