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

Abstract

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.

Unveiling the genetic blueprint of a desert scorpion: A chromosome-level genome ofHadrurus arizonensisprovides the first reference for Parvorder Iurida

“…Following contaminant screening, 63,023 reads (0.46%) were removed (Table S1). The k-mer based genome size estimation was 2.31 Gb from 109.96 Gb of read data (47.6x), double the 1.1 Gb GoaT estimation (Challis et al . 2023) (Table S1).…”

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

“…The goal of the EBP is to create a global network of biodiversity genomics researchers that share a mission to produce a database of openly accessible, standardised, and complete reference resources that span the whole eukaryotic phylogenetic tree. The project has a three-phase approach and to date (Phase I) has produced ~1,213 reference genomes for species across ~1,010 genera 16 . However the rate of production is fast increasing, for instance in 2022 over 316 reference genomes were produced and in the coming years the rate is estimated to increase by at least 10 fold.…”

“…We developed the current portal rapidly to support the goals of the pilot test, but it will be continually and iteratively improved to enhance usability, for example by potentially adding species imagery and distribution ranges, Ensembl 38 and community annotations, interactive geographic map searches, and cross referencing to key resources such as the Global Biodiversity Information Facility (https://www.gbif.org/) and climate data. Progress data is continuously shared through the portal’s public tracking pages (https://portal.erga-biodiversity.eu/status_tracking) and the GoAT database 16 https://goat.genomehubs.org/projects/ERGA-PIL).…”

The BioGenome Portal: a web-based platform for biodiversity genomics data management

“…These projects (or even the nodes within a project) are operationally independent and carry out all of the steps of the genome sequencing process autonomously: from the collection of the biological samples to the production of the genome assembly. The EBP uses Genomes on a Tree (GoaT, (7)) for coordination. GoaT is a centralized resource sponsored by Tree of Life programme (https://www.sanger.ac.uk/programme/tree-of-life/) that collates observed and estimated genome-relevant metadata—including genome sizes and karyotypes—for eukaryotic species, and that also holds declarations of current and planned activity across the EBP nodes.…”