Reference genome for the California ribbed mussel,<i>Mytilus californianus</i>, an ecosystem engineer

Paggeot, Lisa; DeBiasse, Melissa B.; Escalona, Merly; Fairbairn, Colin; Marimuthu, Mohan P A; Nguyen, Oanh; Sahasrabudhe, Ruta; Dawson, Michael N

doi:10.1093/jhered/esac041

Cited by 8 publications

(5 citation statements)

References 43 publications

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“…Mytilectins were present in the genomes of 6 out of 13 species belonging to the order Mytilida. Five of these (Mytilus californianus, Mytilus chilensis, Mytilus coruscus, Mytilus edulis, and Mytilus galloprovincialis) [55][56][57][58][59] are congeneric, confirming the previous reports of MytiLec-1, CGL, and MTL in Mytilus and Crenomytilus spp. [20,26,60].…”

Section: Phylum Mollusca Class Bivalviasupporting

confidence: 88%

Taxonomic Distribution and Molecular Evolution of Mytilectins

Gerdol,

Nerelli,

Martelossi

et al. 2023

Marine Drugs

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R-type lectins are a widespread group of sugar-binding proteins found in nearly all domains of life, characterized by the presence of a carbohydrate-binding domain that adopts a β-trefoil fold. Mytilectins represent a recently described subgroup of β-trefoil lectins, which have been functionally characterized in a few mussel species (Mollusca, Bivalvia) and display attractive properties, which may fuel the development of artificial lectins with different biotechnological applications. The detection of different paralogous genes in mussels, together with the description of orthologous sequences in brachiopods, supports the formal description of mytilectins as a gene family. However, to date, an investigation of the taxonomic distribution of these lectins and their molecular diversification and evolution was still lacking. Here, we provide a comprehensive overview of the evolutionary history of mytilectins, revealing an ancient monophyletic evolutionary origin and a very broad but highly discontinuous taxonomic distribution, ranging from heteroscleromorphan sponges to ophiuroid and crinoid echinoderms. Moreover, the overwhelming majority of mytilectins display a chimera-like architecture, which combines the β-trefoil carbohydrate recognition domain with a C-terminal pore-forming domain, suggesting that the simpler structure of most functionally characterized mytilectins derives from a secondary domain loss.

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Section: Phylum Mollusca Class Bivalviasupporting

confidence: 88%

Taxonomic Distribution and Molecular Evolution of Mytilectins

Gerdol,

Nerelli,

Martelossi

et al. 2023

Marine Drugs

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“…Here, we present a highly contiguous chromosome assembly for Mytilus edulis confirming species-level individual purity through resequencing. To date, our resource has been applied in multiple studies analysing Mytilus genome assemblies (Paggeot et al 2022b; Gallardo-Escarate et al 2023) and cross-species gene orthology analyses (Saco et al 2023). The gene annotations produced in this study were generated using Augustus gene model predictions integrating full transcript Isoseq data and applying stringent filtering parameters.…”

Section: Resultsmentioning

confidence: 99%

“…These characteristics make assembly of these genomes challenging. However, recently genomes for the American oyster, Pacific Oyster, M. corruscus and M. califoniaus have been assembled to chromosome-level using short and long-read sequencing technologies as well as Hi-C-based scaffolding (Yang et al 2021; Paggeot et al 2022a; Penaloza et al 2021; Gomez-Chiarri et al 2015). We used a similar approach in this project to produce a highly contiguous assembly.…”

Section: Introductionmentioning

confidence: 99%

Genome Report: A blue mussel chromosome-scale genome assembly for aquaculture, marine ecology and evolution

Regan

Hori²,

Bean

2022

Preprint

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The blue mussel is commonly described as the Mytilus species complex, encompassing at least three putative species: M. edulis, M. galloprovincialis and M. trossolus. These three species occur on both sides of the Atlantic and hybridize in nature, and both M. edulis and M. galloprovincialis are important aquaculture species. They are also invasive species in many parts of the world. Here, we present the first chromosome-level assembly of the Mytilus species complex. We used a combination of PacBio sequencing and Dovetail's Omni-C technology to generate an assembly with 14 long scaffolds containing 94% of the predicted length of the M. edulis genome (1.6 out of 1.7 Gb). Assembly statistics were total length 1.65 Gb, N50 = 116 Mb, L50 = 7 and, L90 = 13. BUSCO analysis showed 91.3% eukaryote BUSCOs identified. AB-Initio annotation using RNA-seq from mantle, gills, muscle and foot predicted 47,128 genes. Using GBS and shotgun sequencing, we also sequenced 3 North American populations of Mytilus to characterize single-nucleotide as well as structural variance. This high-quality genome for M. edulis provides a platform to develop tools that can be used in breeding, molecular ecology and evolution to address questions of both commercial and environmental perspectives.

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“…Increased effort has been put in the last few years to produce genomic resources in the Mytilus species complex. Quality genomes are available for the following lineages of Mytilus: Atlantic M. galloprovincialis (Gerdol et al, 2020), Southern European M. edulis (Corrochano-Fraile et al, 2022), M. coruscus (R. Li et al, 2020; Yang et al, 2021), M. californianus (Paggeot et al, 2022), and an American M. edulis assembly (unpublished, accession GCA_019925275). This increased effort has highlighted characteristics of interest in those species such as a high proportion of gene presence-absence (Gerdol et al, 2020) or evidence of genome duplication (Corrochano-Fraile et al, 2022).…”

Section: Rationale and Objectivesmentioning

confidence: 99%

Three new genome assemblies of blue mussel lineages: North and South EuropeanMytilus edulisand MediterraneanMytilus galloprovincialis

Simon

2022

Preprint

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The blue mussel species complex (Mytilus edulis) is of particular interest both as model species in population genetics and ecology, but also as an economic resource in many regions. Using 10X genomics pseudo-long reads, I assembled genomes of three closely related blue mussel lineages from the Mytilus species complex in the Northern hemisphere. Given the huge diversity within and between lineages in this complex, the objective was to produce aﬀordable genomic resources for population and evolutionary genomic studies to broaden the coverage of this diverse species complex. I used transcriptome guided corrections and scaﬀolding on a chromosome scale genome of a close species to reduce the fragmentation of the genomes. The result is a set of partially fragmented genomes of equivalent completeness to already published genomes. Three new draft genomes are added to the fast increasing genomic resources of this complex for the Mediterranean M. galloprovincialis, the South-European M. edulis and the the North-European M. edulis.

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Reference genome for the California ribbed mussel,Mytilus californianus, an ecosystem engineer

Cited by 8 publications

References 43 publications

Taxonomic Distribution and Molecular Evolution of Mytilectins

Taxonomic Distribution and Molecular Evolution of Mytilectins

Genome Report: A blue mussel chromosome-scale genome assembly for aquaculture, marine ecology and evolution

Three new genome assemblies of blue mussel lineages: North and South EuropeanMytilus edulisand MediterraneanMytilus galloprovincialis

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