Computational protocol: Anthropogenic marine litter composition in coastal areas may be a predictor of potentially invasive rafting fauna

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Protocol publication

[…] DNA was extracted from a small piece of tissue (about 2×2 mm) using Chelex (Bio Rad BT Chelex® 100 Resin). For DNA extraction from very small individuals with non-tissue parts, like shells (e.g., molluscs), the complete individual was treated with E.Z.N.A® Mollusc DNA Kit. PCRs were performed with the universal primers detailed in . When necessary, the PCR product was purified using EURx® Gene Matrix Agarose Out DNA Purification Kit. DNA sequencing was performed by Macrogen Europe, Amsterdam, Netherlands.Sequence editing and alignment was done using the freeware BIOEDIT Version 7.2.5 []. From the DNA Barcode the species was assigned using the BLAST database [] and the best match with the maximum hit score (minimum 97% nucleotide identity). Phylogenetic trees for confirming species assignation were built with MEGA 7 [] from the sequences obtained in this study and reference sequences of voucher specimens taken from GenBank (https://www.ncbi.nlm.nih.gov/nucleotide/), based on the maximum likelihood reconstruction method, with 500 bootstraps. […]

Pipeline specifications

Software tools BioEdit, MEGA
Application Phylogenetics
Organisms cellular organisms, Crassostrea gigas