title: Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies.
abstract: Contaminations 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.
  
  
  
  Here 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.
  
  
  
  Our 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.
authors.affiliation: Institute of Zoology, Biocenter Grindel, University of Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany. janus.borner@uni-hamburg.de.
authors.forename: Janus
authors.initials: J
authors.lastname: Borner
authors.affiliation: Institute of Zoology, Biocenter Grindel, University of Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany. thorsten.burmester@uni-hamburg.de.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Burmester
mesh_terms: D000818:Animals; D016782:Apicomplexa / Q000145:classification / Q000235:genetics*; D001499:Bayes Theorem; D020451:Contig Mapping; D057225:Data Mining; D016208:Databases, Factual / Q000592:standards*; D003670:Deer / Q000235:genetics; D016678:Genome; D006041:Goats / Q000235:genetics / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D059467:Transcriptome
keywords: Apicomplexa; Coccidia; Contamination; Database analysis; Gregarinasina; Haemosporida; Malaria; Parasites; Phylogeny; Piroplasmida