Abstract
Background By the time our study was completed, the chloroplast genomes of Syringa oblata, S. pubescents subsp . Microphylla, and S. reticulate subsp . Amurensi s had not been sequenced, and their genetic background was not clear. The research content In this study, the chloroplast genomes of Syringa oblata , S. pubescents subsp . Microphylla, S. reticulate subsp . Amurensis , and five other species of Syringa were sequenced for a comparative genomics analysis, inverted repeat (IR) boundary analysis, collinearity analysis, codon preference analysis and a nucleotide variability analysis. Differences in the complete chloroplast genomes of 30 species of Oleaceae were compared with that of S. oblata as the reference species, and Ginkgo biloba was used as the out group to construct the phylogenetic tree. Results The results showed that the chloroplast genomes of S. oblata, S. pubescents subsp . Microphylla, and S. reticulate subsp . Amurensi s were similar to those of other angiosperms and showed a typical four-segment structure, with full lengths of 155,569, 160,491, 155,419, and protein codes of 88, 95, and 87, respectively. Because the IR boundary of S. pubescents subsp . Microphylla was significantly expanded to the large single copy (LSC) region, resulting in complete replication of some genes in the IR region, the LSC region of S. pubescents subsp . Microphylla was significantly shorter than those of S. oblate and S. reticulate subsp . Amurensis . Similar to most higher plants, these three species have a preference for their codons ending with A/T. Conclusions We consider the genus Syringa to be a synphyletic group. The nucleotide variability and phylogenetic analyses showed that Syringa differentiated before Ligustrum and Ligustrum developed from Syringa . We propose removing the existing section division and directly dividing Syringa into five series.