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Genomic databases contain significant protistan contamination, impacting animal genome analysis. This study identified 17,036 contaminated contigs across 1507 metazoan assemblies, revealing host-specific patterns and aiding host-microbe interaction research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Parasitology

Background:

  • Next-generation sequencing (NGS) has led to a massive increase in public genomic data.
  • Exogenous contamination and intracellular parasite sequences in genomic assemblies can hinder accurate analysis.
  • These contaminants, however, offer opportunities to study host-microbe interactions.

Purpose of the Study:

  • To systematically scan the GenBank Whole Genome Shotgun/Transcriptome Shotgun Assembly (WGS/TSA) database for protistan contamination in metazoan assemblies.
  • To analyze the distribution and host specificity of protistan contaminants across different animal taxa.
  • To leverage detected protistan sequences for understanding picoeukaryote diversity and their relationships with Metazoa.

Main Methods:

  • A DNA barcoding strategy was employed to identify protistan sequences within metazoan assemblies.
  • Contigs were analyzed for protistan origin, and contamination rates were calculated for various taxa.
  • Phylogenetic analysis of mitochondrial proteins (COX1 and CYTB) was performed to confirm protistan origin and distribution.

Main Results:

  • A total of 17,036 protistan contaminant contigs were identified in 1507 out of 13,952 metazoan assemblies (10.8% contamination rate).
  • Higher contamination rates were observed in Cnidaria (150/281), Crustacea (237/480), and Mollusca (107/410).
  • Host-specific contamination patterns were evident, with Apicomplexa, Ciliophora, Oomycota, and Symbiodiniaceae showing preferences for mammals/birds, Crustacea, insects, and Cnidaria, respectively.

Conclusions:

  • Protistan contamination is a significant issue in public metazoan genomic databases.
  • The identified contaminants exhibit distinct host associations, providing insights into host-microbe interactions.
  • This large-scale contamination scan offers a valuable resource for exploring protist diversity and their ecological roles within metazoan hosts.