Pearls of wisdom—a Theo Murphy issue on molluscan genomics

Davison, Angus; Neiman, Maurine

doi:10.1098/rstb.2020.0151

Cited by 5 publications

(6 citation statements)

References 26 publications

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“…Ks analysis showed that an ancient WGD event and a more modern WGD event occurred before the divergence of the Bivalvia. This explains why bivalves, and molluscs more generally, present large genomes (Davison and Neiman, 2021). The genomic information for M. edulis presented here, will help clarify the evolutionary processes in Bivalvia species and contribute to improving the understanding of the physiological and morphological diversity of Bivalvia species.…”

Section: Discussionmentioning

confidence: 76%

“…Reference Genome and Whole Genome Duplication Mussels are also known as poor man's shellfish as they are inexpensive and abundant. These features have perhaps contributed to a relative neglect in the investigation of this species' genomic structural variation, and whether such structural changes can play a significant role in their evolution and ecological adaptations (Davison and Neiman, 2021). In the wild, mussels thrive on rocks and stones along the coast, but the majority of mussels consumed are farmed in coastal waters providing food security and employment opportunities to a multitude of fragile coastal communities worldwide (Smaal et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…Similarly to several other molluscs classes, genomic research into M. edulis has been hampered by the lack of a reference genome. This bottleneck is historically linked with the technical difficulties in extracting high molecular weight genomic DNA from Molluscan tissues and thus, allow for long reads sequencing techniques to be successfully applied (Davison and Neiman, 2021). In addition, the relatively large genome size and a high level of heterozygosity further complicates the assembly of high-quality reference genomes in the phylum.…”

Section: Discussionmentioning

confidence: 99%

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Evidence of multiple genome duplication events inMytilusevolution

Corrochano-Fraile

Davie

Carboni

et al. 2021

Preprint

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Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia. Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences. The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises.

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Section: Discussionmentioning

confidence: 76%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Evidence of multiple genome duplication events inMytilusevolution

Corrochano-Fraile

Davie

Carboni

et al. 2021

Preprint

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“…And how is ADAR1 interconnected within the oyster proteome? We highlight the necessity of dedicated projects, which could leverage on existing approaches and implement them to species having specific genome structure, plasticity, repeat contents, and distributions, as bivalves ( 21 ). By producing individual paired DNA/RNA-seq data, useful to discriminate ADAR edits from genomic/transcriptomic variations, it will be possible to develop dedicated SNP databases, such as the human/mouse REDI portal ( 22 ).…”

Section: Discussionmentioning

confidence: 99%

ADAR-Editing during Ostreid Herpesvirus 1 Infection in Crassostrea gigas : Facts and Limitations

Rosani

Bortoletto

Montagnani³

et al. 2022

mSphere

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“…Exploring the evolution of these gene families requires high-quality bivalve reference genomes. Generating such genomes has been impeded by high levels of heterozygosity ( Plough 2016 ; Takeuchi 2017 ; Hollenbeck and Johnston 2018 ), repetitive regions ( Davison and Neiman 2021 ), and structural variations ( Calcino et al 2021 ). A pan-genome based on gene presence–absence variation has recently been suggested for the Mediterranean mussel ( Gerdol et al 2020 ).…”

Section: Main Textmentioning

confidence: 99%

Ancestral Physical Stress and Later Immune Gene Family Expansions Shaped Bivalve Mollusc Evolution

Regan

Stevens

Peñaloza

et al. 2021

Genome Biology and Evolution

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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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Pearls of wisdom—a Theo Murphy issue on molluscan genomics

Cited by 5 publications

References 26 publications

Evidence of multiple genome duplication events inMytilusevolution

Evidence of multiple genome duplication events inMytilusevolution

ADAR-Editing during Ostreid Herpesvirus 1 Infection in Crassostrea gigas : Facts and Limitations

Ancestral Physical Stress and Later Immune Gene Family Expansions Shaped Bivalve Mollusc Evolution

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