Abstract
Styrax japonicus sieb. et Zucc. is widely distributed in China with ornamental and medicinal values. However, the transcriptome of S. japonicus has not yet been reported. In this study, we carried out the first transcriptome analysis of S. japonicus and developed a set of expressed sequence tag–simple sequence repeats (EST–SSRs). We obtained 338,570,222 clean reads in total, of which the mean GC content was 41.58%. In total, 136,071 unigenes were obtained having an average length of 611 bp and 71,226 unigenes were favorably annotated in the database. In total, we identified 55,977 potential EST–SSRs from 38,611 unigenes, of which there was 1 SSR per 6.73 kb. The di-nucleotide repeats (40.40%) were the most identified SSRs. One set of 60 primer pairs was randomly selected, and the amplified products in S. japonicus were validated; 28 primer pairs successfully produced clear amplicons. A total of 21 (35%) polymorphic genic SSR markers were identified between two populations. In total, 15 alleles were detected and the average number was 6. The average of observed heterozygosity and expected heterozygosity was 0.614 and 0.552, respectively. The polymorphism information content (PIC) value fluctuated between 0.074 and 0.855, with a mean value of 0.504, which was also the middle level. This study provides useful information for diversity studies and resource assessments of S. japonicus.
Highlights
Styrax japonicus Sieb. et Zucc. (Japanese snowbell) is a deciduous tree species with white bell-shaped flowers that is widely distributed in eastern Asia and China [1], with high ornamental and medicinal values
Simple sequence repeats (SSRs) markers have been broadly used in genetic structure and genetic diversity evaluations [9], and based on their source, such markers are split into two categories: EST–SSRs, determined from transcribed RNA sequences, and g–SSRs, determined from arbitrary genomic sequences [10]
Nine S. japonicus plants with vigorous growth were collected from the National Forest Genetic Resources Platform (NFGR) of Qingdao Agriculture University
Summary
Styrax japonicus Sieb. et Zucc. (Japanese snowbell) is a deciduous tree species with white bell-shaped flowers that is widely distributed in eastern Asia and China [1], with high ornamental and medicinal values. Despite its importance, limited basic bioinformatics data on S. japonicus are accessible. Previous studies on this species mainly focused on seed germination [2,3] and tissue culture [4]. Simple sequence repeats (SSRs) are usually significantly polymorphic and informative, and abundantly spread across the genome in various plants [7]. SSRs possess abundant information and have high reproducibility, locus specificity, ease of scoring, high intraspecific polymorphism, and multiallelic and good genome coverage [8]. In contrast to genomic SSRs, EST–SSRs have more interspecific transferability, Forests 2018, 9, 748; doi:10.3390/f9120748 www.mdpi.com/journal/forests
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