ArticleG3 (Bethesda, Md.)2020
Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies.
Article in G3 (Bethesda, Md.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- CSI-SSU: phylogenetic contamination screening of genomic datasets, demonstrated on The Protist 10,000 Genomes (P10K) Project.BMC genomics · 2026Article
- Genome of Facultatively Parthenogenetic Harvester (Opiliones) Indicates Frequent Mitonuclear Sequence Transfer and Novel Full-Length Insertions.Genome biology and evolution · 2026Article
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- Discovery of a bacteriophage sequence in a mite genome assembly reveals bacterial contamination and opens new possibilities for exploring arthropod symbionts.Microbial genomics · 2025Article
- Applying a Conservation-Based Approach for Predicting Novel Phosphorylation Sites in Eukaryotes and Evaluating Their Functional Relevance.Journal of proteome research · 2025Article
- Myxozoan parasite genomes assembled from contaminated host data reveal extensive gene order conservation and rapid sequence evolution.G3 (Bethesda, Md.) · 2025Article
- Contamination Survey of Insect Genomic and Transcriptomic Data.Animals : an open access journal from MDPI · 2024Article
- Disentangling cobionts and contamination in long-read genomic data using sequence composition.G3 (Bethesda, Md.) · 2024Article
- Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.G3 (Bethesda, Md.) · 2024Article
- A chromosome-level genome assembly of Zasmidium syzygii isolated from banana leaves.G3 (Bethesda, Md.) · 2024Article
- ContScout: sensitive detection and removal of contamination from annotated genomes.Nature communications · 2024Article
- GenomeFLTR: filtering reads made easy.Nucleic acids research · 2023Article
- Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events.PLoS genetics · 2022Article
- Convergent consequences of parthenogenesis on stick insect genomes.Science advances · 2022Article
- Contamination detection in genomic data: more is not enough.Genome biology · 2022Review
- Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin (Biology · 2021Article
- CONSULT: accurate contamination removal using locality-sensitive hashing.NAR genomics and bioinformatics · 2021Article
- ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.PLoS computational biology · 2021Article
- Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer.Nature communications · 2021Article
- Distribution of Merlin in eukaryotes and first report of DNA transposons in kinetoplastid protists.PloS one · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Thanks to huge advances in sequencing technologies, genomic resources are increasingly being generated and shared by the scientific community. The quality of such public resources are therefore of critical importance. Errors due to contamination are particularly worrying; they are widespread, propagate across databases, and can compromise downstream analyses, especially the detection of horizontally-transferred sequences. However we still lack consistent and comprehensive assessments of contamination prevalence in public genomic data. Here we applied a standardized procedure for foreign sequence annotation to 43 published arthropod genomes from the widely used Ensembl Metazoa database. This method combines information on sequence similarity and synteny to identify contaminant and putative horizontally-transferred sequences in any genome assembly, provided that an adequate reference database is available. We uncovered considerable heterogeneity in quality among arthropod assemblies, some being devoid of contaminant sequences, whereas others included hundreds of contaminant genes. Contaminants far outnumbered horizontally-transferred genes and were a major confounder of their detection, quantification and analysis. We strongly recommend that automated standardized decontamination procedures be systematically embedded into the submission process to genomic databases.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.