13/05/2025

The grooved carpet shell clam (Ruditapes decussatus) is a bivalve of high commercial value distributed throughout the European
coast. Its production has suffered a decline caused by different factors, especially by the parasite Perkinsus olsenii. Improving pro-
duction of R. decussatus requires genomic resources to ascertain the genetic factors underlying resistance/tolerance to P. olsenii.
In this study, the first reference genome of R. decussatus was assembled through long- and short-read sequencing (1677 contigs;
1.386 Mb) and further scaffolded at chromosome level with Hi- C (19 superscaffolds; 95.4% of assembly). Repetitive elements were
identified (32%) and masked for annotation of 38,276 coding- and 13,056 non-coding genes. This genome was used as a reference
to develop a 2bRAD-Seq 13,438 SNP panel for a genomic screening on six shellfish beds distributed across the Atlantic Ocean
and Mediterranean Sea. Beds were selected by perkinsosis prevalence and the infection level was individually evaluated in all the
samples. Genetic diversity was significantly higher in the Mediterranean than in the Atlantic region. The main genetic breakage
was detected between those regions (F ST = 0.224), being the Mediterranean more heterogeneous than the Atlantic. Several loci
under divergent selection (394 outliers; 261 genomic windows) were detected across shellfish beds. Samples were also inspected
to detect signals of selection for resistance/tolerance to P. olsenii by using infection-level and population-genomics approaches,
and 90 common divergent outliers for resistance/tolerance to perkinsosis were identified and used for gene mining. Candidate
genes and markers identified provide invaluable information for controlling perkinsosis and for improving production of the
grooved carpet shell clam.

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