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Int. J. Mol. Sci. 2015, 16(6), 12855-12870; doi:10.3390/ijms160612855

De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis

1
School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China
2
School of Life Sciences, Luoyang Normal University, 71 Longmen Road, Luoyang 471022, China
*
Author to whom correspondence should be addressed.
Academic Editor: Marcello Iriti
Received: 15 April 2015 / Revised: 12 May 2015 / Accepted: 27 May 2015 / Published: 5 June 2015
(This article belongs to the Special Issue Plant Molecular Biology)
View Full-Text   |   Download PDF [2112 KB, uploaded 5 June 2015]   |  

Abstract

Tapiscia sinensis Oliv (Tapisciaceae) is an endangered species native to China famous for its androdioecious breeding system. However, there is a lack of genomic and transcriptome data on this species. In this study, the Tapiscia sinensis transcriptomes from two types of sex flower buds were sequenced. A total of 97,431,176 clean reads were assembled into 52,169 unigenes with an average length of 1116 bp. Through similarity comparison with known protein databases, 36,662 unigenes (70.27%) were annotated. A total of 10,002 (19.17%) unigenes were assigned to 124 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 10,371 simple sequence repeats (SSRs) were identified in 8608 unigenes, with 16,317 pairs of primers designed for applications. 150 pairs of primers were chosen for further validation, and the 68 pairs (45.5%) were able to produce clear polymorphic bands. Six polymorphic SSR markers were used to Bayesian clustering analysis of 51 T. sinensis individuals. This is the first report to provide transcriptome information and to develop large-scale SSR molecular markers for T. sinensis. This study provides a valuable resource for conservation genetics and functional genomics research on T. sinensis for future work. View Full-Text
Keywords: Tapiscia sinensis; transcriptome; Illumina sequencing; EST-SSRs (Expressed sequence tag simple sequence repeats) Tapiscia sinensis; transcriptome; Illumina sequencing; EST-SSRs (Expressed sequence tag simple sequence repeats)
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, X.-J.; Wang, Y.-Y.; Xu, Y.-N.; Yan, R.-S.; Zhao, P.; Liu, W.-Z. De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis. Int. J. Mol. Sci. 2015, 16, 12855-12870.

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