RNA-Seq of rhizosphere soil from Phytophthora symptomatic avocado tree
Duplicate RNA extractions were carried out from all rhizosphere soil samples using the RNAeasy PowerSoil Total RNA Kit by Qiagen. Prior to the first step of the extraction protocol, each sample and its duplicate were centrifuged at 5,000 g for 5 min to remove the LifeGuard Soil Preservation Solution as recommended by the manufacturer. The integrity of the extracted RNA was evaluated with the presence of ribosomal RNA (rRNA) bands by electrophoresis. RNA concentration and purity were measured on the Eppendorf BioSpectrometer. Nine samples with intact RNA from asymptomatic trees were randomly distributed into three equimolar pools and the 10 samples from PRR-symptomatic trees were also distributed into three equimolar pools. Six libraries were then built from the pools and sequenced (paired-end) with a read length of 2  100 bp using the Illumina NovaSeq 6000TM system at Macrogen Inc.
SUB15769310
Symptomatic P5