C. prolifera Hg4
Amplicon libraries were prepared from 0.5 ng of extracted DNA. The adopted strategy is described in detail by Manzari et al. (2015). The primer pair used for amplification of the mitochondrial Cytochrome oxidase subunit 1 (Cox1) gene was mlCOIintF_NextFor and dgHCO2198_NextRev (Next_For: 5-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3, and Next_Rev: 5GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-3) (Leray et al., 2013), designed to contain (from 5 to 3 ends) transposon Nextera sequences (Nextera DNA sample preparation guide, Illumina). RNase/Dnase-free Molecular Biology Grade water (Ambion) was used as a negative control of PCR amplification. Equimolar quantities of the purified amplicons were pooled and subjected to 2250 bp paired-end sequencing on the Illumina MiSeq platform. To increase the genetic diversity of the sequenced samples, as required by the MiSeq platform, a phage PhiX genomic DNA library was added to the mix and co-sequenced (Kozich et al., 2013).