The complete chloroplast (cp) genomes of two Miscanthus species, M. sinensis and M. sacchariflorus, were sequenced and investigated for genes, genome size variation, and polymorphisms. There are 154 genes in both cp genomes, consisting of 122 coding genes, 40 tRNA genes, and 8 rRNA genes. The cp genome contains two inverted repeat (IR) regions, separated by large single copy (LSC) region and small single copy (SSC) region. 112bp indels in M. sinensis and 152bp in M. sacchariflorus were found mainly in LSC and SSC, which are responsible for 40 bp-difference in cp genome size in two species. Likewise, out of 94bp of SNPs, 88bp were found in LSC and SSC regions. Although gene number and sequence structure were quite well conserved, indel distribution and size were different in these two Miscanthus species.

• Gyoungju Nah(Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University) Corresponding Author
• Ji-Hoon Im(Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
• Soo-Hyun Lim(Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
• Kyunghee Kim(Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
• Do-Soon Kim(Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University) Corresponding Author