Development and characterization of 30 microsatellite loci for Plagiorhegma dubium (Berberidaceae).

Bo‐Yun Kim,Yong‐In Kim,Dae‐Hyun Kang,Young‐Dong Kim,Soo‐Rang Lee

doi:10.1002/aps3.1200

Abstract

Premise of the Study Plagiorhegma dubium (Berberidaceae) has been listed as an endangered species in Korea due to extensive collection and destruction of natural habitats. In this study, 30 microsatellite loci, including 25 polymorphic loci, were developed for P. dubium for use in population‐level genetic analyses.Methods and ResultsWe carried out transcriptome sequencing and isolated a total of 30 expressed sequence tag–simple sequence repeat markers from P. dubium using Illumina HiSeq high‐throughput sequencing. To test utility of the developed markers, we genotyped 60 individuals from three populations and estimated the number of alleles and levels of observed and expected heterozygosity. Expected heterozygosity levels ranged from 0.000 to 0.594, 0.000 to 1.000, and 0.000 to 0.744 in the three populations, respectively.ConclusionsThese transcriptome‐derived simple sequence repeat markers are highly polymorphic and can be widely used in characterization of the endangered P. dubium. Population genetic studies with these markers will provide valuable insights for conservation by unraveling evolutionary patterns of P. dubium.

Highlights

PREMISE OF THE STUDY: Plagiorhegma dubium (Berberidaceae) has been listed as an endangered species in Korea due to extensive collection and destruction of natural habitats
We carried out transcriptome sequencing and isolated a total of 30 expressed sequence tag–simple sequence repeat markers from P. dubium using Illumina HiSeq high-throughput sequencing
The plants have a long history of medicinal uses: roots have long been used as folk medicine for stomachache, and the phytochemicals extracted from the plants have shown remedial effects on elevated cholesterol levels (Kong et al, 2004)

Summary

METHODS AND RESULTS

To prepare a cDNA library, total RNA of P. dubium was extracted from a fresh leaf of a single sample from Korea RNA was extracted using the RNeasy Kit version 2.2 (Illumina, San Diego, California, USA) following the manufacturer’s instructions, and was used for TruSeq cDNA library preparation. The RNA libraries were sequenced on the Illumina HiSeq 2000 platform, producing 150-bp paired-end

CONCLUSIONS

F: GCGGACTGTTCTGAAGTGGA R

F: GCCCTCGGAGTTTTTGGAGA R: GCTCCGGCTGCATGAAATAG F: AAGGAGCACAGCGACATGAA R

DATA ACCESSIBILITY

20 NIBRVP0000601483