# BYTE-Sea: the digital infrastructure of ATLASea, the French marine genome sequencing programme

Annie Lebreton, Loraine Brillet-Guéguen, Karine Massau, Alexandre Nicaise, Arthur Le Bars, Lucile Jeusset, Samuel Lalam, Alexandra Louis, Hugues Roest Crollius, Matéo Boudet, et al.

► To cite this version:

Annie Lebreton, Loraine Brillet-Guéguen, Karine Massau, Alexandre Nicaise, Arthur Le Bars, et al. "BYTE-Sea: the digital infrastructure of ATLASea, the French marine genome sequencing programme." JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. 2025. hal-05135947

HAL Id: hal-05135947

https://hal.science/hal-05135947v1

Submitted on 30 Jun 2025

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atlas
sea

# BYTE-Sea: the digital infrastructure of ATLASea, the French marine genome sequencing programme

Annie LEBRETON¹, BYTE-Sea consortium² and Erwan CORRE¹,³

1. ABiMS bioinformatics platform, FR2424, CNRS/Sorbonne Université, Station Biologique de Roscoff, 29680, Roscoff, France

2. BYTE-Sea Consortium: https://gitlab.com/pepr-atlasea/byte-sea_consortium

3. IFB-core, Institut Français de Bioinformatique (IFB), CNRS, INSERM, INRAE, CEA, 94800 Villejuif, France

Corresponding authors: annie.lebreton@sb-roscoff.fr; erwan.corre@france-bioinformatique.fr

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PROGRAMME
DE RECHERCHE
GÉNOMES MARINS

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## ATLASea Program - an atlas of marine genomes

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In the marine sciences, exploring diversity represents a major challenge, as only 10% of marine species are known and few high-quality genomes of marine organisms have been made available to the scientific community. The ATLASea program (PEPR 2023-2030, led by CNRS and CEA) proposes to decipher and exploit the colossal wealth of information from marine biodiversity along the French coast through the sequencing of 4500 genomes of marine species collected in mainland France and the French overseas territories. The Weel-Sea targeted project led by the CNRS coordinates and disseminates the results of the three other targeted projects : DIVE-Sea led by the MNHN, in charge of sampling and sample management, SEQ-Sea led by the CEA, in charge of sample processing to structurally annotated assembly submission and BYTE-Sea led by IFB, structured in 6 work packages, in charge of dissemination and interoperability of the genomic data.

Program
progress status

2025

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● French ZEE

● sampling site

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>1500
species sampled
(27 phyla)

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>400 sequencing
in progress

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>100 genomes
publicly accessible

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IT structure

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Portals v1

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Analysis tools & data

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## BYTE-Sea Work packages (WP)

### WP1: Infrastructure for storage, computing and software

<table><tr><td>Partners</td><td colspan="2">IFB</td><td>IFREMER</td></tr><tr><td>Infrastructures</td><td>BigOuest by ABiMS & GenOuest</td><td>IFB Core Cluster</td><td>DATARMOR</td></tr><tr><td>Storage</td><td colspan="3">Data access and Data Ring</td></tr><tr><td>Computing</td><td colspan="3">Functional annotation & comparative genomics</td></tr><tr><td>Software & services</td><td colspan="3">GitLab repository : Tools and SOP</td></tr><tr><td>Database</td><td colspan="3">Data integrity</td></tr><tr><td>Portal</td><td colspan="3">Services : browsers, web site, API...</td></tr></table>

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PEPR ATLASea

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gitlab.com/pepr-atlasea

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### WP2: ATLASea database

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### WP3: ATLASea portals for data and analysis tools

#### Tracking portal (private)

Tracking portal for the stakeholders
- provide detailed info on the sequencing progress
In production at IFREMER

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#### Data portal

https://portal.atlasea.fr

Tracking portal for the community, gives access to data generated
- provide multiple info on the sampled organisms from collection to publicly available assembly. In production at ABiMS and IFB

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#### Genome portal

Provide access to analysis interface for each genome sequenced in the ATLASea project (BLAST, JBrowse, data access). Automatised with ATLARIS pipeline.

#### Marine genome portal

Provide access to analysis interface for genomic comparison of all marine species publicly available. Three entry points will be developed
- Environmental genomics
- Functional genomics
- Evolutionary genomics
- expected prototype

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### WP4: Automatic functional annotation and expert annotation

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### WP5: Comparative Marine Genomics

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**Ongoing:** Tests to scale up the orthogroup generation. Test of impact of the number of species provided during incrementation, the order of insertion, their phylogeny... OthoFinder3 unstable incrementation. FastOMA ongoing test.

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### WP6: Citizen Annotation

**Manual curation of genome annotation**

**Citizens**

High school / undergraduate students

Introduction to the world of genomics

**Scientific output**

Guided and gamified curation web UI
Release of improved gene annotation

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### Calls for expressions of interest !
2025

Study of...

Ecosystems subject
to invasions

Metabolic
pathways

The Institut Français de Bioinformatique (IFB) is funded by France 2030, via the Agence Nationale de la Recherche grants ANR-11-INBS-0013 (PIA1 RENABI-IFB), and ANR-21-ESRE-0048 (PIA3 ESR/Equipex+ MUDIS4LS). IFB BYTESea project is funded by FRANCE 2030, via Agence Nationale de la Recherche grant 22-EXAT-0004.

Phytoplasms images from phytop.org by T. Michael Keesey, Nix Illustration. Harold N Eyster. Maxime Dahirel. Matt Crook.

https://creativecommons.org/licenses/by-nc/3.0/

ABiMS

GO

GenOuest

Ifremer

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SeBiMER
Bioinformatique marine

DYOGEN

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IFB

INSTITUT FRANÇAIS DE BIOINFORMATIQUE

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FRANCE

cnrs

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Inserm

INRAE

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FRANCE

2030