Metagenome of soil samples from apple orchards
DNA  extracts were sheared to 700 bp using the CovarisE220 (Covaris, USA) according to the manufacturers instructions using the following settings: incident power (W): 175, duty factor:2, cycles per burst: 200, treatment time: 35 sec. Size selection was performed with the Agencourt AMPure XP kit (Beckman Coulter, USA). The fragments were treated by end repair A tailing. Size selection to 400- 500 bp was performed with the Agencourt AMPure XP kit (Beckman Coulter, USA). Ligation of Illumina compatible adapters was done with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, USA) and the samples were multiplexed using NEBNext Multiplex Oligos for Illumina (NEB). Sequencing was performed on an Illumina Miseq (Illumina) sequencing machine using the MiSeq Reagent Kit v3 (600 cycles) (Illumina) for paired end sequencing.