ITS1 metabarcoding revealing Phytophthora diversity in anthropized and natural ecosystems in Sicily, Italy

This dataset on Zenodo contains the raw sequencing data for: La Spada <em>et al.</em> (2022) DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing <em>Phytophthora</em> Diversity in Anthropized and Natural Ecosystems. This a subset of 192 demultiplexed Illumina MiSeq raw sequencing samples run at the James Hutton Institute in January 2020, consisting of two 96-well plates labelled with the Illumina A and D multiplexing kits. There are 61 pairs of raw gzipped compressed FASTQ files (122 files), provided as a 930MB gzipped compressed tar-ball. From the D multiplexing kit, there are 27 Nature Reserve (<em>NR</em>) samples, 16 Botanical Garden (<em>BG</em>) samples, and 6 managed Citrus Orchard (<em>CO</em>) samples containing <em>Phytophthora</em> targeted ITS1 marker sequences, and 6 synthetic controls (prefix <em>GL1D</em>) which should have contained only four known synthetic sequences. Additionally included are the 6 synthetic controls (prefix <em>GL1A</em>) from the A multiplexing kit, which were clean. The filenames start with the sample name, followed by something like <em>DH03_S183_L001_R1_001.fastq.gz</em> where <em>DH03</em> indicates well <em>H03</em> on the 96-well plate labelled with the <em>D</em> multiplexing set, <em>S183</em> is the MiSeq sample number (from 1 to 192), and <em>R1</em> (or <em>R2</em>) indicate the Illumina forward (or reverse) paired read files.