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

Abstract

The European flat oyster (Ostrea edulis L.) is a bivalve naturally distributed across Europe, which was an integral part of human diets for centuries, until anthropogenic activities and disease outbreaks severely reduced wild populations. Despite a growing interest in genetic applications to support population management and aquaculture, a reference genome for this species is lacking to date. Here, we report a chromosomelevel assembly and annotation for the European Flat oyster genome, generated using Oxford Nanopore, Illumina, Dovetail OmniC™ proximity ligation and RNA sequencing. A contig assembly (N50: 2.38 Mb) was scaffolded into the expected karyotype of 10 pseudochromosomes. The final assembly is 935.13 Mb, with a scaffold-N50 of 95.56 Mb, with a predicted repeat landscape dominated by unclassified elements specific to O. edulis. The assembly was verified for accuracy and completeness using multiple approaches, including a novel linkage map built with ddRAD-Seq technology, comprising 4016 SNPs from four full-sib families (eight parents and 163 F1 offspring). Annotation of the genome integrating multitissue transcriptome data, comparative protein evidence and ab-initio gene prediction identified 35,699 protein-coding genes. Chromosome-level synteny was demonstrated against multiple high-quality bivalve genome assemblies, including an O. edulis genome generated independently for a French O. edulis individual. Comparative genomics was used to characterize gene family expansions during Ostrea evolution that potentially facilitated adaptation. This new reference genome for European flat oyster will enable high-resolution genomics in support of conservation and aquaculture initiatives, and improves our understanding of bivalve genome evolution.

Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic resource for aquaculture

“…A total of 35,962 protein‐coding genes were predicted from which 24,302 genes were functionally annotated ( e ‐value < 10 −3 ). The parameters of completeness and main genome features of the assembly are presented in Table 1 and are very close to those obtained in the OE_Roslin_V1 assembly (Gundappa et al, 2022). A phylogenetic tree confirms that Roscoff_O.edulis‐V1 clusters with other Ostreidae and has a closer relationship with the other two Chinese Ostrea species (Figure 1).…”

“…In the digestive gland, 11 genes coding for C1q different from those identified in hemocytes are instead upregulated demonstrating differential regulation of this protein family. C1q domain‐containing proteins are characterized by a large diversity of gene number across species (Farhat et al, 2022; Gerdol et al, 2019; Mun et al, 2017; Peng et al, 2020) and have been shown to be over‐represented in O. edulis genome (Gundappa et al, 2022). Further studies will therefore be necessary to better understand the recognition specificities of this set of molecules.…”

A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae

“…A chromosome‐level flat oyster genome assembly generated and annotated at the Roslin Institute, University of Edinburgh (‘OEROSLIN’; NCBI Bioproject: PRJNA772111; Assembly accession: JAJSPN000000000; Gundappa et al, 2022) was used to map all SNPs and the 715 DEGs previously reported by Ronza et al (2018). The genome assembly was 935.6 Mb in size, comprised of 1365 scaffolds (N50: 94.05 Mb), including 10 large scaffolds (sum: 875.78 Mbp; 93.6% of total genome assembly) corresponding to the haploid chromosome number of flat oyster (2 n = 20; Leitao et al, 2002).…”

Two parallel chromosome‐level reference genomes to support restoration and aquaculture of European flat oyster Ostrea edulis

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This volume of Evolutionary Applications includes the deliberate simultaneous publication of two highly contiguous, chromosomelevel reference genome assemblies for the native European flat oyster Ostrea edulis (Boutet et al, 2022;Gundappa et al, 2022). Ostrea edulis is an iconic native species across Europe where it was heavily fished and consumed through to the early 1900s.

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“…This variation has been observed from the level of marker heterozygosity (Hedgecock et al, 2005) through to significant structural variation (Jiao et al, 2021) including measures of interindividual genomic divergence of 0.21 (calculated by dividing the total length of the divergent regions by genome size, Qi et al, 2021), and gene presence–absence variation suggesting one‐third of genes in a mussel pan‐genome (includes core genes essential for all individuals, and dispensable genes found only in some) are dispensable (Gerdol et al, 2020). This high level of variability results in high heterozygosity, including in the Ostrea genome published in this volume of Evolutionary Applications, which has a heterozygosity rate of 1.07% (Gundappa et al, 2022). As such, the assembly of high‐quality reference genomes for bivalve species has historically proved challenging (Davison & Neiman, 2021), in part due to the difficulty in identifying or breeding inbred animals (Dégremont et al, 2022; Zhang et al, 2012).…”