shotgun metagenome sequencing of rhizosphere microbiome of the peanut

we performed shotgun metagenome sequencing of rhizosphere microbiome of the peanut (Arachis hypogaea) in two conditions, monocropping and crop rotation. To obtain sufficient metagenomic DNA (2 ?g per sample) for all replicates, 4–6 extractions per rhizosphere sample were performed using the FastDNA SPIN kit for the soil (MP Biomedicals, Santa Ana, CA, USA), and pooled. DNA concentration was determined using NanoDrop spectrophotometer (Thermo Scientific, USA) and its quality was assessed by agarose gel electrophoresis. DNA libraries of ca. 300-bp fragments were prepared using Covaris M220 (Thermo Scientific, USA), and were sequenced using the Illumina Hiseq 4000 instrument (Illumina, USA).