Comparative Analysis of Complete Chloroplast Genomes of Gardenia jasminoides and Contribution to the Phylogeny and Adaptive Evolution

Abstract

Gardenia jasminoides, belonging to the Rubiaceae family, is widely distributed and planted in China. It has traditionally been used as an ornamental and medicinal plant in several Asian countries. The rapid development of high-throughput sequencing technology makes it feasible to obtain complete chloroplast (cp) genome sequences and will deepen our understanding of evolution of G. jasminoides. In this study, we sequenced the complete cp genomes of two botanical varieties of G. jasminoides. The complete cp genomes of both botanical varieties of G. jasminoides showed highly conserved structures and the length was 154,954 base pairs (bp) for G. jasminoides var. radicans (GJR) and 155,098 bp for G. jasminoides var. grandiflora (GJG). A total of 132 and 133 genes were identified in GJR and GJG, respectively. The cp genomes of two newly sequenced G. jasminoides were further compared with two published G. jasminoides cp genomes. Multiple repeats and simple sequence repeats (SSRs) were detected among different genotypes of G. jasminoides. The intron sequences of rps16 and rpl16 genes were slightly divergent among four genotypes of G. jasminoides. Phylogenetic analyses based on the complete cp genome sequences showed that G. jasminoides was closely associated with Fosbergia shweliensis, with Coffea as their close relative. Taken together, the complete cp genomes of GJG and GJR provided significant insights and important information that can be used to identify related species and reconstruct their phylogeny.