A Large-Scale Study into Protist-Animal Interactions Based on Public Genomic Data Using DNA Barcodes

SIMPLE SUMMARY: Protists are a group of eukaryotic organisms that are important materials for studies of parasitology, metazoan/animal origin and mitochondrion evolution. However, as they are highly diverse and some species can infect animals with a broad host range, there is still a gap in knowledge regarding protist-animal interactions. Microbe contamination in genomic databases can not only confuse the results of genomic analysis but also provide valuable resources in research of microbe diversity and microbe-host interactions. In this study, we conducted a large-scale scan of protistan contaminations in a public genomic database based on DNA barcodes. The results suggest that there are high numbers of protistan contamination in animal assemblies in public genomic databases. And the heterogeneous distribution of protistan contaminations across different animal taxa reflects complicated protist-host relationships across different animal taxa. ABSTRACT: With the birth of next-generation sequencing (NGS) technology, genomic data in public databases have increased exponentially. Unfortunately, exogenous contamination or intracellular parasite sequences in assemblies could confuse genomic analysis. Meanwhile, they can provide a valuable resource for studies of host-microbe interactions. Here, we used a strategy based on DNA barcodes to scan protistan contamination in the GenBank WGS/TSA database. The results showed a total of 13,952 metazoan/animal assemblies in GenBank, where 17,036 contigs were found to be protistan contaminants in 1507 assemblies (10.8%), with even higher contamination rates in taxa of Cnidaria (150/281), Crustacea (237/480), and Mollusca (107/410). Taxonomic analysis of the protists derived from these contigs showed variations in abundance and evenness of protistan contamination across different metazoan taxa, reflecting host preferences of Apicomplexa, Ciliophora, Oomycota and Symbiodiniaceae for mammals and birds, Crustacea, insects, and Cnidaria, respectively. Finally, mitochondrial proteins COX1 and CYTB were predicted from these contigs, and the phylogenetic analysis corroborated the protistan origination and heterogeneous distribution of the contaminated contigs. Overall, in this study, we conducted a large-scale scan of protistan contaminant in genomic resources, and the protistan sequences detected will help uncover the protist diversity and relationships of these picoeukaryotes with Metazoa.