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Molecules 2016, 21(3), 166; doi:10.3390/molecules21030166

Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae)

1
Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an 710069, China
2
Xi’an Botanical Garden of Shaanxi Province, Xi’an 710061, China
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editor: Derek J. McPhee
Received: 11 December 2015 / Revised: 25 January 2016 / Accepted: 26 January 2016 / Published: 23 February 2016
(This article belongs to the Section Molecular Diversity)
View Full-Text   |   Download PDF [1083 KB, uploaded 23 February 2016]   |  

Abstract

Dipteronia Oliver (Aceraceae) is an endangered Chinese endemic genus consisting of two living species, Dipteronia sinensis and Dipteronia dyeriana. However, studies on the population genetics and evolutionary analyses of Dipteronia have been hindered by limited genomic resources and genetic markers. Here, the generation, de novo assembly and annotation of transcriptome datasets, and a large set of microsatellite or simple sequence repeat (SSR) markers derived from Dipteronia have been described. After Illumina pair-end sequencing, approximately 93.2 million reads were generated and assembled to yield a total of 99,358 unigenes. A majority of these unigenes (53%, 52,789) had at least one blast hit against the public protein databases. Further, 12,377 SSR loci were detected and 4179 primer pairs were designed for experimental validation. Of these 4179 primer pairs, 435 primer pairs were randomly selected to test polymorphism. Our results show that products from 132 primer pairs were polymorphic, in which 97 polymorphic SSR markers were further selected to analyze the genetic diversity of 10 natural populations of Dipteronia. The identification of SSR markers during our research will provide the much valuable data for population genetic analyses and evolutionary studies in Dipteronia. View Full-Text
Keywords: Dipteronia; transcriptome sequencing; de novo assembly; genic SSR; genetic diversity Dipteronia; transcriptome sequencing; de novo assembly; genic SSR; genetic diversity
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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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Zhou, T.; Li, Z.-H.; Bai, G.-Q.; Feng, L.; Chen, C.; Wei, Y.; Chang, Y.-X.; Zhao, G.-F. Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae). Molecules 2016, 21, 166.

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