Amp-Seq of Peganum harmala's roots
Amplicons were purified using Agencourt AMPure XP beads (Beckman Coulter, USA), washed twice with ethanol, air dried, and resuspended in 10 mM Tris (pH 8.5). A second PCR was performed to attach Illumina sequencing adapters and dual index tags using the Fluidigm Access Array Barcode 384 system and KAPA HiFi HotStart ReadyMix (Roche Sequencing Solutions). The 50 L PCRs were run with an initial denaturation at 95 C for 3 min; 8 cycles of 95 C for 30 s, 55 C for 30 s, and 72 C for 30 s; and a final extension at 72 C for 5 min. Indexed amplicons were purified again using AMPure XP beads and quantified with a Qubit DNA HS Assay Kit (ThermoFisher, Tmara, Morocco). Libraries were normalized, pooled, and sequenced on an Illumina MiSeq i100 platform (UM6P CoreLab)