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ERGA-BGE reference genome of Holothuria (Platyperona) sanctori: a sea cucumber from the Mediterranean Sea

Katerina Vasileiadou ,
Thanos Dailianis ,
Grigorios Skouradakis ,
Emmanouela Vernadou
,
Danae Karakasi
,
Astrid Böhne ,
Rita Monteiro ,
Rosa Fernández ,
Nuria Escudero
,
Tereza Manousaki
,
Genomescope Sequencing Team
,
Alice Moussy ,
Corinne Cruaud
,
Karine Labadie
,
Lola Demirdjian ,
Adama Ndar
,
Patrick Wincker
,
Pedro H Oliveira ,
Jean-Marc Aury
,
Chiara Bortoluzzi

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Published

January 27, 2026

DOI

https://doi.org/10.12688/openreseurope.20841.2

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February 3, 2026 (Version of Record 3.0)
January 27, 2026 (Version of Record 2.0)
September 25, 2025 (Version of Record 1.0)

Horizon Europe

Agence nationale de la recherche

Grant ID(s): ANR-10-INBS-09-08, ANR-22-EXAT-0003-SEQ-Sea
UK Research and Innovation (UKRI)
European Commission

Grant ID(s): 101059492
Swiss State Secretariat for Education, Research and Innovation (SERI)

Grant ID(s): 22.00173, 24.00054

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Holothuria (Platyperona) sanctori, genome assembly, European Reference Genome Atlas, Biodiversity Genomics Europe, Earth Biogenome Project, Holothuriidae, sea cucumber

Abstract

Holothuria sanctori is a common species of sea cucumber found in the Mediterranean Sea and the Northeast Atlantic Ocean. It typically inhabits shallow rocky and sandy seabeds, where it plays a key ecological role as a sediment engineer processing organic matter ts and thereby contributing to nutrient cycling. As an edible species, H. sanctori is harvested in several countries. Although it is currently listed as a species of "Least Concern" on the IUCN Red List, the absence of a regulatory framework to prevent overexploitation poses a risk of population decline. Given its ecological significance and economic value , H. sanctori has become a focal point in both marine conservation and aquaculture research. The entirety of the genome sequence was assembled into 23 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 1.2 Gb, composed of 135 contigs and 46 scaffolds, with contig and scaffold N50 values of 19.9 Mb and 50.7 Mb, respectively.

Corresponding author

Chiara Bortoluzzi

0000-0001-6589-6635

chiara.bortoluzzi@sib.swiss

Grant information

Biodiversity Genomics Europe (Grant no.101059492) is funded by Horizon Europe under the Biodiversity, Circular Economy and Environment call (REA.B.3); co-funded by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract numbers 22.00173 and 24.00054; and by the UK Research and Innovation (UKRI) under the Department for Business, Energy and Industrial Strategy’s Horizon Europe Guarantee Scheme. This work was supported by the Genoscope, the Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), France Génomique (ANR-10-INBS-09-08), and the exploratory research programme ‘ATLASea: Atlas of marine genomes and its targeted project SEQ-Sea (ANR-22-EXAT-0003-SEQ-Sea).

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

© 2026 Katerina Vasileiadou (Co-Author); Thanos Dailianis (Co-Author); Grigorios Skouradakis (Co-Author); Emmanouela Vernadou (Co-Author); Danae Karakasi (Co-Author); Astrid Böhne (Co-Author); Rita Monteiro (Co-Author); Rosa Fernández (Co-Author); Nuria Escudero (Co-Author); Tereza Manousaki (Co-Author); Genomescope Sequencing Team (Co-Author); Alice Moussy (Co-Author); Corinne Cruaud (Co-Author); Karine Labadie (Co-Author); Lola Demirdjian (Co-Author); Adama Ndar (Co-Author); Patrick Wincker (Co-Author); Pedro H Oliveira (Co-Author); Jean-Marc Aury (Co-Author); Chiara Bortoluzzi (Corresponding Author, Co-Author)

This work is licensed under a Creative Commons Attribution 4.0 International License.

First version published

September 25, 2025 (https://doi.org/10.12688/openreseurope.20841.1)

Latest version published

February 3, 2026 (https://doi.org/10.12688/openreseurope.20841.3)

Revised

Amendment

In this new version of the Genome Report of Holothuria sanctori, we addressed all reviewers comments by expanding a few sections of the Genome Report.

Introduction

Holothuria (Platyperona) sanctori is distributed throughout the northeastern Atlantic Ocean and is particularly common in the Mediterranean Sea. This nocturnal species inhabits shallow rocky substrates at depths of up to 70 meters (Navarro et al., 2012). Holuthuria sanctori has a cylindrical body that is dark brown in colour, with the posterior end noticeably wider than the anterior. Its thick skin is covered with prominent dark papillae, each encircled by a whitish ring at the base. The species possesses twenty peltate tentacles and features three rows of podia and densely arranged tube feet on its ventral side (Moussa & Wirawati, 2018). While not present in all species within the Holothuriidae family (Caulier et al., 2016), this sea cucumber is equipped with Cuvierian tubules, which serve as defensive structures. Phylogenetic analysis suggests that H. sanctori belongs to a deep evolutionary lineage dating back approximately 155 million years and it forms a distinct clade from other Mediterranean Holothuriidae species (Borrero-Pérez et al., 2010).

The sea cucumber Holothuria sanctori is a deposit feeder that primarily consumes organic matter. It ingests large amounts of sediment, extracting nutrients from bacteria, fungi, and detritus embedded within the particles. Through this activity, it plays a key ecological role as a bioturbator, contributing to sediment oxygenation and overall seabed health. H. sanctori is harvested in the Mediterranean region for its saponins—bioactive compounds likely produced as a chemical defence mechanism. These saponins have attracted pharmaceutical interest due to their anti-tumoral, anti-inflammatory, and antibacterial properties (Caulier et al., 2016). Additionally, the species holds significant value in aquaculture. Its ability to consume high concentrations of organic matter and filter nitrogen enables it to restore sediment quality beneath fish cages, supporting more sustainable farming practices (Moussa & Wirawati, 2018). Holothuria sanctori plays a crucial role in maintaining the stability and ecological integrity of marine ecosystems. Its economic importance in both pharmaceutical and aquaculture sectors highlight the need for effective conservation strategies to ensure the sustainability of its populations in the Mediterranean.

The generation of this reference resource was coordinated by the European Reference Genome Atlas (ERGA) initiative’s Biodiversity Genomics Europe (BGE) project, supporting ERGA’s aims of promoting transnational cooperation to promote advances in the application of genomics technologies to protect and restore biodiversity (Mazzoni et al., 2023).

Materials & methods

ERGA's sequencing strategy includes Oxford Nanopore Technology (ONT) and/or Pacific Biosciences (PacBio) for long-read sequencing, along with Hi-C sequencing for chromosomal architecture, Illumina Paired-End (PE) for polishing (i.e. recommended for ONT-only assemblies), and RNA sequencing for transcriptome profiling, to facilitate genome assembly and annotation.

Sample and sampling information

On 13 July 2023, Katerina Vasileiadou sampled one specimen of Holothuria sanctori (sex unknown). The specimen was identified by Katerina Vasileiadou in Lasithi, Elounda bay, Crete, Greece based on the characteristics described by Moussa & Wirawati (2018). Sampling was performed under permission ΥΠΕΝ/ΔΔΔ/34284/1131 issued by the Ministry for Environment and Energy, Secretariat General for Natural Environment & Water, Directorate General for Forests & Forest Environment, Directorate for Forest Management, Greece.

Tissues were removed from the living specimen following the legal framework for scientific specimens, flash frozen in liquid nitrogen, and stored at -80°C until DNA extraction. The specimen was euthanized following the Greek and EU legal framework.

Vouchering information

Physical reference materials for the here sequenced specimen have been deposited in the Natural History Museum of Crete https://www.nhmc.uoc.gr/en/ under accession number NHMC.65.25.

Frozen reference tissue material of the here sequenced specimen is available from the same individual at the Biobank of the Natural History Museum of Crete https://www.nhmc.uoc.gr/en/ under the voucher ID NHMC.65.25.

Genetic information

The estimated genome size, based on ancestral taxa, is 2.25 Gb. This is a diploid genome with a haploid number of 21 chromosomes (2n=42). All information for this species was retrieved from Genomes on a Tree (Challis et al., 2023).

DNA/RNA processing

DNA was extracted from 300 mg of intestinal tissue using a Genomic-tip 100/G Kit (QIAGEN, MD, USA) following manufacturer instructions. DNA fragment size selection was performed using Short Read Eliminator (PacBio, CA, USA). Quantification was performed using a Qubit dsDNA HS Assay kit (Thermo Fisher Scientific) and integrity was assessed in a FemtoPulse system (Agilent). DNA was stored at 4 °C. RNA was extracted from intestinal tissue (50 mg) using the RNeasy Plus Universal kit (Qiagen) following manufacturer instructions. Residual genomic DNA was removed with 6U of TURBO DNase (2 U/μL) (Thermo Fisher Scientific). Quantification was performed using a Qubit RNA HS Assay kit and integrity was assessed in a Bioanalyzer system (Agilent). RNA was stored at -80 °C.

Library preparation and sequencing

Long-read DNA libraries were prepared with the SMRTbell prep kit 3.0 following manufacturers' instructions and sequenced on a Revio system (PacBio). Hi-C libraries were generated from intestinal tissue (50 mg) using the Arima High Coverage HiC kit (following the Animal Tissues low input protocol v01) and sequenced on a NovaSeq X Plus instrument (Illumina) with 2x150 bp read length. Poly(A) RNA-Seq libraries were constructed using the Illumina Stranded mRNA Prep, Ligation Prep kit (Illumina) and sequenced on an Illumina NovaSeq X Plus instrument (Illumina) with 2x150 bp read length.

In total 90x PacBio HiFi and 47x HiC data were sequenced to generate the assembly.

Genome assembly methods

The genome of Dendarus foraminosus was assembled using the Genoscope GALOP pipeline (https://workflowhub.eu/workflows/1200). Briefly, raw PacBio HiFi reads were assembled using Hifiasm v0.19.8-r603 (Cheng et al., 2021). Remaining allelic duplications were removed using purge_dups v1.2.5 (Guan et al., 2020) with default parameters and the proposed cutoffs. The purged assembly was scaffolded using YaHS v1.2.2 (Zhou et al., 2023) and assembled scaffolds were then curated through manual inspection using PretextView v0.2.5 to remove false joins and incorporate sequences not automatically scaffolded into their respective locations within the chromosomal pseudomolecules. This step included the removal of a bacterial contig and a substantial number of duplications. Chromosome-scale scaffolds confirmed by Hi-C data were named in order of size. The mitochondrial genome was assembled as one circular contig using Oatk v1.0 (Zhou et al., 2024) and included in the released assembly. Summary analysis of the released assembly was performed using the ERGA-BGE Genome Report ASM Galaxy workflow (https://doi.org/10.48546/workflowhub.workflow.1104.1).

Results

Genome assembly

The genome assembly has a total length of 1,171,681,863 bp in 46 scaffolds including the mitogenome (Figure 1 & Figure 2), with a GC content of 39.4%. The assembly has a contig N50 of 19,932,592 bp and L50 of 21 and a scaffold N50 of 50,699,391 bp and L50 of 10. The assembly has a total of 89 gaps, totalling 15.0 kb in cumulative size. The single-copy gene content analysis using the Eukaryota database with BUSCO (Manni et al., 2021) resulted in 98.4% completeness (97.6% single and 0.8% duplicated). 73.3% of reads k-mers were present in the assembly and the assembly has a base accuracy Quality Value (QV) of 62.3 as calculated by Merqury (Rhie et al., 2020).

Figure 1. Snail plot summary of assembly statistics.

The main plot is divided into 1,000 size-ordered bins around the circumference, with each bin representing 0.1% of the 1,171,681,863 bp assembly including the mitochondrial genome. The distribution of sequence lengths is shown in dark grey, with the plot radius scaled to the longest sequence present in the assembly (110 Mb, shown in red). Orange and pale-orange arcs show the scaffold N50 and N90 sequence lengths (50,699,391 and 39,181,847 bp), respectively. The pale grey spiral shows the cumulative sequence count on a log-scale, with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT, and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated, and missing BUSCO genes found in the assembled genome from the Eukaryota database (odb10) is shown in the top right.

Figure 2. Hi-C contact map showing spatial interactions between regions of the genome.

The diagonal corresponds to intra-chromosomal contacts, depicting chromosome boundaries. The frequency of contacts is shown on a logarithmic heatmap scale. Hi-C matrix bins were merged into a 150 kb bin size for plotting. The Hi-C contact map shows the 23 autosomes and the mitochondrial genome (GenBank accession: OZ199603.1).

Data availability

H. sanctori and the related genomic study were assigned to Tree of Life ID (ToLID) 'ehHolSanc2' and all sample, sequence, and assembly information are available under the umbrella BioProject PRJEB77253. The sample information is available at the following BioSample accessions: SAMEA115125951 and SAMEA115125945. The genome assembly is accessible from ENA under accession number GCA_964304565.2 and the annotated genome will be made available through the Ensembl website (https://projects.ensembl.org/erga-bge/).

Sequencing data produced as part of this project are available from ENA at the following accessions: ERX14170116, ERX14170117, ERX13549354, ERX13549355, ERX14096391, ERX14096392, and ERX14096393. Documentation related to the genome assembly and curation can be found in the ERGA Assembly Report (EAR) document available at https://github.com/ERGA-consortium/EARs/tree/main/Assembly_Reports/Holothuria_sanctori/ehHolSanc2. Further details and data about the project are hosted on the ERGA portal at https://portal.erga-biodiversity.eu/data_portal/491806.

Author contributions

KV and TM coordinated the project; TD, GS and EV collected the species; TD, GS and EV identified the species; KV, TM, and DK sampled and preserved biological material and provided metadata; AsB, RM, RF, and NE provided support in sampling, shipping of biological material, metadata collection, and management; GST extracted DNA, prepared libraries, and performed sequencing under the supervision of AM, CC, KL, PHO, and PW; LD and AN performed genome assembly and curation under the supervision of JMA; CB generated the analysis and report. All authors contributed to the writing, review, and editing of this genome note and read and approved the final version. This work is part of the species assigned to Genoscope, which was instrumental in the wet lab, sequencing, and assembly processes, and represents a key contribution to BGE's outputs.

Author information

Members of the Genoscope Sequencing Team are listed here: https://zenodo.org/records/14611490.

Acknowledgements

We acknowledge the support of the Freiburg Galaxy Team: Saim Momin and Björn Grüning, Bioinformatics, University of Freiburg (Germany), funded by the German Federal Ministry of Education and Research BMBF grant 031 A538A de.NBI-RBC and the Ministry of Science, Research and the Arts Baden-Württemberg (MWK) within the framework of LIBIS/de.NBI Freiburg. We would like to acknowledge the assembly reviewer, Fernando Cruz from the Centro Nacional de Análisis Genómic (CNAG).

Faculty Opinions recommended

References

Borrero-Pérez GH, Gómez-Zurita J, González-Wangüemert M, et al.: Molecular systematics of the genus Holothuria in the Mediterranean and Northeastern Atlantic and a molecular clock for the diversification of the Holothuriidae (Echinodermata: Holothuroidea). Mol Phylogenet Evol. 2010; 57(2): 899–906. PubMed Abstract | Publisher Full Text
Caulier G, Mezali K, Soualili DL, et al.: Chemical characterization of saponins contained in the body wall and the Cuvierian tubules of the sea cucumber Holothuria (Platyperona) sanctori (Delle Chiaje, 1823). Biochem Syst Ecol. 2016; 68: 119–127. Publisher Full Text
Challis R, Kumar S, Sotero-Caio C, et al.: Genomes on a Tree (GoaT): a versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic Tree of Life [version 1; peer review: 2 approved]. Wellcome Open Res. 2023; 8: 24. PubMed Abstract | Publisher Full Text | Free Full Text
Cheng H, Concepcion GT, Feng X, et al.: Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021; 18(2): 170–175. PubMed Abstract | Publisher Full Text | Free Full Text
Guan D, McCarthy SA, Wood J, et al.: Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020; 36(9): 2896–2898. PubMed Abstract | Publisher Full Text | Free Full Text
Manni M, Berkeley MR, Seppey M, et al.: BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021; 38(10): 4647–4654. PubMed Abstract | Publisher Full Text | Free Full Text
Mazzoni CJ, Ciofi C, Waterhouse RM: Biodiversity: an atlas of European reference genomes. Nature. 2023; 619(7969): 252. PubMed Abstract | Publisher Full Text
Moussa R, Wirawati I: Observations on some biological characteristics of Holothuria polii and Holothuria sanctori from Mediterranean Egypt. Int J Fish Aquat Stud. 2018; 6(3): 351–357. Reference Source
Navarro PG, Garcia-Sanz S, Tuya F: Reproductive biology of the sea cucumber Holothuria sanctori (Echinodermata: Holothuroidea). Sci Mar. 2012; 76(4): 741–752. Publisher Full Text
Rhie A, Walenz BP, Koren S, et al.: Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020; 21(1): 245. PubMed Abstract | Publisher Full Text | Free Full Text
Zhou C, Brown M, Blaxter M, et al.: Oatk: a de novo assembly tool for complex plant organelle genomes. bioRxiv. 2024; 2024–10. Publisher Full Text
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Comments

Publication information

Section

Data Note

Published

January 27, 2026

DOI

https://doi.org/10.12688/openreseurope.20841.2

Versions

February 3, 2026 (Version of Record 3.0)
January 27, 2026 (Version of Record 2.0)
September 25, 2025 (Version of Record 1.0)

Included in

Horizon Europe

Funding data

Agence nationale de la recherche

Grant ID(s): ANR-10-INBS-09-08, ANR-22-EXAT-0003-SEQ-Sea
UK Research and Innovation (UKRI)
European Commission

Grant ID(s): 101059492
Swiss State Secretariat for Education, Research and Innovation (SERI)

Grant ID(s): 22.00173, 24.00054

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Keywords

Holothuria (Platyperona) sanctori, genome assembly, European Reference Genome Atlas, Biodiversity Genomics Europe, Earth Biogenome Project, Holothuriidae, sea cucumber

Comments

Katerina Vasileiadou

Institute of Oceanography, Hellenic Centre for Marine Research, Heraklion, Crete, 70014, Greece

Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, 70014, Greece

Roles

Co-Author, Investigation, Resources, Writing – Original Draft Preparation, Writing – Review & Editing

0000-0002-5057-6417

kvasileiadou@hcmr.gr

Thanos Dailianis

Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, 70014, Greece

Roles

Co-Author, Investigation, Resources, Writing – Review & Editing

0000-0002-4102-9331

thanosd@hcmr.gr

Grigorios Skouradakis

Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, 70014, Greece

Roles

Co-Author, Investigation, Resources, Writing – Review & Editing

0000-0002-8482-460X

gskouradakis@hcmr.gr

Emmanouela Vernadou

Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, 70014, Greece

Roles

Co-Author, Resources

e.vernadou@hcmr.gr

Danae Karakasi

Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion, GR-70013, Greece

Natural History Museum of Crete, School of Sciences and Engineering,, University of Crete, Knossos Avenue, Heraklion, GR-71409, Greece

Roles

Co-Author, Investigation, Resources, Writing – Review & Editing

danae@nhmc.uoc.gr

Astrid Böhne

Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, Museum Koenig Bonn, Bonn, 53113, Germany

Roles

Co-Author, Methodology, Project Administration, Supervision, Writing – Review & Editing

0000-0002-1284-3115

A.Boehne@leibniz-lib.de

Rita Monteiro

Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, Museum Koenig Bonn, Bonn, 53113, Germany

Roles

Co-Author, Methodology, Project Administration, Supervision, Writing – Review & Editing

0000-0003-1374-4474

R.Monteiro@leibniz-lib.de

Rosa Fernández

Metazoa Phylogenomics Lab, Institute for Evolutionary Biology (CSIC-UPF). Passeig marítim de la Barceloneta 37-49., Barcelona, 08003, Spain

Roles

Co-Author, Methodology, Project Administration, Supervision, Writing – Review & Editing

0000-0002-4719-6640

rmfernandezgarcia00@gmail.com

Nuria Escudero

Metazoa Phylogenomics Lab, Institute for Evolutionary Biology (CSIC-UPF). Passeig marítim de la Barceloneta 37-49., Barcelona, 08003, Spain

Roles

Co-Author, Methodology, Project Administration, Supervision, Writing – Review & Editing

nuria.escudero@ibe.upf-csic.es

Tereza Manousaki

Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, 70014, Greece

Roles

Co-Author, Methodology, Project Administration, Supervision, Writing – Review & Editing

tereza@hcmr.gr

Genomescope Sequencing Team

Roles

Co-Author

admin@ore.testing.publicknowledgeproject.org

Alice Moussy

Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France

Roles

Co-Author, Investigation, Supervision, Writing – Review & Editing

0009-0006-3405-7074

amoussy@genoscope.cns.fr

Corinne Cruaud

Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France

Roles

Co-Author, Investigation, Supervision, Writing – Review & Editing

cruaud@genoscope.cns.fr

Karine Labadie

Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France

Roles

Co-Author, Investigation, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing

klabadie@genoscope.cns.fr