Complete chloroplast genomes of four Syzygium species and comparative analysis with other Syzygium species

Syzygium Gaertn., the largest genus in Myrtaceae, is the most species-rich tree genus worldwide. Despite some attempts at phylogenetic work on this genus, the phylogenetic positions of many endemic species are difficult to determine due to the sample collection difficulties. In this study, we assembled four complete chloroplast (cp.) genomes of Syzygium and annotated one published cp. genome without an available annotation. The Syzygium cp. genomes were highly conserved in genome size structure, GC content, gene content, and gene order. The single-copy regions and intergenic regions were more diverged than the inverted repeat regions and gene regions. We identified eight hyper-variable regions in the Syzygium cp. genomes, which could be used to develop accurate and cost-effective molecular markers. By using the recently published phylogenetic tree as the backbone structure, we reconstructed a phylogenetic tree to detect the phylogenetic positions of some endemic or narrowly distributed species. The 13 newly analyzed species fell into three different subgenera. We found that the Chinese endemic Syzygium species did not cluster into a monophyletic clade and instead belonged to three subgenus. This study reported the phylogenetic position of Chinese endemic Syzygium species for the first time and revealed that China may be one of the main diversity centers of this genus.