Genetic divergence of the endangered seagrass Zostera japonica Ascherson & Graebner between temperate and subtropical coasts of China based on partial sequences of matK and ITS

• Zostera japonica occurs both in the temperate and subtropical coastal waters in China.
• Genetic divergence of Z. japonica was studied based on sequences of matK and ITS.
• There was significant population divergence between the northern and southern areas.

The seagrass Zostera japonica Ascherson & Graebner is a unique species that occurs both in the northern temperate and southern subtropical/tropical coastal areas of China. The nuclear rDNA-internal transcribed spacer (ITS) and the chloroplast matK-intron were used to survey the genetic diversity and structure of Z. japonica from the northern and southern populations. The ITS and matK sequences contained 15 (including four indels) and 2 polymorphic sites, respectively. The genetic distance FST (0.993–1.000) based on the ITS suggested a significant genetic divergence between the northern and southern populations. Limited dispersal ability, occurrence of a large geographic gap of the species’ distribution range, and the isolation effects of marginal seas along China’s coastline during the Pleistocene glaciations, may be the main reasons for this divergence. In addition, the southern populations showed significant genetic divergence between both sides of the Qiongzhou Strait and showed a higher genetic diversity than those from the north based on ITS. A recovery or conservation strategy for this species in China should be planned based on the genetic information among/within populations.