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Molecules 2015, 20(12), 21214-21231; doi:10.3390/molecules201219758

Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae)

1
Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi’an 710069, China
2
College of Biopharmaceutical and Food Engineering, Shangluo University, Beixin Street, Shangluo 726000, China
*
Author to whom correspondence should be addressed.
Academic Editor: Derek J. McPhee
Received: 8 October 2015 / Revised: 5 November 2015 / Accepted: 9 November 2015 / Published: 30 November 2015
(This article belongs to the Section Molecular Diversity)
View Full-Text   |   Download PDF [1774 KB, uploaded 30 November 2015]   |  

Abstract

Gynostemma pentaphyllum is an important medicinal herb of the Cucurbitaceae family, but limited genomic data have hindered genetic studies. In this study, transcriptomes of two closely-related Gynostemma species, Gynostemma cardiospermum and G. pentaphyllum, were sequenced using Illumina paired-end sequencing technology. A total of 71,607 nonredundant unigenes were assembled. Of these unigenes, 60.45% (43,288) were annotated based on sequence similarity search with known proteins. A total of 11,059 unigenes were identified in the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. A total of 3891 simple sequence repeats (SSRs) were detected in 3526 nonredundant unigenes, 2596 primer pairs were designed and 360 of them were randomly selected for validation. Of these, 268 primer pairs yielded clear products among six G. pentaphyllum samples. Thirty polymorphic SSR markers were used to test polymorphism and transferability in Gynostemma. Finally, 15 SSR makers that amplified in all 12 Gynostemma species were used to assess genetic diversity. Our results generated a comprehensive sequence resource for Gynostemma research. View Full-Text
Keywords: Gynostemma; transcriptome; illumina paired-end sequencing; de novo assembly; EST-SSR Gynostemma; transcriptome; illumina paired-end sequencing; de novo assembly; EST-SSR
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Zhao, Y.-M.; Zhou, T.; Li, Z.-H.; Zhao, G.-F. Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae). Molecules 2015, 20, 21214-21231.

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