Fig. 1From: Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of RhamnaceaeV. harmandiana chloroplast genome assembly and correction. A Identification of IRs in the chloroplast genome by dot plot. B A quadripartite structure of V. harmandiana chloroplast. There are four IR boundaries of A, B, C and D, each marked with the chloroplast genome position. An amplicon covering each boundary is indicated by the red arrows. Boundary A divides LSC and IRb. Boundary B and Boundary C separate SSC from IRb and IRa, respectively. Boundary D partitions IRa and LSC. Table S1 provides primer details, in which the primer set VharA to VharD are for the validation of the IR boundaries. C Validation of the IR boundaries by PCR amplification of regions spanning over the four IR boundaries. Approximate sizes of amplicons in each boundary region are 951, 1189, 1035 and 1193 nt, respectively. D Correction of mismatched nucleotide bases between IRs. All 45 mismatched bases and the correct DNA bases determined by Sanger sequencing are illustrated. IRb base position is uses as reference. The primer set VharIR1 to VharIR14 are to determine mismatched nucleotide bases between IRs (Additional file 2 Table S1). Large single-copy (LSC); inverted repeats (IRs), reversed inverted repeat (revIR) and small single-copy (SSC)Back to article page