Illumina sequencing data from fungal (ITS) and bacterial (16S) endophyte meta-communities associated with Parkinsonia spp. in North America and Australia

This dataset contains the raw FASTQ files from multiplex dual-index Illumina sequencing of fungal, bacterial and oomycete communities associated with Parkinsonia spp. in North America and Australia. Fungal reads were obtained via sequencing of the ITS amplicon using ITS1F and ITS2 primers, bacterial reads were obtained via sequencing of the 16s rRNA gene using primers 515F and 806R primers, and oomycete reads were obtained via sequencing of the ITS region using ITS6 and ITS7 primers. Samples were taken from multiple plant parts of healthy and dieback-affected Parkinsonia aculeata in Australia (QLD, WA, NT), and healthy P. aculeata, P. microphylla and P. florida in the USA (AZ, TX). FASTQ files can be cleaned up and curated after Bissett et al. (2016). The quality of all Illumina R1 and R2 reads can be assessed visually using FastQC (Andrews 2016), merged using FLASH (Magoč & Salzberg 2011), and converted to FASTA format. For 16S rRNA sequences, extract and edit using MOTHUR v1.34.1 (Schloss et al. 2009). For ITS region sequences, extract and edit using ITSx (Bengtsson-Palme et al. 2013). For a more detailed protocol, refer to Chapter 5 and Appendix C of the PhD thesis “Investigating the cause of dieback in the invasive plant, Parkinsonia aculeata”, by Tracey V. Steinrucken (2017).