Characterization of Chloroplast Genomes, Nuclear Ribosomal DNAs, and Polymorphic SSR Markers Using Whole Genome Sequences of Two Euonymus hamiltonianus Phenotypes

• 발행기관: 한국육종학회
• 저자명: Junki Lee Shin-Jae Kang Hyeonah Shim Sang-Choon Lee Nam-Hoon Kim Woojong Jang Jee Young Park Jeong Hwa Kang Wan Hee Lee Taek Joo Lee Gyoungju Nah Tae-Jin Yang
• 간행물 정보: 『Plant breeding and biotechnology』Vol.7 No.2, 50~61쪽, 전체 12쪽
• 주제분류: 농수해양 > 기타농수해양
• 파일형태: PDF
• 발행일자: 2019.06.01

영문 초록

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.

목차

INTRODUCTION

MATERIALS AND METHODS

RESULTS

DISCUSSION

ACKNOWLEDGEMENTS

REFERENCES

키워드

Euonymus hmiltonianus Chloroplast nrDNA Polymorphic SSR Bioinformatic pipeline