Pearls of wisdom—a Theo Murphy issue on molluscan genomics

1. Introduction

This issue of Philosophical Transactions began with a mistake. Back in late 2017, Maurine Neiman and myself had not met in person or even chatted online, although we had a shared interest in snails and so followed each other on Twitter. One day, Maurine's former Ph.D. student Joel Sharbrough tweeted a link (figure 1) showing Potamopyrgus antipodarum snails on the front cover of a Theo Murphy issue of Journal of Heredity dedicated to the ‘Evolutionary Genomics of Sex'. The fortuitous mistake that I made—likely wishful thinking—was to misread the title as the ‘Evolutionary Genomics of Snails'.

Figure 1.

The misunderstanding that launched the meeting, from https://twitter.com/jsharbro/status/940722284972535808. (Online version in colour.)

After a brief exchange on Twitter, Maurine and I realized that it was an opportune moment to have a focused meeting on molluscan genomics. Indeed, there never had been a themed conference or journal Theo Murphy issue on molluscan genomics that could showcase the emerging advances, highlight the challenges and help formulate solutions to the unique issues facing this phylum. Further motivated by a near future in which well-assembled molluscan genomes would soon be commonplace—arguably where long-read DNA-sequencing technologies have put us now—we set out to bring together a broad group of junior and senior geneticists, genomicists and evolutionary biologists. This effort resulted in a Royal Society Theo Murphy Discussion meeting, ‘Pearls of Wisdom: Synergising Leadership and Expertise in Molluscan Genomics' (figure 2), which took place on the 16–17th September 2019 at the Kavli Royal Society Centre, Chicheley Hall, UK. Our goal was to identify common themes and barriers in molluscan biology and genomics and, at the same time, bring together a community of people who might help raise the phylum to the prominence that it deserves. Both the meeting and this Theo Murphy issue are therefore a direct consequence of the interactions that followed the fortunate misreading of a tweet¹.

Figure 2.

Graphic for the Theo Murphy meeting, artwork by Emily Jalinsky, reproduced with permission. (Online version in colour.)

The papers featured in this issue reflect the breadth of molluscan genomics research, using a diversity of methodological innovations to summarize and synthesize a host of issues, discoveries, and questions that will be of interest to both molluscan biologists and the wider biological community.

2. Structure and overview of contributions

While molluscs are an extraordinarily diverse group of biologically, economically and medically important organisms, research on their genomes has lagged behind other animal groups. Molluscs are the second-largest animal phylum, with perhaps over 100 000 living species, but with only around 53 genome assemblies in NCBI GenBank, representing only four of the eight extant classes [1].

A possible explanation for the lack of representation is the presumption that molluscs are ‘difficult'. In particular, molluscs are infamous for challenges facing the extraction of quality, high-molecular weight DNA, and they often have large, repetitive and heterozygous genomes. In turn, these challenges have probably contributed to the almost complete lack of genomic technologies (e.g. gene editing) that can be readily applied to molluscs. These actual and perceived challenges, and the absence of technologies and tools, may prevent the acquisition of funding, which further impedes progress.

Of course, as some of the leading authorities on molluscan genomics, the contributing authors of this issue are united in their belief that molluscs are valuable as biological models and therefore should be of interest to the wider scientific community. The authors are also well aware of the challenges that molluscan genomics face; in consequence, several of the papers in this issue directly address these systemic issues and describe or investigate solutions.

The necessary DNA-sequencing technologies for use with molluscan samples are now relatively mature, especially short-read methods, and e.g. transcriptomics. Now, the quality of the output mainly depends upon the input material (DNA), the bioinformatic methods that are used to extract the data and assemble the genomes, and the platforms upon which we store and make the data accessible for (re)use. This Theo Murphy issue therefore opens with a timely review on the extraction of nucleic acids from molluscs [2], the value of which was noted by a referee as ‘very rare, yet of extremely high value: the collection of informal knowledge, which is essentially fed by experiments and experiences that, because they were unsuccessful, never made it into official literature’.

With sequencing data in hand (especially long-read), molluscan researchers are faced with a plethora of possible assembly options, most of which have not been tested on molluscan species. Sun et al. [3] helpfully present an optimized pipeline for molluscan genome assembly using Oxford Nanopore data, in itself only possible because of their careful application of DNA extraction methodologies for this platform. Given that there are ambitious plans to sequence every species on earth [4,5], there is an urgent need to make such data accessible. A partial solution to this problem, MolluscDB, is presented here, providing an easy-to-use and openly accessible data platform for the mollusc research community [6]. The importance of the general idea is highlighted by the fact that another group happened upon the same title for a similar resource at the same time [7].

The issue highlights newly emerging axes of discovery in molluscs, some of which may be well characterized in other phyla. These papers also illustrate the danger of ignoring molluscs: rigorous studies of comparative evolution across phyla require appropriate sampling. Rosani et al. [8] review the comparative genomics of non-coding RNAs, especially microRNAs, in bivalves. Likewise, Maenner et al. [9] highlight the very limited knowledge of epigenetic mechanisms in molluscs, inferring DNA methylation patterns in the genomes of 140 species across all eight classes of molluscs and identifying DNA methyltransferases. Finally, Sigwart et al. [1] make the case that improved taxonomic sampling within the Mollusca will improve the outcomes and resolution of phylogenies within the group—and also benefit studies in other phyla.

Improving long-read DNA-sequencing technologies and economical genome resequencing are together increasing our ability to detect structural variation in genome architecture. Recent analyses of multiple genomes from the same species have shown that differences in gene content can be substantial, especially in prokaryotes [10]. Such variation has led to an appreciation of the ‘pangenome', the complete set of genes present in a species, although still with relatively few studies in metazoans. Thus, work by Calcino et al. [11] and others [12] using recently published complete genomes from representatives of eight wild-caught mollusc species to investigate the prevalence of hemizygous regions has implications for understanding genome dynamics across the other animal phyla. For similar benefit, Modak et al. [13] assess copy number variation in oyster.

Although rigorous characterization of genomic architecture across all but model eukaryotes is at an early stage of cataloguing, it is likely that this is the beginning of a deluge as data generation becomes more straightforward. A note of caution, however, is that future comparative studies should use genome assemblies built with consistent assembly and annotation pipelines [11].

A primary motivation for many studies of genomic structural variation is whether such structural changes play a significant role in evolution and adaptation. Ultimately, answers may only be revealed by putting genome resequencing into an ecological context, required to understand how mollusc species adapt and speciate. Genome resequencing is now routine in other taxa, but large genome size and lack of reference assemblies have limited the ability to apply resequencing to molluscs. The study by Chueca et al. [14] is thus an illustration of what will soon be commonplace: the wider application of resequencing methods in molluscs. Indeed, we anticipate the execution of studies that are as ambitious as those that have used Littorina as a model to understand speciation over many years [15], but requiring considerably less resources.

The Mollusca are replete with exceptionalism in even the most universal biological systems [16], including their mitochondria [17,18]. Ghiselli et al. [19] highlight the remarkable nature of the mitochondrial genomes of some molluscs, which provide a model system for studying mitochondrial evolution. The mitochondrial genomes of molluscs highlight the manifold roles that mitochondria play in organismal physiology and the many ways that the study of mitochondrial genomes is useful for phylogeny and population biology.

Perhaps one of the main challenges affecting the widespread use of molluscs as research organisms is that no individual mollusc species (or, indeed, any animal from the much larger lophotrochozoan group) has emerged as a broadly used model system in biology. In our own contribution to this issue [20], we make the case that both perceptual and methodological barriers have played a role in their relative neglect. We illustrate important research questions to which molluscs can be usefully applied and how the study of model molluscs and their genomes may impact our understanding of this phylum and the much wider group of animal life, as well as considering the barriers that prevent further take-up. As an example of the research questions, potential applications and the rapid progress that is being made, McCartney [21] presents an analysis of the zebra mussel byssus, a key innovation that enables molluscs to attach to a substrate, characterizing the main genes involved using a near chromosome-level assembly. Such studies have potential applications in the control of invasive bivalves, but also should be of wider interest because the silk-like byssus proteins have similar motifs in spiders, silkworms and other animals.

Finally, one of the ongoing limitations in working with molluscs is that transgenic technologies are poorly developed (featured in [20]), which hinders both fundamental biological discovery and limits the commercial application or control of intermediate vectors of human parasites such as schistosomes. In their review, Potts et al. [22] specifically discuss the current state and future potential of genomic technologies to improve disease resistance in aquaculture. Similarly, Seppälä et al. [23] argue that the understanding of the evolution of immune defence traits in natural host populations is crucial for predicting their long-term performance under continuous infection risk. They review the opportunities and challenges in ecoimmunology across gastropods, indicating research opportunities in gastropod molluscs for which well-established ecological understanding and/or ‘immune-omics' resources are already available. Such understanding is, of course, a necessary prerequisite to the development of disease control methods that may benefit from transgenesis.

3. Conclusion

In the early years of high-throughput DNA-sequencing technologies, the limitations of available sequencing techniques and algorithms meant that the first forays into molluscan genomics often resulted in fragmented assemblies. A completed genome of any kind was in itself a remarkable achievement. In the few years between the conception of the meeting (e.g. [24]) and this published outcome, it is remarkable to see the progress that has been made (e.g. [25–27]) and the wide variety of applications for which these genomes are being used. A genome—irrespective of the quality of the assembly—is rightly seen as a staging point on which to base biologically interesting questions, not an end goal. One issue is that a ‘high-quality genome assembly' is also a rapidly moving target; an assembly that was good enough for a high-profile publication in 2017 may be difficult to publish as a standalone resource in 2021, unless the assembly is chromosome anchored (achieved in just a few molluscs; [25–27]).

This issue is timely because the papers integrate across the breadth of molluscan genomics research, using a diversity of methodological innovations to summarize and synthesize a host of issues, discoveries and questions that will be of interest to both molluscan biologists and the wider biological community. The directions outlined in these papers may directly shape decisions regarding project design (e.g. how to best extract DNA [2] and which genomic technologies to use [3]). They should also inspire research aimed at testing hypotheses posed and questions raised by our authors.

This collection of papers should also demonstrate that molluscan genomics is now providing the resources needed to begin comparative work across all major animal groups. By bringing together scientists who have not previously worked together, and putting ideas and problems into the public domain, we hope that this issue will facilitate an appreciation of molluscan genomics across the wider community, and in time, drive further advances in this phylum, bringing molluscs to the forefront of modern biology.

Data accessibility

This article has no additional data.

Authors' contributions

A.D. wrote the first draft, with both authors then working together to complete the article.

Competing interests

We declare we have no competing interests.

Funding

We received no funding for this article.