Chloroplast (cp) genome sequences provide a valuable source for DNA barcoding. Molecular phylogenetic studies have concentrated on DNA sequencing of conserved gene loci. However, this approach is time consuming and more difficult to implement when gene organization differs among species. Here we report the complete re-sequencing of the cp genome of Capsicum pepper (Capsicum annuum var. glabriusculum) using the Illumina platform. The total length of the cp genome is 156,817 bp with a 37.7% overall GC content. A pair of inverted repeats (IRs) of 50,284 bp were separated by a small single copy (SSC; 18,948 bp) and a large single copy (LSC; 87,446 bp). The number of cp genes in C. annuum var. glabriusculum is the same as that in other Capsicum species. Variations in the lengths of LSC, SSC and IR regions were the main contributors to the size variation in the cp genome of this species. A total of 125 simple sequence repeat (SSR) and 48 insertions or deletions variants were found by sequence alignment of Capsicum cp genome. These findings provide a foundation for further investigation of cp genome evolution in Capsicum and other higher plants.

• Sebastin Raveendar(National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration)
• Jung-Ro Lee(National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration)
• Donghwan Shim(The Agriculture Genome Center, National Academy Agriculture Science, RDA)
• Kyung Jun Lee(National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration)
• Kyung-Ho Ma(National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration)
• Sok-Young Lee(National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration)
• Jong-Wook Chung(National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration) Corresponding Author