ArticleGigaScience2022
Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Molting in Pancrustacea Is Characterized by Both Deeply Conserved and Recently Evolved Gene Modules.Genome biology and evolution · 2026Article
- Evolutionary dynamics of the arthropod molting machinery.Molecular biology and evolution · 2026Review
- Snail plots are badges of genome assembly quality.G3 (Bethesda, Md.) · 2026Article
- Whole genome sequence analysis supports the genomic mosaicism of the endangered Hawaiian duck (Anas wyvilliana).Scientific reports · 2026Article
- Bioinformatics of Combined Nuclear and Mitochondrial Phylogenomics to Define Key Nodes for the Classification of Coleoptera.Systematic biology · 2026Article
- MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes.GigaScience · 2026Article
- Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins.Bioinformatics advances · 2026Article
- Limited population structure but signals of recent selection in introduced African Fig Fly (Zaprionus indianus) in North America.G3 (Bethesda, Md.) · 2025Article
- Draft genome of the endemic alpine ground beetle Carabus (Platycarabus) depressus (Coleoptera: Carabidae) from long-read sequencing of a frozen archived specimen.G3 (Bethesda, Md.) · 2025Article
- A full genome assembly reveals drought stress effects on gene expression and metabolite profiles in blackcurrant (Horticulture research · 2025Article
- Chromosome-Scale Genomes of the Flightless Caterpillar Hunter Beetles Calosoma tepidum and Calosoma wilkesii From British Columbia (Coleoptera: Carabidae).Genome biology and evolution · 2025Article
- From literature to biodiversity data: mining arthropod organismal traits with machine learning.Biodiversity data journal · 2025Article
- Genome assembly of a nocturnal butterfly (Macrosoma leucophasiata) reveals convergent adaptation of visual genes.Communications biology · 2024Article
- Genomic signatures of sensory adaptation and evolution in pangolins.BMC genomics · 2024Article
- Satellitome Analysis ofInternational journal of molecular sciences · 2024Article
- Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes.Nature communications · 2024Article
- A reference quality genome assembly for the jewel scarab Chrysina gloriosa.G3 (Bethesda, Md.) · 2024Article
- Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda.FEMS microbiology ecology · 2024Article
- Lepidopteran Synteny Units reveal deep chromosomal conservation in butterflies and moths.G3 (Bethesda, Md.) · 2023Article
- A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index.AoB PLANTS · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAmbitious 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.
findingsHere 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.
conclusionsThese 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.
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