DOI: 10.5061/dryad.mn338
title: Data from: Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies

description: Background: 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.
 Results: 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.
 Conclusion: 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.
description: extracted
 contigsFasta files containing
 the extracted, parasite-derived contigs. Contigs from each Assembly are
 stored in a separate file.extracted_contigs.zippredicted amino acidsFasta files containing the predicted amino acid sequences based on the extracted contigs. Sequences from each Assembly are stored in a separate file.predicted_aa.zipdataset 1 single genesFasta files containing the single gene amino acid alignments of dataset 1 prior to processing by Gblocks.dataset_1_single_genes.zipdataset 1 single genes after gblocksFasta files containing the single gene amino acid alignments of dataset 1 after processing by Gblocks.dataset_1_single_genes_gblocks.zipdataset 2 single genesFasta files containing the single gene amino acid alignments of dataset 2 prior to processing by Gblocksdataset_2_single_genes.zipdataset 2 single genes after gblocksFasta files containing the single gene amino acid alignments of dataset 2 after processing by Gblocks.dataset_2_single_genes_gblocks.zipdataset 1 superalignment in FASTA formatConcatenated superalignment of all 1420 single gene amino acid alignments of dataset 1 after processing by Gblocks.dataset_1_superalignment.fadataset 2 superalignment in FASTA formatConcatenated superalignment of all 301 single gene amino acid alignments of dataset 2 after processing by Gblocks.dataset_2_superalignment.famitochondrial sequences from gorilla Plasmodium in FASTA formatNucleotide alignment of mitochondrial Plasmodium sequences including two sequences that were extraceted from the gorilla genome. The alignment is based on data from Liu et al. (2010) and only contains sequences from Clades G1 and C1.mito_gorilla.fa18S rRNA Piroplasmida in FASTA formatNucleotide alignment of 18s rRNA sequences from Piroplasmida including a sequences that was extraceted from the platypus genome. The alignmnet is based on data from Paparini et al. (2015) and was processed by Gblocks.18s_piroplasmida.fa