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

Manu Kumar Gundappa*, Carolina Penaloza, Tim Regan, Isabelle Boutet, Arnaud Tanguy, Ross Houston, Tim Bean, Dan Macqueen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

The European flat oyster (Ostrea edulis L.) is a bivalve naturally distributed across Europe that 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 chromosome-level assembly and annotation for the European Flat oyster genome, generated using Oxford Nanopore, Illumina, Dovetail OmniCTM proximity ligation and RNA sequencing. A contig assembly (N50: 2.38Mb) was scaffolded into the expected karyotype of 10 pseudo-chromosomes. 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 4,016 SNPs from four full-sib families (8 parents and 163 F1 offspring). Annotation of the genome integrating multi-tissue 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.
Original languageEnglish
Pages (from-to)1713-1729
JournalEvolutionary Applications
Issue number11
Early online date4 Aug 2022
Publication statusPublished - Nov 2022

Keywords / Materials (for Non-textual outputs)

  • European flat oyster
  • aquaculture
  • bivalves
  • comparative genomics
  • conservation and restoration
  • genetic map
  • reference genome


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