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

Abstract

The European flat oyster (Ostrea edulis L.) is a native bivalve of the European coasts. Harvest of this species has declined during the last decades because of the appearance of two parasites that have led to the collapse of the stocks and the loss of the natural oyster beds. O. edulis has been the subject of numerous studies in population genetics and on the detection of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated immune responses to these parasites at the molecular and cellular levels. Several genetic improvement programs have been initiated especially for parasite resistance. Within the framework of a European project (PERLE 2) that 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 in the foreshore, obtaining a reference genome becomes 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, 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 pseudochromosomes. Annotation of the genome revealed the presence of 35,962 protein-coding genes. We analyzed in detail the transposable element (TE) diversity in the flat oyster genome, highlighted some specificities in tRNA and miRNA composition, and provided the first insight into the molecular response of O. edulis to M. refringens. This genome provides a reference for genomic studies on O. edulis to better understand its basic physiology and as a useful resource for genetic breeding in support of aquaculture and natural reef restoration.

Keywords: Martelia; aquaculture; flat oyster; genome; transposable elements.

FIGURE 1

Phylogenetic tree of Mollusca species based on the alignment of 114 OGs. The tree scale is 0.1, and the bootstrap is represented at each node.

FIGURE 2

Phylogenetic relationships of Copia retrotransposons. The tree is based on neighbor‐joining analysis of RT/RNaseH domain amino acid sequences. The Copia subfamilies from oysters are indicated in color: Crassostrea gigas in dark blue, Crassostrea virginica in light blue, Ostrea edulis in red, Pinctada martensii in purple, and Saccostrea glomerata in green. Node statistical support values (>70%) come from nonparametric bootstrapping using 100 replicates.

FIGURE 3

Phylogenetic relationships of Gypsy retrotransposons. The tree is based on neighbor‐joining analysis of RT/RNaseH domain amino acid sequences. The clades that have elements of oysters are indicated in color, and the clades not present in oysters are represented by the black lines. Node statistical support values (>70%) come from nonparametric bootstrapping using 100 replicates.

FIGURE 4

Heat maps of the most upregulated DEGs (a) and the most downregulated DEGs (b) in hemocytes of M. refringens‐infected O. edulis individuals. The heat map shows the matrix of fold changes that were calculated for each condition and each DEG by normalizing the expression of each condition and DEG to the expression of the DEG in all conditions. Positive fold changes are in red, and negative fold changes are in green.

FIGURE 5

Heat maps of the most upregulated DEGs (a) and the most downregulated DEGs (b) in the digestive gland of M. refringens‐infected O. edulis individuals. The heat map shows the matrix of fold changes that were calculated for each condition and each DEG by normalizing the expression of each condition and DEG to the expression of the DEG in all conditions. Positive fold changes are in red, and negative fold changes are in green.

FIGURE 6

Heat map of the 30 most upregulated SLCs in the digestive gland (Digl) of Ostrea edulis compared with palp (Palp), mantle (MT), adductor muscle (Mus), gills (Gill), gonads (Gon), and hemocytes (Hemo). The heat map shows the matrix of fold changes that were calculated for each tissue by normalizing the expression of each SLC within a tissue to the expression of the SLC in all tissues. Positive fold changes are in red, and negative fold changes are in green.