Complete chloroplast genomic sequence of Citrus platymamma determined by combined analysis of Sanger and NGS data

Citrus platymamma (Byeonggyul) of the family Rutacease is one of the most important genetic resources of Korean Citrus. To characterize the chloroplast (cp) genetic makeup of this species, the cp genome was sequenced by both Sanger and next generation sequencing (NGS) methods. The characterized cp genome is 160,121 bp in size: the large single copy (LSC) region is 87,732 bp, the inverted repeat (IR) is 26,998 bp, and the small single copy (SSC) region is 18,393 bp. The cp genome contains 114 genes and 21 introns, including 80 protein-coding genes, four RNA genes, 30 tRNA genes, 19 group II introns, and one group I intron. Based on phylogenetic analysis with six known cp genomes from the Sapindales order, to which the Rutaceae belongs, the cp genome of C. platymamma is closest to that of Citrus sinensis. When directly comparing the cp genomes of C. platymamma and C. sinenesis, we detected size variation in the psbC and rps4 genes, four SNPs, and eight 1-bp simple sequence repeats (SSRs). Additionally, we found that the cp genomic structures of C. platymamma and C. sinensis are identical in regards to the junction sequences of LSC-IRs and SSC-IRs, and provide evidence that the junction sequences of the SSC-IRs originated from the common ancestor of C. platymamma, C. sinensis, and C. aurantifolia. Further study of other species will provide enhanced understanding of cp genome evolution in the Citrus genus.