The complete chloroplast genome sequence of the endangered species Syringa pinnatifolia (Oleaceae)

22 January 2019

Zhang, Jingwen; Jiang, Zaimin; Zhao, Han; Su, Hao; Cai, Jing

Syringa pinnatifolia is an endangered endemic species with important ornamental and medicinal value in China that needs urgent protection. In this article, we report the complete chloroplast (cp) genome structure of the S. pinnatifolia and its evolution inferred through comparative studies with other related species. The S. pinnatifolia cp genome was 155,326 bp and contained a large single copy region (LSC) of 86,167 bp and a small single copy region (SSC) of 17,775 bp and a pair of inverted repeat regions (IRs) of 25,692 bp. A total of 113 unique genes were annotated, including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. The GC content of the S. pinnatifolia cp genome was 37.9%, and the corresponding values in the LSC, SSC and IR regions were 36.0%, 32.1%, 43.2% respectively. Along repetitive sequences analysis revealed that the S. pinnatifolia cp genome contained 38 repeats. In addition, Microsatellite marker detection analysis identified 253 simple sequence repeats (SSRs), which provides opportunities for future studies of the population genetics and phylogenetic relationships of Syringa plants. Phylogenetic analysis of 29 selected cp genomes revealed that S. pinnatifolia was closely related to Syringa vulgaris and all 27 Lamiales species formed a lineage separate from the two outgroup species. This newly characterized S. pinnatifolia chloroplast genome will provide useful genomic resource of phylogenetic inference and develop more genetic markers for species discrimination in the genus Syringa.