Chromosome level reference genome for European flat oyster (<i>Ostrea edulis</i> L.)

Gundappa, Manu Kumar; Peñaloza, Carolina; Regan, Tim; Boutet, Isabelle; Tanguy, Arnaud; Houston, Ross D.; Bean, Tim P.; Macqueen, Daniel J.

doi:10.1101/2022.06.26.497633

Cited by 5 publications

(9 citation statements)

References 108 publications

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“…The down-regulation of those genes could indicate a lower capacity of immune response by the oyster. C1q domain containing proteins have been largely characterized in mollusk genomes, are characterized by a large diversity gene number across species (Mun et al, 2017; Gerdol et al, 2019, Peng et al, 2020; Farhat et al, 2022) and have been shown to be overrepresented in O. edulis genome (Gundappa et al, 2022the over-expression of genes involved in apoptosis is coherent with previous results obtained on O. edulis in response to B. ostreae (Gervais et al, 2019) or in C . virginica in response to Perkinsus marinus (Lau et al, 2018)…”

Section: Discussionsupporting

confidence: 86%

“…A total of 35962 protein-coding genes were predicted from which 24302 genes were functionally annotated (e-value<0.001). The parameters of completeness and main genome features of the assembly are presented in Table 1 and are very close from those obtained in the OE_Roslin_V1 assembly (Gundappa et al, 2022). Phylogenetic tree confirms that Roscoff_O .…”

Section: Resultssupporting

confidence: 72%

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Chromosomal assembly of the flat oyster (Ostrea edulisL.) genome as a new genetic ressource for aquaculture

Boutet

Monteiro

Takeuchi

et al. 2022

Preprint

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The European flat oyster (Ostrea edulis L.) is the endemic species of the European coasts. Its exploitation has been reduced during the last decades, because of the appearance of two parasites that have led to the collapse of the stocks and the strong decline of the natural oyster beds. O. edulis has been the subject of numerous studies and programs in population genetics and on the presence of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated the effects of these parasites mainly on immunity at the molecular and cellular levels. Several genetic selection programs especially related to resistance to the parasite have been initiated. Within the framework of a European project (PERLE 2) which aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species on the foreshore, obtaining a reference genome has proved to be essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio technology, Illumina, 10X linked and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudo-chromosomes. Annotation of the genome revealed the presence of 35962 protein-coding genes. We analyzed in details the transposable elements (TE) diversity in the flat oyster genome, highlight some specificities in tRNA and miRNA composition and provide first insights in the molecular response of O. edulis to M. refringens. This genome will serve as a reference for genomic studies on O. edulis to better understand its basic physiology or developing genetic markers in breeding projects for aquaculture or natural reef restoration.

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Section: Discussionsupporting

confidence: 86%

Section: Resultssupporting

confidence: 72%

Chromosomal assembly of the flat oyster (Ostrea edulisL.) genome as a new genetic ressource for aquaculture

Boutet

Monteiro

Takeuchi

et al. 2022

Preprint

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“…The genotype concordance rate among replicates was 99.7%, demonstrating a high reproducibility of the genotyping assays. The flanking region of these markers were mapped to the O. edulis chromosome-level genome assembly ( Gundappa et al, 2022 ). Of the 11,808 SNPs, 10,025 had uniquely mapping probes and were retained for downstream analysis.…”

Section: Methodsmentioning

confidence: 99%

“…These resources have been applied to examine the genetic basis of growth ( Jones et al, 2014 ; Gutierrez et al, 2018 ; He et al, 2021 ), low salinity tolerance ( McCarty et al, 2022 ), disease resistance ( Gutierrez et al, 2020 ; Yang et al, 2022 ) and nutritional content ( Meng et al, 2019 ). For the European flat oyster, high-quality genomes have recently been released ( Boutet et al, 2022 ; Gundappa et al, 2022 ), which along with available high-throughput genotyping techniques (e.g., SNP arrays and genotype-by-sequencing approaches), provide the opportunity for gaining insight into the genomic architecture of relevant production traits. Most of the traits of economic importance in aquaculture species have a polygenic architecture ( Zenger et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis)

et al. 2022

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The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed across Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to overexploitation and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was in the low-moderate range, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels was assessed. Genomic prediction accuracies using the full density panel were high (> 0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e., 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relatedness should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

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“…FUN_017843; Gundappa et al 2022). The predicted protein product of this gene contains an AAA domain, hence can bind and hydrolyse ATP (Lupas and Martin 2002).…”

Section: Genome-wide Association Analysis For Growth-related Traitsmentioning

confidence: 99%

Genome-wide association and genomic prediction of growth traits in the European flat oyster (Ostrea edulis)

Peñaloza

Barría

Papadopoulou

et al. 2022

Preprint

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The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed in Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to anthropogenic activities and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was moderate-low, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic genetic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels (down to 100 SNPs) was assessed. Genomic prediction accuracies using the full density panel were high (>0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e. 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relationship should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

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Chromosome level reference genome for European flat oyster (Ostrea edulis L.)

Cited by 5 publications

References 108 publications

Chromosomal assembly of the flat oyster (Ostrea edulisL.) genome as a new genetic ressource for aquaculture

Chromosomal assembly of the flat oyster (Ostrea edulisL.) genome as a new genetic ressource for aquaculture

Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis)

Genome-wide association and genomic prediction of growth traits in the European flat oyster (Ostrea edulis)

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