The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Abstract

A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

Fig. 1

. Establishing an inclusive, accessible, distributed and pan-European genomic infrastructure that could support the streamlined and scalable production of genomic resources for all European species.

Fig. 2. Sample, country and partnering institution distribution across Europe.

a Taxonomic distribution of the species included into infrastructure testing. b Top: Distribution of sample ambassadors per participating country. Bottom-left: self identified sex distribution across sample ambassadors, Bottom-right: frequency of genome teams that have international collaborators i.e. collaborators that are outside of the country of origin that the sample was obtained from. c Map illustrating the distribution of sampling localities, cryopreserved specimens, collections holding vouchered specimens, sequencing library preparation hubs and sequencing facilities across Europe.

Fig. 3. Pilot test data production per species progression.

a total data production progress across all 98 species included, noting that data not planned/required for 12 species for proximity ligation, and 15 species for annotation data. b species distribution of species with genome assemblies available, both draft and curated assemblies are shown here. The data-type distribution for these species is also supplied. See Supplementary Fig. 3 for complete species tree.

Fig. 4. Quality control and status of the 38 genome assemblies evaluated.

a Genome assemblies are represented according to their Scaffold N50 (y-axis, log₁₀) and number of the longest scaffolds that comprise at least 95% of the assembly (x-axis, log₂). Bubble size is proportional to assembly span. Empty bubbles depict HiFi-based genomes, while full bubbles are ONT-based. Colours are according to assembly status (Curated, Pre-curation, Non-final draft). Lower values for both axes indicate better assembly contiguity. Assemblies not reaching the EBP-recommended One Megabase Contig N50 (log₁₀1,000,000 = 6) or 10 Megabase Scaffold N50 (log₁₀10,000,000 = 7) here a proxy for chromosome-level scaffolds are labelled with their ToLIDs* (https://id.tol.sanger.ac.uk/). b Completed HiFi- and ONT-based genomes assemblies are represented according to their Quality value (QV, y-axis) and number of gaps per Gbp (log₁₀, x-axis). The bubble size is proportional to assembly size. Colour grade of the bubbles is according to the K-mer completeness score. ToLIDs are reported for the assemblies that are below the recommended EBP metric for QV (40), Gaps/Gbp (log₁₀1000 = 3) or K-mer completeness (90%). Quality values are calculated differently for HiFi-based assemblies than for ONT-based assemblies and should not be compared directly. c BUSCO completeness scores for genome assemblies with ‘Curated’ and ‘Pre-curation’ status. Using two orthologs databases, one for a more recent last common ancestor encompassing related species (blue), and one for all eukaryotes (grey), we seek a more comprehensive estimation of the assembly completeness. Number of single-copy orthologs present on each database is reported. *Briefly, a ToLID is a unique identifier for an individual organism within a species sampled for genome sequencing, consisting of one or two lowercase letters for high-level taxonomic rank and clade, respectively, followed by three letters for genus and species each. Thus, within insects (i), the Hemiptera (i) includes Andrena humilis (iyAndHumi1) and Osmia cornuta (iyOsmCorn1). The Coleoptera (c) contains Carabus granulatus (icCarGran1), C. intricatus (icCarIntr1), and Leptodirus hochenwarti (icLepHoch2). Ephemeroptera (e) features Epeorus assimilis (ieEpeAssi1), and among Strepsiptera (v) it is found Stylops ater (ivStyAter1). Lepidoptera (l) includes Coenonympha glycerion (ilCoeGlyc1), Helleia helle (ilHelHell1), and Parnassius mnemosyne (ilParMnem1). Within the fungi (g), Agaricomycetes (f) are represented by Spongipellis delectans (gfSpoDele1). For sponges (o), Demospongiae (d) includes Phakellia ventilabrum (odPhaVent1), and among algae (u), Heterokontophyta (o) are represented by Phaeosaccion multiseriatum (uoPhaMult1). The fishes (f) include Alburnus alburnus (fAlbAlb2), Ammodytes marinus (fAmmMar1), Anaecypris hispanica (fAnaHis1), Argentina silus (fArgSil1), Knipowitschia panizzae (fKniPan1), Perca sp.‘yellow fin Alpine’ (fPerYfa1), Salvelinus alpinus (fSalAlp1), Silurus aristotelis (fSilAri1), Solea solea (fSolSol8), Tripterygion tripteronotum (fTriTrp1), and Zingel asper (fZinAsp1). Birds (b) are represented by Haliaeetus albicilla (bHalAlb1), Oenanthe leucura (bOenLec1), and Tetrao urogallus (bTetUro2). Mammals (m) include Canis aureus (mCanAur2), Chionomys nivalis (mChiNiv1), Lepus granatensis (mLepGra1), Lepus europaeus (mLepEur2), and Mustela lutreola (mMusLut1). Among reptiles (r) is Vipera ursinii (rVipUrs1). Within dicotyledons (d), the Ericales (d) include Hottonia palustris (ddHotPalu1), and Rosales and Fabales (r) features Prunus brigantina (drPruBrig1) and Trifolium dubium (drTriDubi1), respectively. Finally, among ‘other chordates’ (k), Ascidiacea (a) includes Botryllus schlosseri (kaBotSchl2), while in the category ‘other animal phyla’ (t), Nematomorpha (f) is exemplified by Gordionus montsenyensis (tfGorSpeb1).