Standards recommendations for the Earth BioGenome Project.

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

A chromosome-level genome assembly of the common eider, Somateria mollissima (Linnaeus, 1758).

The common eider, Somateria mollissima mollissima (Chordata; Aves; Anseriformes; Anatidae), is a large sea duck with a circumpolar distribution. We here describe a chromosome-level genome assembly from an individual female. The haplotype-resolved assembly contains one pseudo-haplotype spanning 1205 megabases (with both Z and W sex chromosomes) and one pseudo-haplotype spanning 1080 megabases. Most of these two assemblies (91.13% and 93.18%, respectively) are scaffolded into 32 autosomal chromosomal pseudomolecules plus Z and W for pseudo-haplotype one. The BUSCO completeness scores are 94.0% and 89.9%, respectively, and gene annotations of the assemblies identified 17,479 and 16,315 protein coding genes. Annotation of repetitive sequences classify 17.84 % and 14.62 % of pseudo-haplotype one and two, respectively, as repeats. The genome of the common eider will be a useful resource for the widely distributed northern species in light of climate change and anthropogenic threats.

The Earth BioGenome project: opportunities and challenges for plant genomics and conservation.

Sequencing them all. That is the ambitious goal of the recently launched Earth BioGenome project (Proceedings of the National Academy of Sciences of the United States of America, 115, 4325-4333), which aims to produce reference genomes for all eukaryotic species within the next decade. In this perspective, we discuss the opportunities of this project with a plant focus, but highlight also potential limitations. This includes the question of how to best capture all plant diversity, as the green taxon is one of the most complex clades in the tree of life, with over 300 000 species. For this, we highlight four key points: (i) the unique biological insights that could be gained from studying plants, (ii) their apparent underrepresentation in sequencing efforts given the number of threatened species, (iii) the necessity of phylogenomic methods that are aware of differences in genome complexity and quality, and (iv) the accounting for within-species genetic diversity and the historical aspect of conservation genetics.

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera).

Field-collected specimens were used to obtain nine high-quality genome assemblies from a total of 10 insect species native to prairies and savannas of central Illinois (USA): Mellilla xanthometata (Lepidoptera: Geometridae), Stenolophus ochropezus (Coleoptera: Carabidae), Forcipata loca (Hemiptera: Cicadellidae), Coelinius sp. (Hymenoptera: Braconidae), Thaumatomyia glabra (Diptera: Chloropidae), Brachynemurus abdominalus (Neuroptera: Myrmeleontidae), Catonia carolina (Hemiptera: Achilidae), Oncometopia orbona (Hemiptera: Cicadellidae), Flexamia atlantica (Hemiptera: Cicadellidae) and Stictocephala bisonia (Hemiptera: Membracidae). Sequencing library preparation from single specimens was successful despite extremely small DNA yields (<0.1 µg) for some samples. Additional sequencing and assembly workflows were adapted to each sample depending on the initial DNA yield. PacBio circular consensus (CCS/HiFi) or continuous long reads (CLR) libraries were used to sequence DNA fragments up to 50 kb in length, with Illumina sequenced linked-reads (TellSeq libraries) and Omni-C libraries used for scaffolding and gap-filling. Assembled genome sizes ranged from 135 MB to 3.2 GB. The number of assembled scaffolds ranged from 47 to >13,000, with the longest scaffold per assembly ranging from ~23 to 439 Mb. Genome completeness was high, with BUSCO scores ranging from 85.5% completeness for the largest genome (Stictocephala bisonia) to 98.8% completeness for the smallest genome (Coelinius sp.). The unique content was estimated using RepeatMasker and GenomeScope2, which ranged from 50.7% to 75.8% and roughly decreased with increasing genome size. Structural annotation predicted a range of 19,281-72,469 protein models for sequenced species. Sequencing costs per genome at the time ranged from US$3-5k, averaged ~1600 CPU-hours on a high-performance cluster and required approximately 14 h of bioinformatics analyses with samples using PacBio HiFi data. Most assemblies would benefit from further manual curation to correct possible scaffold misjoins and translocations suggested by off-diagonal or depleted signals in Omni-C contact maps.

Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life.

As genomic data transform our understanding of biodiversity, the Earth BioGenome Project (EBP) has set a goal of generating reference quality genome assemblies for all ~1.9 million described eukaryotic taxa. Meeting this goal requires coordination among many individual regional and taxon-focussed projects working under the EBP umbrella. Large-scale sequencing projects require ready access to validated genome-relevant metadata, such as genome sizes and karyotypes, but these data are dispersed across the literature, and directly measured values are lacking for most taxa. To meet these needs, we have developed Genomes on a Tree (GoaT), an Elasticsearch-powered datastore and search index for genome-relevant metadata and sequencing project plans and statuses. GoaT indexes publicly available metadata for all eukaryotic species and interpolates missing values through phylogenetic comparison. GoaT also holds target priority and sequencing status information for many projects affiliated to the EBP to aid project coordination. Metadata and status attributes in GoaT can be queried through a mature API, a web front end, and a command line interface. The web front end additionally provides summary visualisations for data exploration and reporting (see https://goat.genomehubs.org). GoaT currently holds direct or estimated values for over 70 taxon attributes and over 30 assembly attributes across 1.5 million eukaryotic species. The depth and breadth of curated data, frequent updates, and a versatile query interface make GoaT a powerful data aggregator and portal to explore and report underlying data for the eukaryotic tree of life. We illustrate this utility through a series of use cases from planning through to completion of a genome-sequencing project.

A sampling strategy for genome sequencing the British terrestrial arthropod fauna.

The Darwin Tree of Life (DToL) project aims to sequence and assemble high-quality genomes from all eukaryote species in Britain and Ireland, with the first phase of the project concentrating on family-level coverage plus species of particular ecological, biomedical or evolutionary interest. We summarise the processes involved in (1) assessing the UK arthropod fauna and the status of individual species on UK lists; (2) prioritising and collecting species for initial genome sequencing; (3) handling methods to ensure that high-quality genomic DNA is preserved; and (4) compiling standard operating procedures for processing specimens for genome sequencing, identification verification and voucher specimen curation. We briefly explore some lessons learned from the pilot phase of DToL and the impact of the Covid-19 pandemic.