MOSH_FSP_FOOD_CHAIN_METHOD_DEVELOPMENT_AMPLICON

Sampling method development to identify an appropriate sampling method for baby spinach utilising 16S and ITS amplicon sequencing.\nLineage: Illumina paired-end 2 x 300 bp sequencing was performed on the Miseq platform by Australian Centre for Ecogenomics, University of Queensland (Brisbane, Australia) targeting the V3-V4 region of the bacterial 16S gene using primers 515F and 806wR with PNA blockers pPNA and mPNA and primers ITS3 and ITS4 targeting the ITS2 region. Library preparation for both amplicon targets were performed as per Illumina protocol 15044223 Rev.B which is a 2 stage PCR workflow, PCR amplicons were purified using Agencourt AMPure XP beads (Beckman Coulter) with 16S amplicons indexed with NEBNext® Ultra™ II Q5® Mastermix and ITS amplicon indexed with Q5 Hot Start High-Fidelity 2X Master Mix (New England Biolabs). Demultiplexed paired-end reads were provided by Australian Centre for Ecogenomics. These are the raw reads provuded by ACE Sequencing.