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.
Highlights
Contaminations from various exogenous sources are a common problem in next-generation sequencing
The former approach is not suited for the identification of contaminations by parasites for which only distantly related species are available in the public databases, whereas the latter approach is especially useful for quantitative estimates of genome abundance but can only find a small number of predefined genes
We drastically reduced the computational complexity of this problem by first filtering the genome data to extract only those contigs that show significant sequence similarity to proteins from apicomplexan parasites (Fig. 1a)
Summary
Contaminations from various exogenous sources are a common problem in next-generation sequencing. As the amount of read data in next-generation sequencing (NGS) projects is enormous and the reads are short and of low quality, the programs either rely on near exact matches at the nucleotide level [11], or employ smaller databases containing only selected marker genes [12] or genes that are specific to certain clades [13] The former approach is not suited for the identification of contaminations by parasites for which only distantly related species are available in the public databases, whereas the latter approach is especially useful for quantitative estimates of genome abundance but can only find a small number of predefined genes. This is obviously only feasible when high-quality genome data is already available for the host species
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