Illumina raw reads were collected using an Illumina Hiseq 2500 platform. The quality-trim with all of the raw reads was performed using CLC Genomics Workbench v7.5 (CLC bio, Aarhus, Denmark) with the default parameter set. The programs MITObim v1.7 (University of Oslo, Oslo, Norway) [96 (link)] and MIRA v4.0.2 (DKFZ, Heidelberg, Germany) [97 (link)] were used to perform the reference-guided assembly twice, to reconstruct the CPGs with published G. pentaphyllum (KX852298) and C. melo (JF412791) as references, respectively. A few gaps, dubious bases, and low-coverage regions in the assembled CPGs were corrected by Sanger sequencing, whereby pairs of primers were designed (Table S1 ) using Primer 3 version 4.0.0 (Whitehead Institute for Biomedical Research, Massachusetts, USA) [98 (link)]. The software DOGMA, Dual Organellar Genome Annotator (University of Texas at Austin, Austin, TX, USA) [99 (link)], was used to annotate the complete CPGs, and corrected by comparing with the complete CPGs of the references mentioned above using GENEIOUS R8 (Biomatters Ltd., Auckland, New Zealand). The circular CPG maps were drawn using online software OGDRAW (http://ogdraw.mpimp-golm.mpg.de ) (Max planck Institute of Molecular Plant Physiology, Potsdam, Germany). All of the newly generated complete CPG sequences were submitted to GenBank (Table 1 ).
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