Specimen and sample metadata standards for biodiversity genomics: a proposal from the Darwin Tree of Life project

Abstract

The vision of the Earth BioGenome Project1 is to complete reference genomes for all of the planet’s ~2M described eukaryotic species in the coming decade. To contribute to this global endeavour, the Darwin Tree of Life Project (DToL2) was launched in 2019 with the aim of generating complete genomes for the ~70k described eukaryotic species that can be found in Britain and Ireland. One of the early tasks of the DToL project was to determine, define, and standardise the important metadata that must accompany every sample contributing to this ambitious project. This ensures high-quality contextual information is available for the associated data, enabling a richer set of information upon which to search and filter datasets as well as enabling interoperability between datasets used for downstream analysis. Here we describe some of the key factors we considered in the process of determining, defining, and documenting the metadata required for DToL project samples. The manifest and Standard Operating Procedure that are referred to throughout this paper are likely to be useful for other projects, and we encourage re-use while maintaining the standards and rules set out here.

Genome sequence ofOphryocystis elektroscirrha, an apicomplexan parasite of monarch butterflies: cryptic diversity and response to host-sequestered plant chemicals

“…However, given that repetitive sequences such as transposable elements (TEs) may be shared between host and parasite, we do not expect a complete lack of homology between parasite and host scaffolds. Based on visual inspection of the data, scaffolds were defined as confidently representing Ophryocystis if (1) alignments to O. elektroscirrha comprised at least half the scaffold length (after accounting for overlapping alignments), and (2) alignments to the uninfected D. chrysippus comprised less than a third of the scaffold length aligned to O. elektroscirrha .…”

“…Eukaryotic genomics has overwhelmingly focused on multicellular organisms (1), in spite of the staggering diversity of unicellular eukaryotes. Furthermore, although animal genome sequencing efforts are increasingly aiming to systematically characterize extant species' genomes (2)(3)(4), when unicellular eukaryotes are studied, it is still mostly in connection to human health or economic interests; in other words, by putting most of the effort into studying pathogens of human-importance, the scientific community has left large gaps in our knowledge of these ubiquitous organisms.…”

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

“…Five genomes exceeded the recommended metric Gaps/Gbp 23 as they all had >1,000 remaining ( Argentina silus (fArgSil1), Knipowitschia panizzae (fKniPan1), Ammodytes marinus (fAmmMar1), Salvelinus alpinus (fSalAlp1) and Vipera ursinii rakosiensis (rVipUrs1)). Despite this, for all the completed assemblies, Ns accounted for less than 0.05% of the genome, with the exception of Mustela lutreola (mMusLut1).…”

“…During sample collection important metadata concerning the species collection event were expected to be documented by the sample collector. To standardise this process a robust metadata schema was developed, using the DToL metadata schema as a foundation 23 . The tailored ERGA schema, including unique ERGA specimen identifiers as well as ToLID (https://id.tol.sanger.ac.uk/), was codified into a .csv formatted ‘manifest’ and made publicly available (https://github.com/ERGA-consortium/ERGA-sample-manifest).…”

The European Nucleotide Archive in 2022

“…We have also seen success through our biodiversity collaborations. For example, the COPO service ( 8 ) developed at the Earlham Institute in the UK provides a centralised service for sample metadata management including for many biodiversity monitoring projects such as the Darwin Tree of Life (DToL) ( 9 ) and the Aquatic Symbiosis Genomics (ASG) ( 10 ) projects. Both these projects aim to generate sequence data and reference genomes for a large set of organisms and have required a large collaborative effort to collect and coordinate samples from different locations, collected and identified by many different people.…”