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

Tao Zhou,Gui-Fang Zhao,Zhong-Hu Li,Li Feng,Yong-Xia Chang,Yue Wei,Chen Chen,Guo-Qing Bai

doi:10.3390/molecules21030166

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.

Highlights

Dipteronia Oliver (Aceraceae) [1] is an endangered endemic genus found in southwestern and central China with only two living species, D. sinensis Oliver and D. dyeriana Henry [2]
After filtering and evaluating the raw reads, a total of 40.6 and 52.6 million reads were generated for D. sinensis and D. dyeriana, with 88.50% Q20 bases and 90.14% Q20 bases, respectively
D. dyeriana were deposited in the NCBI Sequence Read Archive (SRA) under the accession numbers

Summary

Introduction

Dipteronia Oliver (Aceraceae) [1] is an endangered endemic genus found in southwestern and central China with only two living species, D. sinensis Oliver and D. dyeriana Henry [2]. Both species are members of the order Sapindales and family Aceraceae and are perennial woody plants with different natural ranges. D. sinensis is mainly found in central and southwestern China, whereas D. dyeriana is only located in the Yunnan Province in southwestern China. The two living species have small population sizes due to deforestation and weak natural regeneration. D. sinensis and D. dyeriana are listed among Chinese Rare and Endangered Plants and China Species

Results

Discussion

Conclusion