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

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....

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Autores principales: Zhou, Tao, Li, Zhong-Hu, Bai, Guo-Qing, Feng, Li, Chen, Chen, Wei, Yue, Chang, Yong-Xia, Zhao, Gui-Fang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6272838/
https://www.ncbi.nlm.nih.gov/pubmed/26907245
http://dx.doi.org/10.3390/molecules21030166
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author Zhou, Tao
Li, Zhong-Hu
Bai, Guo-Qing
Feng, Li
Chen, Chen
Wei, Yue
Chang, Yong-Xia
Zhao, Gui-Fang
author_facet Zhou, Tao
Li, Zhong-Hu
Bai, Guo-Qing
Feng, Li
Chen, Chen
Wei, Yue
Chang, Yong-Xia
Zhao, Gui-Fang
author_sort Zhou, Tao
collection PubMed
description 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.
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spelling pubmed-62728382018-12-28 Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae) Zhou, Tao Li, Zhong-Hu Bai, Guo-Qing Feng, Li Chen, Chen Wei, Yue Chang, Yong-Xia Zhao, Gui-Fang Molecules Article 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. MDPI 2016-02-23 /pmc/articles/PMC6272838/ /pubmed/26907245 http://dx.doi.org/10.3390/molecules21030166 Text en © 2016 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons by Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhou, Tao
Li, Zhong-Hu
Bai, Guo-Qing
Feng, Li
Chen, Chen
Wei, Yue
Chang, Yong-Xia
Zhao, Gui-Fang
Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae)
title Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae)
title_full Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae)
title_fullStr Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae)
title_full_unstemmed Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae)
title_short Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae)
title_sort transcriptome sequencing and development of genic ssr markers of an endangered chinese endemic genus dipteronia oliver (aceraceae)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6272838/
https://www.ncbi.nlm.nih.gov/pubmed/26907245
http://dx.doi.org/10.3390/molecules21030166
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