Lindera glauca (Lauraceae) is an economically important East Asian forest tree characterized by a dioecy in China and apomixis in Japan. However, patterns of population genetic diversity and structure of this species remain unknown for this species due to a lack of efficient molecular markers. In this study, we employed Illumina sequencing to analyze the transcriptomes of the female and male flower buds of L. glauca. We retrieved 59,753 and 75,075 unigenes for the female and male buds, respectively. Based on sequence similarity, 44,379 (74.27 %) unigenes for the female and 45,414 (60.49 %) unigenes for the male were matched to public databases. We identified 11,127 putative differentially expressed genes between the female and male buds and 20,048 expressed sequence tag-simple sequence repeats (EST-SSRs). From 3147 primer pairs designed successfully, 120 were selected for validation of polymorphism, and 13 could reliably amplify polymorphic bands and exhibited moderate levels of genetic diversity (e.g., NA = 4.42; HE = 0.56) when surveyed across 96 individuals of altogether six L. glauca populations from China and Japan. One of the three population genetic clusters identified in China was fixed in Japan, suggesting a historical population bottleneck following island immigration. The present study has generated a wealth of transcriptome data for future functional genomic research focused on the variable reproductive system of L. glauca (dioecy, apomixis) as well as EST-SSR markers for population genetics studies and its intriguing evolutionary shift from dioecy to apomixis in the wake of island colonization.
