Chimera_richness_phylo_diversity
Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses
This submission underpins the associated research questions and comprises four 18S nSSU PCR amplicon pools, described the associated metadata.
Eukaryotic diversity in environmental samples is often assessed via PCR-based  amplification of nSSU genes. However, estimates of diversity derived from  pyrosequencing environmental datasets are often inflated, mainly because of the  formation of chimeric sequences during PCR amplification. Chimeras are hybrid  products composed of distinct parental sequences that can lead to the  misinterpretation of diversity estimates. We have analyzed the effect of sample  richness, evenness and phylogenetic diversity on the formation of chimeras using a  nSSU dataset derived from 454 Roche pyrosequencing of replicated, large control  pools of closely and distantly related nematode mock communities, of known  intragenomic identity and richness. To further investigate how chimeric molecules are  formed the nSSU gene secondary structure was analyzed in several individuals. We  observed for the first time that chimera formation proved to be higher in both richer  and more genetically diverse samples, thus providing a novel perspective of chimera  formation in (nSSU) pyro-sequenced environmental datasets. Nonetheless, the region  where the chimera forms has to have sufficient conservation to favour hybridization  and chimera formation. We anticipate that this study will significantly contribute to a  better understanding of the nature and mechanisms involved in chimera formation  during the PCR amplification of environmentally derived DNA.