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De novo transcriptome assembly and development of EST-SSR markers of the endangered Dendrebium nobile (Orchidaceae)

Bin Zhu, Xi Luo, Zuomin Gao, Xin Hu and Qingbei Weng


Dendrobium nobile of the family Orchidaceae has been widely used as an important traditional Chinese herbal medicine and a popular garden flower worldwide. It is mainly distributed in southern Tsinling Mountains of China. However, the wild D. nobile is getting endangered due to its habitat destruction and overexploitation. Deciphering genomic information of D. nobile and developing genetic markers are essential for the formulation of scientific protection measures. Here, the comprehensive transcriptome data of a wild D. nobile ecotype, “chishuijinchai”, was obtained by de novo assembly based on Illumina RNA-seq data. A total of 138,628,272 clean reads were generated after removing the adapters and low-quality reads. All the reads were assembled into 114,191 unigenes with an average length of 918 base pairs (bp). Out of 114,191 unigenes, 39,373 unigenes (34.5%) were annotated based on any of the COG, KEGG, KOG, Pfam, Swiss-Prot and Nr databases. Additionally, 27,614 (24.18%) unigenes were annotated into 3 main GO categories. Moreover, a total of 29,380 SSR (simple sequence repeats) loci located on 22,572 unigenes were identified by MISA. Around 100 primers were randomly selected for polymorphism validation across 8 Dendrobium species. Out of these selected primers, 62 and 29 primers showed inter- and intra-specific polymorphisms, respectively. These findings provide fundamental basis for evolution and population genetic diversity studies of D. nobile, which should be beneficial for the protection of its germplasm resources  

To Cite this article: Zhu, B., X. Luo, Z. Gao, X. Hu and Q. Weng. 2022. De novo transcriptome assembly and development of EST-SSR markers of the endangered Dendrebium nobile (Orchidaceae). Pak. J. Bot., 54(2): DOI:  

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