Signatures of Selection for Resistance/Tolerance to Perkinsus olseni in Grooved Carpet Shell Clam ( Ruditapes decussatus ) Using a Population Genomics Approach

Sambade, Inés M.; Estêvão, João; Pampín, Marina; Cruz, Andreia; Guévélou, Eric; Blanco, Andrés; Câmara, Francisco; Gómez‐Garrido, Jessica; Cruz, Fernando; Bargelloni, Luca; Carboni, Stefano; Alioto, Tyler; Costas, Benjamin; Fernández‐Boo, Sergio; Martínez, Paulino

doi:10.1111/eva.70106

Title: Signatures of Selection for Resistance/Tolerance to Perkinsus olseni in Grooved Carpet Shell Clam ( Ruditapes decussatus ) Using a Population Genomics Approach

Journal Article · 12 May 2025 · Evolutionary Applications

DOI: https://doi.org/10.1111/eva.70106 · OSTI ID:2566004

Sambade, Inés M. ^[1]; Estêvão, João ^[2]; Pampín, Marina ^[1]; Cruz, Andreia ^[3]; Guévélou, Eric ^[3]; Blanco, Andrés ^[1]; Câmara, Francisco ^[4]; Gómez‐Garrido, Jessica ^[4]; Cruz, Fernando ^[4]; Bargelloni, Luca ^[5]; Carboni, Stefano ^[6]; Alioto, Tyler ^[4]; Costas, Benjamin ^[7]; Fernández‐Boo, Sergio ^[7];

^[1]

Department of Zoology, Genetics and Physical Anthropology, Facultad de Veterinaria, Campus Terra Universidade de Santiago de Compostela Lugo Spain
Department of Zoology, Genetics and Physical Anthropology, Facultad de Veterinaria, Campus Terra Universidade de Santiago de Compostela Lugo Spain, Aquatic Animal Health (A2S) CIIMAR—University of Porto Porto Portugal
Oceano Fresco S.A Nazaré Portugal
Centre Nacional d'Anàlisi Genòmica (CNAG) Barcelona Spain, Universitat de Barcelona (UB) Barcelona Spain
University of Padova Padova Italy
IMC Foundation Sardinia Italy
Aquatic Animal Health (A2S) CIIMAR—University of Porto Porto Portugal

ABSTRACT 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 production of R . decussatus requires genomic resources to ascertain the genetic factors underlying resistance/tolerance to P. olseni i . 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. olseni i 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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Sponsoring Organization:: USDOE

OSTI ID:: 2566004

Journal Information:: Evolutionary Applications, Journal Name: Evolutionary Applications Journal Issue: 5 Vol. 18; ISSN 1752-4571

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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