ArticleBMC genomics2017
Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 58 citations in OpenAlex.
- Hemoglobin Digestion Genes Are Conserved in Lizard-InfectiveEcology and evolution · 2026Article
- ParaRef: a decontaminated reference database for parasite detection in ancient and modern metagenomic datasets.Genome biology · 2025Article
- Apicortin, a Putative Apicomplexan-Specific Protein, Is Present in Deep-Branching Opisthokonts.Biology · 2025Article
- PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era.Molecular biology and evolution · 2024Article
- Diversity and Distribution of Mites (ACARI) Revealed by Contamination Survey in Public Genomic Databases.Animals : an open access journal from MDPI · 2023Article
- Presence of p25alpha-Domain in Seed Plants (Spermatophyta): Microbial/Animal Contaminations and/or Orthologs.Life (Basel, Switzerland) · 2023Article
- A Large-Scale Study into Protist-Animal Interactions Based on Public Genomic Data Using DNA Barcodes.Animals : an open access journal from MDPI · 2023Article
- Killer Knots: Molecular Evolution of Inhibitor Cystine Knot Toxins in Wandering Spiders (Araneae: Ctenidae).Toxins · 2023Article
- Where Have All the Diagnostic Morphological Parasitologists Gone?Journal of clinical microbiology · 2022Article
- Evolutionary Adjustment of tRNA Identity Rules in Bacillariophyta for Recognition by an Aminoacyl-tRNA Synthetase Adds a Facet to the Origin of Diatoms.Journal of molecular evolution · 2022Article
- An unexpected tenant: contamination in a Physeter catodon (Physeteridae, Artiodactyla) genome indicates undescribed species of Sarcocystis Lankester, 1882 (Sarcocystidae, Eucoccidiorida) in the marine environment.Folia parasitologica · 2022Article
- Apicortin, a Constituent of Apicomplexan Conoid/Apical Complex and Its Tentative Role in Pathogen-Host Interaction.Tropical medicine and infectious disease · 2021Review
- Mining Public Metagenomes for Environmental Surveillance of Parasites: A Proof of Principle.Frontiers in microbiology · 2021Article
- Fungus-originated glucanase and monooxygenase genes in creeping bent grass (Agrostis stolonifera L.).PloS one · 2021Article
- Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding.Parasites & vectors · 2020Article
- Article
- Horizontal Transfer and Gene Loss Shaped the Evolution of Alpha-Amylases in Bilaterians.G3 (Bethesda, Md.) · 2020Article
- Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies.G3 (Bethesda, Md.) · 2020Article
- Phylogenomics from transcriptomic "bycatch" clarify the origins and diversity of avian trypanosomes in North America.PloS one · 2020Article
- Metatranscriptomics yields new genomic resources and sensitive detection of infections for diverse blood parasites.Molecular ecology resources · 2020Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundContaminations from various exogenous sources are a common problem in next-generation sequencing. Another possible source of contaminating DNA are endogenous parasites. On the one hand, undiscovered contaminations of animal sequence assemblies may lead to erroneous interpretation of data; on the other hand, when identified, parasite-derived sequences may provide a valuable source of information.
resultsHere we show that sequences deriving from apicomplexan parasites can be found in many animal genome and transcriptome projects, which in most cases derived from an infection of the sequenced host specimen. The apicomplexan sequences were extracted from the sequence assemblies using a newly developed bioinformatic pipeline (ContamFinder) and tentatively assigned to distinct taxa employing phylogenetic methods. We analysed 920 assemblies and found 20,907 contigs of apicomplexan origin in 51 of the datasets. The contaminating species were identified as members of the apicomplexan taxa Gregarinasina, Coccidia, Piroplasmida, and Haemosporida. For example, in the platypus genome assembly, we found a high number of contigs derived from a piroplasmid parasite (presumably Theileria ornithorhynchi). For most of the infecting parasite species, no molecular data had been available previously, and some of the datasets contain sequences representing large amounts of the parasite's gene repertoire.
conclusionOur study suggests that parasite-derived contaminations represent a valuable source of information that can help to discover and identify new parasites, and provide information on previously unknown host-parasite interactions. We, therefore, argue that uncurated assembly data should routinely be made available in addition to the final assemblies.
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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.