Tropical Journal of Pharmaceutical Research

Original Research Article | OPEN ACCESS

Comparative transcriptome analysis and simple sequence repeat marker development for two closely related Isodon species used as Xihuangcao herbs

Shanshan Huang^1,2, Weiming Hu¹, Shaohua Zeng¹, Xiaolu Mo², Ying Wang¹

¹Guangdong Provincial Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510610; ²Guangdong Food and Drug Vocational College, Guangzhou 510520, PR China.

For correspondence:- Ying Wang Email: yingwang@scib.ac.cn

Accepted: 14 December 2018 Published: 31 January 2019

Citation: Huang S, Hu W, Zeng S, Mo X, Wang Y. Comparative transcriptome analysis and simple sequence repeat marker development for two closely related Isodon species used as Xihuangcao herbs. Trop J Pharm Res 2019; 18(1):75-84 doi: 10.4314/tjpr.v18i1.12

© 2019 The authors.
This is an Open Access article that uses a funding model which does not charge readers or their institutions for access and distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0) and the Budapest Open Access Initiative (http://www.budapestopenaccessinitiative.org/read), which permit unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited..

Abstract

Purpose: To facilitate the molecular identification of original plants, resolve taxonomic problems and identify standards for ‘Xihuangcao’-based products on the market.

Methods: A transcriptomic analysis of two closely related species, i.e., Isodon serra (Maxim.) (IS) and I. lophanthoides (Buch.-Ham. ex D. Don) Hara, was conducted by using the Illumina HiSeq 2500 platform, and expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on these transcriptomes.

Results: In total, 149,650 and 103,221 contigs were obtained, with N50 values of 1,400 and 1,516, from the IS and I. lophanthoides RNA-Seq datasets, respectively. These contigs were clustered into 107,777 and 68,220 unigenes, which were functionally annotated to identify the genes involved in therapeutic components. In total, 14,138 and 11,756 EST-SSR motifs were identified, and of these motifs, 7,453 and 6,428 were used to design primers for IS and I. lophanthoides, respectively. After PCR verification and fluorescence-based genotyping, 24 SSR markers with bright bands, high polymorphism, and single amplification were obtained and used to identify closely related Isodon species/varieties.

Conclusion: These data could help herbal scientists identify high-quality herbal plants and provide a reference for genetic improvement and population genetic and phylogenetic studies investigating ‘Xihuangcao’ herbs.

Keywords: Xihuangcao, Transcriptome, EST-SSR, Molecular markers