Using next-generation sequencing technology, 26 microsatellite markers were developed and genotyped by capillary electrophoresis for Hopea hainanensis Merrill & Chun, an endangered tree species in Hainan Island and northern Vietnam. Twelve markers were found to be polymorphic in this species. Primer transferability was tested with H. chinensis Hand.-Mazz. and H. reticulata Tardieu, in which 3 and 7 microsatellite markers were found to be polymorphic, separately. The 12 polymorphic microsatellite markers could be applied to population genetic studies aimed at H. hainanensis as well as its close relatives, facilitating the conservation and restoration of these endangered but valuable Hopea species.

Fifty individuals of Hopea hainanensis were collected from 10 natural populations at Hainan Island, China. Two additional species, H. chinensis and H. reticulata, were included for cross-species amplification. The genomic DNA of one H. hainanensis sample was used for Illumina Paired-end sequencing. A genomic DNA library with 350-450bp inserts was constructed, and then was sequenced by an Illumina HiSeq 2500 system. Raw sequencing data were filtered, merged and clustered, and screened by MISA to identify microsatellite motifs. Primers were designed using Primer Premier 5.0. Primers specificity were tested by PCR amplification, and then labeled with the fluorescent dye to conduct genotyping analysis by capillary electrophoresis on an ABI 3730xl DNA Analyzer.

This file contains SSR genotypes of three Hopea species used in this study. Two Hopea species, H. hainanensis and H. reticulata are putative autotetraploids, while H. chinensis is a diploid species. Missing genotypes are represented using four or two zeros according to the ploidy of the species. For tetraploid species, SSR loci lacking dosage information are represented by the corresponding allelic phenotypes, and missing alleles in those loci are coded using zeros.