Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

Abstract

Background Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. To guide forthcoming genome generation efforts and promote efficient prioritization of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Findings Here we present an automated analysis workflow that surveys genome assemblies from the United States NCBI, assesses their completeness using the relevant BUSCO datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, examine how key assembly metrics relate to gene content completeness, and compare results from using different BUSCO lineage datasets. Conclusions These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritizations for ongoing and future sampling, sequencing, and genome generation initiatives.

Standardized nuclear markers improve and homogenize species delimitation in Metazoa

“…Therefore, metazoan‐level universal single‐copy orthologs (metazoan USCOs) have been proposed as a core set of nuclear‐encoded protein‐coding genes for species delimitation in Metazoa (Eberle et al, 2020). USCOs are under strong selection for occurring only in single copy within a genome (Feron & Waterhouse, 2022; Waterhouse et al, 2011, 2013). In Metazoa, 978 USCOs were recognized based on a representative selection of 65 high‐quality genomes (Simão et al, 2015).…”

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

“…Core information derived from publicly available (INSDC) assemblies and updates to the underlying taxonomy (including new taxon registrations) are updated every weekday, while target and status lists supplied by EBP-affiliate projects are included in the next daily release after they have been pushed to the goat-data GitHub repository. This enables GoaT to be integrated into pipelines, such as the DToL production pipeline which uses the latest available estimated genome sizes to plan sequencing effort for each species, and the Arthropoda Assembly Assessment Catalogue 28 at https://evofunvm.dcsr.unil.ch/upcoming_assemblies.html , that uses information about sequencing status. Frequent updates of status lists, in particular, are fundamental to GoaT achieving its objective of helping to reduce duplication of sequencing efforts as the number and pace of large-scale sequencing projects continue to increase.…”

Chromosome‐level genome assembly of the aster leafhopper (Macrosteles quadrilineatus) reveals the role of environment and microbial symbiosis in shaping pest insect genome evolution

“…The inferred size of the ALF genome is 1.3 Gbp with a BUSCO score of 96.08%, suggesting a complete high‐quality assembly (Table 2) (Feron & Waterhouse, 2022; Li et al., 2022; Yan et al., 2021). ALF's genome encodes 21,979 protein‐coding genes, which is in alignment with previous leafhopper genomes (e.g., GWSS has 19,904 genes, and TGLH has 19,642 genes; Li et al., 2022; Zhao et al., 2022).…”