title: Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae).
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.
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China. woody196@163.com.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China. lizhonghu@nwu.edu.cn.
authors.forename: Zhong-Hu
authors.initials: ZH
authors.lastname: Li
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China. bgq@ms.xab.ac.cn.|Xi'an Botanical Garden of Shaanxi Province, Xi'an 710061, China. bgq@ms.xab.ac.cn.
authors.forename: Guo-Qing
authors.initials: GQ
authors.lastname: Bai
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China. jjfl.007@163.com.
authors.forename: Li
authors.initials: L
authors.lastname: Feng
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China. Estelleplus@163.com.
authors.forename: Chen
authors.initials: C
authors.lastname: Chen
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China. weiyue0101@sina.com.
authors.forename: Yue
authors.initials: Y
authors.lastname: Wei
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China. changyongxia_mia@sina.com.
authors.forename: Yong-Xia
authors.initials: YX
authors.lastname: Chang
authors.affiliation: Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China. gfzhao@nwu.edu.cn.
authors.forename: Gui-Fang
authors.initials: GF
authors.lastname: Zhao
mesh_terms: D031001:Aceraceae / Q000145:classification / Q000235:genetics*; D002681:China; D017931:DNA Primers / Q000737:chemistry / Q000235:genetics; D056727:Endangered Species; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005819:Genetic Markers; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D011110:Polymorphism, Genetic; D059467:Transcriptome
chemical_list: D017931:DNA Primers; D005819:Genetic Markers
keywords: Dipteronia; de novo assembly; genetic diversity; genic SSR; transcriptome sequencing