Abstract:As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities with a focus on particular taxa or ecosystems need solutions capable of aggregating genomic resources and serving them in a standardized and analysis-friendly manner. Taxon-focussed resources can be more flexible in addressing the needs of a research community than can universal or general databases. Here, we present MolluscDB, a genome and tra… Show more
“…The take-home message is that model species, including but not limited to molluscs, should continue to be selected according to the biological question. At the same time, we should push for permanent and reusable data, resources and web tools [8,51], including high-quality contiguous genomes [9–11], portable genome browsers [52], and pipelines that can be used for other taxa [2].…”
Section: Making a Model Molluscmentioning
confidence: 99%
“…Figure 2Idealized ‘ELCTR’ criteria for the making of a model mollusc. Images from top: Cepaea nemoralis at the University of Nottingham (Daniel Ramos Gonzalez); Potamopyrgus antipodarum laboratory culture at the University of Iowa (Justin Torner); attendees at the Royal Society ‘Pearls of Wisdom’ molluscan genome meeting 2019 (Liam Helm); CRISPR-Cas9 cartoon (National Human Genome Research Institute, CC-BY-2.0); investigators using the MolluscDB [8] database (Chelsea Higgins). (Online version in colour.…”
Molluscs are among the most ancient, diverse, and important of all animal taxa. Even so, no individual mollusc species has emerged as a broadly applied model system in biology. We here make the case that both perceptual and methodological barriers have played a role in the relative neglect of molluscs as research organisms. We then summarize the current application and potential of molluscs and their genomes to address important questions in animal biology, and the state of the field when it comes to the availability of resources such as genome assemblies, cell lines, and other key elements necessary to mobilising the development of molluscan model systems. We conclude by contending that a cohesive research community that works together to elevate multiple molluscan systems to ‘model’ status will create new opportunities in addressing basic and applied biological problems, including general features of animal evolution.
This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
“…The take-home message is that model species, including but not limited to molluscs, should continue to be selected according to the biological question. At the same time, we should push for permanent and reusable data, resources and web tools [8,51], including high-quality contiguous genomes [9–11], portable genome browsers [52], and pipelines that can be used for other taxa [2].…”
Section: Making a Model Molluscmentioning
confidence: 99%
“…Figure 2Idealized ‘ELCTR’ criteria for the making of a model mollusc. Images from top: Cepaea nemoralis at the University of Nottingham (Daniel Ramos Gonzalez); Potamopyrgus antipodarum laboratory culture at the University of Iowa (Justin Torner); attendees at the Royal Society ‘Pearls of Wisdom’ molluscan genome meeting 2019 (Liam Helm); CRISPR-Cas9 cartoon (National Human Genome Research Institute, CC-BY-2.0); investigators using the MolluscDB [8] database (Chelsea Higgins). (Online version in colour.…”
Molluscs are among the most ancient, diverse, and important of all animal taxa. Even so, no individual mollusc species has emerged as a broadly applied model system in biology. We here make the case that both perceptual and methodological barriers have played a role in the relative neglect of molluscs as research organisms. We then summarize the current application and potential of molluscs and their genomes to address important questions in animal biology, and the state of the field when it comes to the availability of resources such as genome assemblies, cell lines, and other key elements necessary to mobilising the development of molluscan model systems. We conclude by contending that a cohesive research community that works together to elevate multiple molluscan systems to ‘model’ status will create new opportunities in addressing basic and applied biological problems, including general features of animal evolution.
This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
“…Paired-end sequences were preferably chosen over single reads when possible. Moreover, raw data published in MolluscDB (Liu et al 2021), and molluscDB (Caurcel et al 2021) repositories were manually downloaded.…”
Section: Compilation Of Transcriptomic Data Ensemblesmentioning
With the advent of high throughput sequencing, the amount of genomic data available for animals (Metazoa) species has bloomed over the last decade, especially from transcriptomes due to lower sequencing costs and easier assembling process compared to genomes. Transcriptomic data sets have proven useful for phylogenomic studies, such as inference of phylogenetic interrelationships (eg, species tree reconstruction) and comparative genomics analyses (e.g., gene repertoire evolutionary dynamics). However, these data sets are often analyzed following different analytical pipelines, particularly including different software versions, leading to potential methodological biases when analyzed jointly in a comparative framework. Moreover, these analyses are computationally expensive and not affordable for a large part of the scientific community. More importantly, assembled transcriptomes are usually not deposited in public databases. Furthermore, the quality of these data sets is hardly ever taken into consideration, potentially impacting subsequent analyses such as orthology and phylogenetic or gene repertoire evolution inference. To alleviate these issues, we present Metazoan Assemblies from Transcriptomic Ensembles (MATEdb), a curated database of 335 high-quality transcriptome assemblies from different animal phyla analyzed following the same pipeline. The repository is composed, for each species, of (1) a de novo transcriptome assembly, (2) its candidate coding regions within transcripts (both at the level of nucleotide and amino acid sequences), (3) the coding regions filtered using their contamination profile (i.e., only metazoan content), (4) the longest isoform of the amino acid candidate coding regions, (5) the gene content completeness score as assessed against the BUSCO database, and (6) an orthology-based gene annotation. We complement the repository with gene annotations from high-quality genomes, which are often not straightforward to obtain from individual sequencing projects, totalling 423 high-quality genomic and transcriptomic data sets. We invite the community to provide suggestions for new data sets and new annotation features to be included in subsequent versions, that will be analyzed following the same pipeline and be permanently stored in public repositories. We believe that MATEdb will accelerate research on animal phylogenomics while saving thousands of hours of computational work in a plea for open and collaborative science.
“…A pan-genome based on gene presence–absence variation has recently been suggested for the Mediterranean mussel ( Gerdol et al 2020 ). However, long-read sequencing ( Sun et al 2021 ) has somewhat overcome these issues, leading to an increasing number of improved assemblies ( Caurcel et al 2021 ; Peñaloza et al 2021 ). These resources present a new opportunity; here, using the genomes of 32 species representing each molluscan class, including 15 bivalve species, we identify gene families which have expanded during early and recent bivalve evolution.…”
Bivalve molluscs comprise 20,000 species occupying a wide diversity of marine habitats. As filter feeders and detritivores they act as ecosystem engineers clarifying water, creating reefs and protecting coastlines. The global decline of natural oyster reefs has led to increased restoration efforts in recent years. Bivalves also play an important role in global food security contributing to > 20% of worldwide aquaculture production. Despite this importance, relatively little is known about bivalve evolutionary adaptation strategies. Difficulties previously associated with highly heterozygous and repetitive regions of bivalve genomes have been overcome by long read sequencing, enabling the generation of accurate bivalve assemblies. With these resources we have analysed the genomes of 32 species representing each molluscan class, including 15 bivalve species, to identify gene families that have undergone expansion during bivalve evolution. Gene family expansions across bivalve genomes occur at the point of evolutionary pressures. We uncovered two key factors that shape bivalve evolutionary history: expansion of bivalvia into environmental niches with high stress followed by later exposure to specific pathogenic pressures. The conserved expansion of protein recycling gene families we found across bivalvia is mirrored by adaptations to a sedentary lifestyle seen in plants. These results reflect the ability of bivalves to tolerate high levels of environmental stress and constant exposure to pathogens as filter feeders. The increasing availability of accurate genome assemblies will provide greater resolution to these analyses allowing further points of evolutionary pressure to become clear in other understudied taxa and potentially different populations of a single species.
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