This study reveals artifactual pyrosequencing reads produced by MDA amplication.

Multiple Displacement Amplification (MDA) protocol is reported to introduce different artifacts to DNA samples with impurities. In this study, we report an artifactual effect of MDA with raw sediment DNA from a deep-sea brine basin. In the metagenomes, we showed the presence of abundant artifactual 454 pyrosequencing reads in sizes of 50 to 220 bp. Translocated gene fragments were identified in these reads and were derived from neighboring regions in a gene. Occasionally, the translocation occurred between the gene fragments from different species. The gene fragments in these reads could form a strong stem-loop structure. More than 60% of the artifactual reads could fit the structural model. MDA amplification is probably responsible for massive generation of the artifactual reads with the secondary structure in the metagenomes. Possible sources of the translocations and structures were discussed.