Unexpected cross-species contamination in genome sequencing projects

The raw data from a genome sequencing project sometimes contains DNA from contaminating organisms, which may be introduced during sample collection or sequence preparation. In some instances, these contaminants remain in the sequence even after assembly and deposition of the genome into public datab...

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Bibliographic Details
Published in:PeerJ (San Francisco, CA) CA), 2014-11, Vol.2, p.e675-e675
Main Authors: Merchant, Samier, Wood, Derrick E, Salzberg, Steven L
Format: Article
Language:English
Subjects:
Analysis
Anopheles
Bacteria
Bioinformatics
Biology
Bos taurus
Cattle
Chromosomes
Computational Biology
Computer science
Contaminants
Contamination
Deoxyribonucleic acid
DNA
DNA sequencing
Experiments
Genome assembly
Genomes
Genomics
Microbiology
Microbiome
Neisseria gonorrhoeae
Nucleotide sequence
Organisms
Sequence analysis
Sheep
Software
Studies
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Description
Summary:The raw data from a genome sequencing project sometimes contains DNA from contaminating organisms, which may be introduced during sample collection or sequence preparation. In some instances, these contaminants remain in the sequence even after assembly and deposition of the genome into public databases. As a result, searches of these databases may yield erroneous and confusing results. We used efficient microbiome analysis software to scan the draft assembly of domestic cow, Bos taurus, and identify 173 small contigs that appeared to derive from microbial contaminants. In the course of verifying these findings, we discovered that one genome, Neisseria gonorrhoeae TCDC-NG08107, although putatively a complete genome, contained multiple sequences that actually derived from the cow and sheep genomes. Our findings illustrate the need to carefully validate findings of anomalous DNA that rely on comparisons to either draft or finished genomes.
ISSN:2167-8359
2167-8359
DOI:10.7717/peerj.675