Cp DNA-seq of Ambrosia artemisiifolia
The intact cell chloroplast from plant leaf tissues were isolated using the chloroplast isolation kit (Sigma-Aldrich, USA) according to manufacturer's instructions (Takara Bio Inc; Japan). Isolation of cp DNA was performed as described by do Nascimento Vieria et al, 2014  with the following modifications: the dissolved DNA in NFW was kept on ice for 2 hours and treated with Plazmid-Safe ATP-Dependent Dnase (EpiCentre,USA ) to get intact circular cp DNA. An Illumina paired-end cp DNA library (average insert size of 500 bp) was constructed using the Illumina TruSeq library preparation kit according to manufacturers protocoll. The cp DNA libraries were sequenced with 2 × 300 bp on the MiSeq instrument at Xenovea Ltd., Hungary (http://xenovea.com/).