Hard to get, easy to lose: Evolution of mantle photoreceptor organs in bivalves (Bivalvia, Pteriomorphia)

A chromosome-level genome assembly of the disco clam, Ctenoides ales

The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales (C. ales), which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and reported a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein-coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, is a valuable resource for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.

Opsin expression varies across larval development and taxa in pteriomorphian bivalves

Introduction

Many marine organisms have a biphasic life cycle that transitions between a swimming larva with a more sedentary adult form. At the end of the first phase, larvae must identify suitable sites to settle and undergo a dramatic morphological change. Environmental factors, including photic and chemical cues, appear to influence settlement, but the sensory receptors involved are largely unknown. We targeted the protein receptor, opsin, which belongs to large superfamily of transmembrane receptors that detects environmental stimuli, hormones, and neurotransmitters. While opsins are well-known for light-sensing, including vision, a growing number of studies have demonstrated light-independent functions. We therefore examined opsin expression in the Pteriomorphia, a large, diverse clade of marine bivalves, that includes commercially important species, such as oysters, mussels, and scallops.

Methods

Genomic annotations combined with phylogenetic analysis show great variation of opsin abundance among pteriomorphian bivalves, including surprisingly high genomic abundance in many species that are eyeless as adults, such as mussels. Therefore, we investigated the diversity of opsin expression from the perspective of larval development. We collected opsin gene expression in four families of Pteriomorphia, across three distinct larval stages, i.e., trochophore, veliger, and pediveliger, and compared those to adult tissues.

Results

We found larvae express all opsin types in these bivalves, but opsin expression patterns are largely species-specific across development. Few opsins are expressed in the adult mantle, but many are highly expressed in adult eyes. Intriguingly, opsin genes such as retinochrome, xenopsins, and Go-opsins have higher levels of expression in the later larval stages when substrates for settlement are being tested, such as the pediveliger.

Conclusion

Investigating opsin gene expression during larval development provides crucial insights into their intricate interactions with the surroundings, which may shed light on how opsin receptors of these organisms respond to various environmental cues that play a pivotal role in their settlement process.

Molluscan Genomes Reveal Extensive Differences in Photopigment Evolution Across the Phylum

In animals, opsins and cryptochromes are major protein families that transduce light signals when bound to light-absorbing chromophores. Opsins are involved in various light-dependent processes, like vision, and have been co-opted for light-independent sensory modalities. Cryptochromes are important photoreceptors in animals, generally regulating circadian rhythm, they belong to a larger protein family with photolyases, which repair UV-induced DNA damage. Mollusks are great animals to explore questions about light sensing as eyes have evolved multiple times across, and within, taxonomic classes. We used molluscan genome assemblies from 80 species to predict protein sequences and examine gene family evolution using phylogenetic approaches. We found extensive opsin family expansion and contraction, particularly in bivalve xenopsins and gastropod Go-opsins, while other opsins, like retinochrome, rarely duplicate. Bivalve and gastropod lineages exhibit fluctuations in opsin repertoire, with cephalopods having the fewest number of opsins and loss of at least 2 major opsin types. Interestingly, opsin expansions are not limited to eyed species, and the highest opsin content was seen in eyeless bivalves. The dynamic nature of opsin evolution is quite contrary to the general lack of diversification in mollusk cryptochromes, though some taxa, including cephalopods and terrestrial gastropods, have reduced repertoires of both protein families. We also found complete loss of opsins and cryptochromes in multiple, but not all, deep-sea species. These results help set the stage for connecting genomic changes, including opsin family expansion and contraction, with differences in environmental, and biological features across Mollusca.

'Distributed' vision and the architecture of animal visual systems

More than a century of research, of which JEB has published a substantial selection, has highlighted the rich diversity of animal eyes. From these studies have emerged numerous examples of visual systems that depart from our own familiar blueprint, a single pair of lateral cephalic eyes. It is now clear that such departures are common, widespread and highly diverse, reflecting a variety of different eye types, visual abilities and architectures. Many of these examples have been described as 'distributed' visual systems, but this includes several fundamentally different systems. Here, I re-examine this term, suggest a new framework within which to evaluate visual system distribution in both spatial and functional senses, and propose a roadmap for future work. The various architectures covered by this term reflect three broad strategies that offer different opportunities and require different approaches for study: the duplication of functionally identical eyes, the expression of multiple, functionally distinct eye types in parallel and the use of dispersed photoreceptors to mediate visual behaviour without eyes. Within this context, I explore some of the possible implications of visual system architecture for how visual information is collected and integrated, which has remained conceptually challenging in systems with a large degree of spatial and/or functional distribution. I highlight two areas that should be prioritised in future investigations: the whole-organism approach to behaviour and signal integration, and the evolution of visual system architecture across Metazoa. Recent advances have been made in both areas, through well-designed ethological experiments and the deployment of molecular tools.

The effects of artificial light at night on behavioral rhythm and related gene expression are wavelength dependent in the oyster Crassostrea gigas

Artificial light at night (ALAN) constitutes a growing threat to coastal ecosystems by altering natural light cycles, which could impair organisms' biological rhythms, with resulting physiological and ecological consequences. Coastal ecosystems are strongly exposed to ALAN, but its effects on coastal organisms are poorly studied. Besides ALAN's intensity, ALAN's quality exposure may change the impacts on organisms. This study aims to characterize the effects of different ALAN's spectral compositions (monochromatic wavelength lights in red (peak at 626 nm), green (peak at 515 nm), blue (peak at 467 nm), and white (410-680 nm) light) at low and realistic intensity (1 lx) on the oyster Crassostrea gigas daily rhythm. Results reveal that all ALAN's treatments affect the oysters' daily valve activity rhythm in different manners and the overall expression of the 13 studied genes. Eight of these genes are involved in the oyster's circadian clock, 2 are clock-associated genes, and 3 are light perception genes. The blue light has the most important effects on oysters' valve behavior and clock and clock-associated gene expression. Interestingly, red and green lights also show significant impacts on the daily rhythm, while the lowest impacts are shown with the green light. Finally, ALAN white light shows the same impact as the blue one in terms of loss of rhythmic oysters' percentage, but the chronobiological parameters of the remaining rhythmic oysters are less disrupted than when exposed to each of the monochromatic light's treatments alone. We conclude that ALAN's spectral composition does influence its effect on oysters' daily rhythm, which could give clues to limit physiological and ecological impacts on coastal environments.

Genome-Wide Identification of 5-HT Receptor Gene Family in Razor Clam Sinonovacula constricta and Their Circadian Rhythm Expression Analysis

Serotonin (5-HT) is primarily distributed in the gastrointestinal and central nervous systems, where it plays a crucial role in regulating various physiological functions such as digestion, reproduction and establishing animal emotions. 5-HT is an effective oxytocin widely used in molluscan aquaculture, and its physiological functions are performed by binding to corresponding 5-HT receptors (5-HTRs). In this study, seven 5-HTR genes of Sinonovacula constricta (Sc5-HTRs) were identified and analyzed, and they were designated as Sc5-HT1A, Sc5-HT1D, Sc5-HT2-1, Sc5-HT2-2, Sc5-HT2-3, Sc5-HT4 and Sc5-HT6. Phylogenetic analysis showed that the seven Sc5-HTRs were conserved among mollusks, and the Sc5-HTRs were all transmembrane proteins. The seven Sc5-HTR genes were distributed on chromosome 1, 2, 13 and 14. After injecting 5-HT, there was a significant increase in mRNA expression levels of Sc5-HT1A (p < 0.05) and Sc5-HT2-3 (p < 0.01), while Sc5-HT4 decreased significantly (p < 0.01) compared to control groups which might be effective 5-HT receptors. Furthermore, two of the receptors (Sc5-HT2-3 and Sc5-HT4) were expressed in the circadian rhythm patterns, indicating their potential influence on the nocturnal spawning of S. constricta. Overall, these findings provide a theoretical basis for understanding the structures and functions of 5-HTR gene family members, and may facilitate the artificial propagation of mollusks.

The effects of artificial light at night (ALAN) on the gaping activity and feeding of mussels

Artificial Light at Night (ALAN) is a common environmental pollutant which affects >22 % of the world's coastlines. However, the impact of ALAN wavelengths on coastal organisms is under-investigated. Here, we tested the impact of red, green, and white ALAN on the gaping activity and phytoplankton consumption of Mytilus edulis mussels and compared these to dark night. Mussels exhibited a semi-diel activity pattern. Although ALAN did not significantly affect the time open nor the phytoplankton consumption, it did have a colour-specific effect on the gaping frequency with red and white ALAN resulting in lower activity compared to the dark night. Green ALAN caused higher gaping frequency and a negative relationship between consumption and proportion of time open compared to the other treatments. Our findings suggest colour-specific ALAN effects on mussels and call for further investigation on the associated physiological mechanisms and potential ecological consequences.

Variation in eye abundance among scallops reveals ontogenetic and evolutionary convergence associated with life habits

Eyes are remarkable systems to investigate the complex interaction between ecological drivers and phenotypic outcomes. Some animals, such as scallops, have many eyes for visual perception, but to date, the evolution of multiple-eye systems remains obscure. For instance, it is unclear whether eye number changes over a lifetime or varies among species. Scallops are a suitable model group to investigate these questions considering the interspecific variation of adult size and ecological diversity. We tested whether eye abundance scales with body size among individuals and species and whether it varies with life habits. We performed comparative analyses, including a phylogenetic ANCOVA and evolutionary model comparisons, based on eye count and shell height (as a proxy of body size) across 31 scallop species. Our analyses reveal that patterns of increasing relationship with body size are not concordant among taxa and suggest ontogenetic convergence caused by similar ecologies. Accordingly, selective optima in eye numbers are associated with shifts in life habits. For instance, species with increased mobility have significantly more eyes than less mobile species. The convergent evolution of greater eye abundance in more mobile scallops likely indicates a visual improvement based on increased levels of oversampling of the surrounding environment.

The Evolution of Visual Roles – Ancient Vision Versus Object Vision

Just like other complex biological features, image vision (multi-pixel light sensing) did not evolve suddenly. Animal visual systems have a long prehistory of non-imaging light sensitivity. The first spatial vision was likely very crude with only few pixels, and evolved to improve orientation behaviors previously supported by single-channel directional photoreception. The origin of image vision was simply a switch from single to multiple spatial channels, which improved the behaviors for finding a suitable habitat and position itself within it. Orientation based on spatial vision obviously involves active guidance of behaviors but, by necessity, also assessment of habitat suitability and environmental conditions. These conditions are crucial for deciding when to forage, reproduce, seek shelter, rest, etc. When spatial resolution became good enough to see other animals and interact with them, a whole range of new visual roles emerged: pursuit, escape, communication and other interactions. All these new visual roles require entirely new types of visual processing. Objects needed to be separated from the background, identified and classified to make the correct choice of interaction. Object detection and identification can be used actively to guide behaviors but of course also to assess the over-all situation. Visual roles can thus be classified as either ancient non-object-based tasks, or object vision. Each of these two categories can also be further divided into active visual tasks and visual assessment tasks. This generates four major categories of vision into which I propose that all visual roles can be categorized.