Illumina-based chloroplast genome assembly

All genome data were sequenced using an Illumina Hiseq 2500 platform by Biomarker Technologies, Inc (Beijing, China). High-quality reads were obtained using the CLC Genomics Workbench v7.5 (CLC Bio, Aarhus, Denmark). Reference-guided assembly was then performed to reconstruct the chloroplast genomes using the program MITObim v1.7 (Christoph et al., 2013 (link)). In order to obtain accurate sequences, each species was assembled four times with the reference genomes A. cepa (KM088014), A. sativum (KY085913), A. victorialis (NC_037240), and A. obliquum (LT699701). Gaps that appeared in the assembled cp genomes were corrected by Sanger sequencing and the primers were designed using Lasergene 7.1 (DNASTAR, Madison, WI, United States). The primers and amplifications were shown in Supplementary Table S2. The program DOGMA (Wyman et al., 2004 (link)) was used to annotate the whole cp genome, and subsequently corrected within GENEIOUS R11 (Biomatters, Ltd., Auckland, New Zealand). Final plastid genome maps were drawn using OGDRAW (Lohse et al., 2013 (link)).