Toward standardization in arthropod and biodiversity genome projects

In recent years, many high-quality reference genome sequences for arthropod species have been generated. Although most genome papers describe their protocols and metrics, no consensus exists on the data that should be included in genome reports. Here, we review current standards across seven key stages of an arthropod genome project (budgeting, sourcing and vouchering, sample preparation and sequencing, genome assembly, analysis reproducibility, databasing, and genome annotation) and identify persistent gaps in standards as well as their implementation. To assess current standards reporting in the community, we surveyed 100 arthropod genome papers published in 2024. The use of long reads to assemble highly contiguous arthropod genomes is now standard practice when adequate input DNA is available, and basic assembly contiguity and conserved gene content statistics are consistently reported. However, there is less standardization in pre- and post-assembly procedures and metrics. When comparing Darwin Tree of Life (DToL) genome notes to other journals, publications from the latter group were less likely to describe compliance with ethical collection practices, sample vouchering, post-assembly curation steps, and assembly quality metrics beyond basic contiguity and completeness values. Genome annotation practices are highly variable: some genome note formats do not explicitly require annotation, and while the reporting rate of protein-coding gene annotations is higher in non-DToL publications, the submission rate of annotations to centralized sequence databases is much lower. Our findings highlight critical opportunities to harmonize reporting standards and promote their dissemination, ensuring that future arthropod genomes are both comparable and maximally reusable for large-scale comparative and applied research.