Differentiated population structure of a genetically depauperate mangrove species Ceriops tagal revealed by both Sanger and deep sequencing

► We use both chloroplast and nuclear genes to examine the genetic variation of Ceriops tagal across Indo-West Pacific. ► Both sanger and deep sequencing are adopted, representing the first large-scale sequencing study in this species. ► An extremely low level of genetic diversity but a highly differentiated population structure among regions was revealed. ► Such pattern may result from the genetic bottlenecks followed by subsequent recolonization. ► Genetic information obtained from this study is essential for conservation and breeding strategies of C. tagal.