Two recently sequenced vertebrate genomes are contaminated with apicomplexan species of the Sarcocystidae family

• Published in: International journal for parasitology 2015-11, Vol.45 (13), p.871-878
• Main Author: Orosz, Ferenc
• Format: Article
• Language: English
• Subjects: Animals; Apicomplexa; Apicoplast; Apicortin; Base Sequence; Bat; Bird Diseases; Chiroptera - genetics; Chiroptera - parasitology; Chromosome Mapping; Colinus - genetics; Colinus - parasitology; Computer Simulation; DNA Contamination; Host; Host-Parasite Interactions; Nephroisospora; Phylogenetic tree; Phylogeny; RNA, Ribosomal, 18S - genetics; Sarcocystidae - classification; Sarcocystidae - genetics; Sarcocystidae - isolation & purification; Sarcocystis; Sarcocystis - parasitology; Sequence Alignment; Sequence Analysis, DNA
• ISSN: 0020-7519; 1879-0135
• DOI: 10.1016/j.ijpara.2015.07.002

[Display omitted] •The draft genome of Colinus virginianus, a bird, is contaminated by a Sarcocystis species.•That parasite is related to ones known to cycle between avian and mammalian hosts.•The draft genome of Myotis davidii, a bat, is contaminated by a species of Sarcocystidae.•That parasite is the second (tentative) member of the Nephroisospora genus.•Several contigs of both hosts originated from the apicomplexan organelle, the apicoplast. This paper highlights a general problem, namely that host genome sequences can easily be contaminated with parasite sequences, thus careful isolation of genetic material and careful bioinformatics analysis are needed in all cases. Two recently published genomes are shown here to be contaminated with sequences of apicomplexan parasites which belong to the Sarcocystidae family. Sequences of the characteristic apicomplexan organelle, the apicoplast, were used as queries in BLASTN searches against nucleotide sequences of various animal groups looking for possible contamination. Draft genomes of a bird, Colinus virginianus (Halley et al., 2014), and a bat, Myotis davidii (Zhang et al., 2013) were found to contain at least six and 17 contigs, respectively, originating from the apicoplast of an apicomplexan species, and other genes specific to this phylum can also be found in the published genomes. Obviously, the sources of the genetic material, the muscle and the kidney of the animals, respectively, contained the parasitic cysts. Phylogenetic analyses using 18S rRNA and internal transcribed spacer 1 genes show that the parasite contaminating C. virginianus is a species of Sarcocystis related to ones known to cycle between avian and mammalian hosts. In the case of M. davidii it belongs to the Nephroisospora genus, the only member of which, Nephroisospora eptesici, has been recently identified from the kidney of big brown bats (Eptesicus fuscus).