Eukaryote, Prokaryote and Metazoan datasets for comparing DNA extraction protocols for environmental DNA-based monitoring of sediment biota

Brief description

18S rDNA (Eukaryote), 16S rDNA (Prokaryote) and COI (Metazoan) amplicons data from sediment DNA used to compare DNA extraction protocols for the purpose of environmental DNA-based monitoring of sediment biota. DNA was extracted using two extraction methods (with variations in the initial volume of material): a bespoke method targeting only extracellular DNA and a commercially available kit-based method for extracting total DNA.
16S Prokaryote amplicons were amplified with primers 515F (5’-GTGYCAGCMGCCGCGGTAA-3’) and 806R (5’-GGACTACNVGGGTWTCTAAT-3’) (Parada et al. 2016; Apprill et al. 2015). 18S Eukaryote amplicons were amplified with primers All18SF (5’-GGTGCATGGCCGTTCTTAGT-3’) and All18SR (5’-CATCTAAGGGCATCACAGACC-3') (Hardy et al. 2010). COI Metazoa amplicons were amplified with primers mlCOIintF (5’-GGWACWGGWTGAACWGTWTAYCCYCC-3’) and jgHCO2198 (5’-TAIACYTCIGGRTGICCRAARAAYCA-3’) (Leray et al. 2013).
Sequences were obtained by a 2 x 250 bp paired-end sequencing on Illumina MiSeq 2500 platform.
https://www.publish.csiro.au/MF/justaccepted/MF20269
Lineage: For raw data, demultiplexing of original sequencing files was performed using the GHAP pipeline (Greenfield 2017; available at https://doi.org/10.4225/08/59f98560eba25).
Filtered data were processed according to the filtering procedure described in Pansu et al. (2021): ‘Comparison of an extracellular vs. total DNA extraction approach for environmental DNA-based monitoring of sediment biota’ (Marine & Freshwater Research). For each mOTU, the number of reads per sample post-filtering is reported.