Zhang Yue, Zhang Xue, Wang Yue-Hua, Shen Shi-Kang
School of Life Sciences and Laboratory of Ecology and Evolutionary Biology, Yunnan University, Yunnan, China.
Front Plant Sci. 2017 Sep 26;8:1664. doi: 10.3389/fpls.2017.01664. eCollection 2017.
Transcriptome sequences generated by next-generation sequencing (NGS) technologies can be utilized to rapidly detect and characterize a large number of gene-based microsatellites from different plants. Lévl. is a perennial woody species from the family Ericaceae and an endangered plant with high ornamental value endemic to Southwestern China. Nevertheless, the genetic and genomic information of remain unknown. In this study, we performed transcriptome sequencing for leaf samples, and generated large transcript sequences for functional characterization and development gene-associated SSR markers. A total of 164,242 unigenes were assembled and 115,089 (70.07%) unigenes were successfully annotated in public databases. In addition, a total of 15,314 potential EST-SSRs were identified, and the frequency of SSRs in the unigenes was 9.32%, with an average of one EST-SSR per 5.65 kb. The most abundant type was repeated di-nucleotide (54.63%), followed by mono- (26.03%) and tri-nucleotide (18.51%) repeats. Based on the SSR-containing sequence, 100 primer pairs were randomly selected and synthesized and used for assessment of the polymorphism. Thirty-six primer pairs were polymorphic and revealed polymorphism among 20 individuals from four populations. A total of 197 alleles were identified, with an average of 5.472 alleles per locus. The Polymorphism Information Content ranged from 0.154 to 0.870, with a mean of 0.482. The newly developed EST-SSR markers exhibited high transferability (58.33-83.33%) among the six subgenera. Thus, these novel EST-SSR markers developed would provide valuable sequence resources for population structure, genetic diversity analysis, and genetic resource assessments of and its related species.
通过下一代测序（NGS）技术生成的转录组序列可用于快速检测和表征来自不同植物的大量基于基因的微卫星。Lévl.是杜鹃花科的一种多年生木本植物，是中国西南地区特有的具有高观赏价值的濒危植物。然而，其遗传和基因组信息仍然未知。在本研究中，我们对叶片样本进行了转录组测序，并生成了大量转录序列用于功能表征和开发与基因相关的SSR标记。总共组装了164,242个单基因，其中115,089个（70.07%）单基因在公共数据库中成功注释。此外，共鉴定出15,314个潜在的EST-SSR，单基因中SSR的频率为9.32%，平均每5.65 kb有一个EST-SSR。最丰富的类型是二核苷酸重复（54.63%），其次是单核苷酸（26.03%）和三核苷酸（18.51%）重复。基于含SSR的序列，随机选择并合成了100对引物，用于评估多态性。36对引物具有多态性，并在来自四个种群的20个个体中显示出多态性。共鉴定出197个等位基因，每个位点平均有5.472个等位基因。多态性信息含量范围为0.154至0.870，平均值为0.482。新开发的EST-SSR标记在六个亚属中表现出高转移性（58.33 - 83.33%）。因此，开发的这些新型EST-SSR标记将为该植物及其相关物种的种群结构、遗传多样性分析和遗传资源评估提供有价值的序列资源。
