The Whole-Genome Sequencing and Hybrid Assembly of Mytilus coruscus

Li, Ronghua; Zhang, Weijia; Lu, Junkai; Zhang, Zhouyi; Mu, Changkao; Song, Weiwei; Migaud, Hervé; Bekaert, Michaël

doi:10.3389/fgene.2020.00440

Cited by 47 publications

(48 citation statements)

References 29 publications

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“…Curiously, the genome of the congeneric non-invasive mussel M. coruscus [20], whose geographical distribution is limited to the Yellow Sea, displays a significantly lower number of protein-coding genes and a much lower level of heterozygosity compared with M. galloprovincialis (Additional file 1: Data Note 3 and 6), which suggests that the prevalence of PAV may vary from species to species. Future investigations, which will hopefully benefit from the release of additional chromosome-scale genome assemblies, should be aimed at investigating whether the pan-genomic architecture we described in the Mediterranean mussel is shared by other mollusks.…”

Section: Discussionmentioning

confidence: 99%

“…Although M. galloprovincialis displays a morphologically conserved karyotype compared with other mussels and has not undergone known whole-genome duplication or allopolyploidization events [11], it shares with other bivalves a relatively large and complex genome, characterized by high heterozygosity and numerous mobile elements [12][13][14][15][16][17]. These factors posed a serious challenge to previous assembly efforts, which resulted in extremely fragmented genome sequences for this species [18,19] which, unlike the congeneric Mytilus coruscus [20] and a few other mussel species [15], still lacks a highly contiguous reference genome assembly.…”

Section: Introductionmentioning

confidence: 99%

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Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

et al. 2020

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Background The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, the factors underlying the evolutionary success of this species remain unclear. Results Here, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture in M. galloprovincialis, with a core set of 45,000 genes plus a strikingly high number of dispensable genes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals. We show that dispensable genes are associated with hemizygous genomic regions affected by structural variants, which overall account for nearly 580 Mb of DNA sequence not included in the reference genome assembly. As such, this is the first study to report the widespread occurrence of gene presence-absence variation at a whole-genome scale in the animal kingdom. Conclusions Dispensable genes usually belong to young and recently expanded gene families enriched in survival functions, which might be the key to explain the resilience and invasiveness of this species. This unique pan-genome architecture is characterized by dispensable genes in accessory genomic regions that exceed by orders of magnitude those observed in other metazoans, including humans, and closely mirror the open pan-genomes found in prokaryotes and in a few non-metazoan eukaryotes.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

et al. 2020

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“…Analyses of Illumina data with Genome Scope 25 estimated the genome size at 726 Mb (Supplementary Fig. S1), which is less than half the size of genomes from other mussel species, Mytilus galloprovincialis (1.28 Gb), Mytilus coruscus (1.90 Gb), Bathymodiolus platifrons (1.66 Gb), Modiolus philippinarum (2.63 Gb), and L. fortunei (1.67 Gb) 26 – 29 . Genome Scope also estimated heterozygosity at 0.63%, and repetitive portions of the genome at 19.57% (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

Genomics and transcriptomics of the green mussel explain the durability of its byssus

Inoue

Yoshioka

Tanaka

et al. 2021

Sci Rep

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Mussels, which occupy important positions in marine ecosystems, attach tightly to underwater substrates using a proteinaceous holdfast known as the byssus, which is tough, durable, and resistant to enzymatic degradation. Although various byssal proteins have been identified, the mechanisms by which it achieves such durability are unknown. Here we report comprehensive identification of genes involved in byssus formation through whole-genome and foot-specific transcriptomic analyses of the green mussel, Perna viridis. Interestingly, proteins encoded by highly expressed genes include proteinase inhibitors and defense proteins, including lysozyme and lectins, in addition to structural proteins and protein modification enzymes that probably catalyze polymerization and insolubilization. This assemblage of structural and protective molecules constitutes a multi-pronged strategy to render the byssus highly resistant to environmental insults.

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“…Raw ONT reads in the .fast5 format from the published Scaly-foot Snail genome sequencing project (PRJNA523462) [8] were re-basecalled using Guppy version 3.6.0 with the high-accuracy (HAC) mode on a GeForce® RTX 1080 Ti (NVIDIA) GPU. The Illumina and ONT reads from the Mytilus coruscus genome sequencing project were downloaded from the NCBI SRA database (ERR3415816 and ERR3431204) [9]. Illumina reads were cleaned to remove bacterial contamination using Kraken2 [10], and the genome size and heterozygosity was calculated by Jellyfish v2.3.0 with the k-mer size of 17, 19, and 21 and GenomeScope 2.0 [11].…”

Section: Methodsmentioning

confidence: 99%

Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes

Sun

Chen

et al. 2021

Preprint

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SummaryChoosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations. Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) also brought about a large variety of assemblers. Although these have been extensively tested on model species such as Homo sapiens and Drosophila melanogaster, such benchmarking has not been done in Mollusca which lacks widely adopted model species. Molluscan genomes are notoriously rich in repeats and are often highly heterozygous, making their assembly challenging. Here, we benchmarked 10 assemblers based on ONT raw reads from two published molluscan genomes of differing properties, the gastropod Chrysomallon squamiferum (356.6Mb, 1.59% heterozygosity) and the bivalve Mytilus coruscus (1593Mb, 1.94% heterozygosity). By optimising the assembly pipeline, we greatly improved both genomes from previously published versions. Our results suggested that 40-50X of ONT reads are sufficient for high-quality genomes, with Flye being the recommended assembler for compact and less heterozygous genomes exemplified by C. squamiferum, while NextDenovo excelled for more repetitive and heterozygous molluscan genomes exemplified by M. coruscus. A phylogenomic analysis utilising the two updated genomes with other 32 published high-quality lophotrochozoan genomes resulted in maximum support across all nodes, and we show that improved genome quality also leads to more complete matrices for phylogenomic inferences. Our benchmarking will ensure the efficiency in future assemblies for molluscs and perhaps also other marine phyla with few genomes available.

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The Whole-Genome Sequencing and Hybrid Assembly of Mytilus coruscus

Cited by 47 publications

References 29 publications

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

Genomics and transcriptomics of the green mussel explain the durability of its byssus

Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes

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