Zhou Xiao-Jun, Wang Yue-Yue, Xu Ya-Nan, Yan Rong-Shan, Zhao Peng, Liu Wen-Zhe
School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
School of Life Sciences, Luoyang Normal University, 71 Longmen Road, Luoyang 471022, China.
Int J Mol Sci. 2015 Jun 5;16(6):12855-70. doi: 10.3390/ijms160612855.
Tapiscia sinensis Oliv (Tapisciaceae) is an endangered species native to China famous for its androdioecious breeding system. However, there is a lack of genomic and transcriptome data on this species. In this study, the Tapiscia sinensis transcriptomes from two types of sex flower buds were sequenced. A total of 97,431,176 clean reads were assembled into 52,169 unigenes with an average length of 1116 bp. Through similarity comparison with known protein databases, 36,662 unigenes (70.27%) were annotated. A total of 10,002 (19.17%) unigenes were assigned to 124 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 10,371 simple sequence repeats (SSRs) were identified in 8608 unigenes, with 16,317 pairs of primers designed for applications. 150 pairs of primers were chosen for further validation, and the 68 pairs (45.5%) were able to produce clear polymorphic bands. Six polymorphic SSR markers were used to Bayesian clustering analysis of 51 T. sinensis individuals. This is the first report to provide transcriptome information and to develop large-scale SSR molecular markers for T. sinensis. This study provides a valuable resource for conservation genetics and functional genomics research on T. sinensis for future work.
银鹊树（省沽油科）是中国特有的濒危物种，以其雄花两性花同株的繁育系统而闻名。然而，该物种缺乏基因组和转录组数据。在本研究中，对两种性别的花芽的银鹊树转录组进行了测序。共97431176条clean reads被组装成52169个单基因，平均长度为1116 bp。通过与已知蛋白质数据库的相似性比较，注释了36662个单基因（70.27%）。使用京都基因与基因组百科全书（KEGG）通路数据库，共有10002个（19.17%）单基因被分配到124条通路。此外，在8608个单基因中鉴定出10371个简单序列重复（SSR），设计了16317对引物用于应用。选择150对引物进行进一步验证，其中68对（45.5%）能够产生清晰的多态性条带。使用6个多态性SSR标记对51个银鹊树个体进行贝叶斯聚类分析。这是首次报道为银鹊树提供转录组信息并开发大规模SSR分子标记。本研究为银鹊树未来的保护遗传学和功能基因组学研究提供了宝贵的资源。
