Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies

Castro LF, Froufe E. The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Contiguous assemblies are fundamental to deciphering the composition of extant genomes. In molluscs, this is considerably challenging owing to the large size of their genomes, heterozygosity, and widespread repetitive content. Consequently, long-read sequencing technologies are fundamental for high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, was recently generated. However, the resulting genome is highly fragmented since the assembly relied on short-read approaches. Here, an improved reference genome assembly was generated using a combination of PacBio CLR long reads and Illumina paired-end short reads. This genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4 Mbp. The ab initio gene prediction resulted in 48,314 protein-coding genes. Our new assembly is a substantial improvement and an essential resource for studying this species' unique biological and evolutionary features, helping promote its conservation.

Development and Interrogation of a Transcriptomic Resource for the Giant Triton Snail (Charonia tritonis)

Gastropod molluscs are among the most abundant species that inhabit coral reef ecosystems. Many are specialist predators, along with the giant triton snail Charonia tritonis (Linnaeus, 1758) whose diet consists of Acanthaster planci (crown-of-thorns starfish), a corallivore known to consume enormous quantities of reef-building coral. C. tritonis are considered vulnerable due to overexploitation, and a decline in their populations is believed to have contributed to recurring A. planci population outbreaks. Aquaculture is considered one approach that could help restore natural populations of C. tritonis and mitigate coral loss; however, numerous questions remain unanswered regarding their life cycle, including the molecular factors that regulate their reproduction and development. In this study, we have established a reference C. tritonis transcriptome derived from developmental stages (embryo and veliger) and adult tissues. This was used to identify genes associated with cell signalling, such as neuropeptides and G protein-coupled receptors (GPCRs), involved in endocrine and olfactory signalling. A comparison of developmental stages showed that several neuropeptide precursors are exclusively expressed in post-hatch veligers and functional analysis found that FFamide stimulated a significant (20.3%) increase in larval heart rate. GPCRs unique to veligers, and a diversity of rhodopsin-like GPCRs located within adult cephalic tentacles, all represent candidate olfactory receptors. In addition, the cytochrome P450 superfamily, which participates in the biosynthesis and degradation of steroid hormones and lipids, was also found to be expanded with at least 91 genes annotated, mostly in gill tissue. These findings further progress our understanding of C. tritonis with possible application in developing aquaculture methods.

Molecular Methods as Potential Tools in Ecohydrological Studies on Emerging Contaminants in Freshwater Ecosystems

Contaminants of emerging concern (CECs) present a threat to the functioning of freshwater ecosystems. Their spread in the environment can affect both plant and animal health. Ecohydrology serves as a solution for assessment approaches (i.e., threat identification, ecotoxicological assessment, and cause–effect relationship analysis) and solution approaches (i.e., the elaboration of nature-based solutions: NBSs), mitigating the toxic effect of CECs. However, the wide array of potential molecular analyses are not fully exploited in ecohydrological research. Although the number of publications considering the application of molecular tools in freshwater studies has been steadily growing, no paper has reviewed the most prominent studies on the potential use of molecular technologies in ecohydrology. Therefore, the present article examines the role of molecular methods and novel omics technologies as essential tools in the ecohydrological approach to CECs management in freshwater ecosystems. It considers DNA, RNA and protein-level analyses intended to provide an overall view on the response of organisms to stress factors. This is compliant with the principles of ecohydrology, which emphasize the importance of multiple indicator measurements and correlation analysis in order to determine the effects of contaminants, their interaction with other environmental factors and their removal using NBS in freshwater ecosystems.