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Characterization of Chloroplast Genomes, Nuclear Ribosomal DNAs, and Polymorphic SSR Markers Using Whole Genome Sequences of Two Euonymus hamiltonianus Phenotypes
Plant Breeding and Biotechnology 2019;7:50-61
Published online March 1, 2019
© 2019 Korean Society of Breeding Science.

Junki Lee1,2, Shin-Jae Kang1, Hyeonah Shim1, Sang-Choon Lee3, Nam-Hoon Kim3, Woojong Jang1, Jee Young Park1, Jeong Hwa Kang4, Wan Hee Lee4, Taek Joo Lee4, Gyoungju Nah2, Tae-Jin Yang1,5*

1Deptartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea, 2Genome Analysis Center at National Instrumentation Center for Environmental Management, Seoul National University, Seoul 08826, Korea, 3Phyzen Genomics Institute, Seongnam 13558, Korea, 4Hantaek Botanical Garden, Yongin 17183, Korea, 5Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
Corresponding author: Tae-Jin Yang, tjyang@snu.ac.kr, Tel: +82-2-880-4547, Fax: +82-2-873-2056
Received February 20, 2019; Revised February 23, 2019; Accepted February 23, 2019.
This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Although genomics provides useful tools for crops, most wild resource plants still lack molecular data. To retrieve useful genomic data and thus provide fundamental information for a resource plant, we established a multi-directional approach using two low coverage whole-genome shotgun sequence (WGS) data of Euonymus hamiltonianus, which is a wild resource plant with potential as a medicinal and ornamental plant. We assembled complete chloroplast genome and nuclear ribosomal DNA (nrDNA) sequences and analyzed polymorphic simple sequence repeats (pSSRs) in the nuclear genome based on the comparison of WGS data between two different phenotypes. We developed a bioinformatics pipeline to identify pSSR motifs by systematic comparison of two WGS datasets. The pipeline is composed of multiple steps including end-joining of paired reads, isolation of joined reads harboring SSR motifs derived from unique non-repetitive regions, identification of pSSR via in silico comparison with counterpart WGS reads, design of pSSR primer sets, and validation. The pipeline was applied to WGS data of E. hamiltonianus and identified 161 contigs with pSSR motifs between the two different phenotypes. Based on the pSSR motifs, 20 primer pairs were designed, of which seven were successfully validated as real pSSR markers. We expect this information to be applicable to genomic resources of E. hamiltonianus.
Keywords : Euonymus hmiltonianus, Chloroplast, nrDNA, Polymorphic SSR, Bioinformatic pipeline


March 2019, 7 (1)
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