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.

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  PLOS ONE.2022; 17(10): e0275590.     CrossRef
• Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae
  Yongtan Li, Yan Dong, Yichao Liu, Xiaoyue Yu, Minsheng Yang, Yinran Huang
  Frontiers in Plant Science.2021;[Epub]     CrossRef
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Eclipta prostrata and E. alba are annual herbal medicinal plants and have been used as Chinese medicinal tonics. Both species are widely distributed in tropical and subtropical regions as well as in Korea. Both species have similar morphological features but E. alba has smoother leaf blade margins compared with E. prostrata. Although both species are utilized as oriental medicines, E. prostrata is more widely used than E. alba. Morphological semblances have confounded identification of either species. Here, we report the complete chloroplast genomes of both species to provide an authentication system between the two species and understand their diversity. Both chloroplast genomes were 151,733–151,757 bp long and composed of a large single copy (83,285–83,300 bp), a small single copy (18,283–18,346 bp), and a pair of inverted repeats (25,075–25,063 bp). Gene annotation revealed 80 protein coding genes, 30 tRNA genes and four rRNA genes. A phylogenetic analysis revealed that the genus Eclipta is grouped with Heliantheae tribe species in the Asteraceae family. A comparative analysis verified 29 InDels and 58 SNPs between chloroplast genomes of E. prostrata and E. alba. The low chloroplast genome sequence diversity indicates that both species are really close to each other and are not completely diverged yet. We developed six DNA markers that distinguish E. prostrata and E. alba based on the polymorphisms of chloroplast genomes between E. prostrata and E. alba. The chloroplast genome sequences and the molecular markers generated in this study will be useful for further research of Eclipta species and accurate classification of medicinal herbs.

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• A review on the phytochemicals of Eclipta prostrata and Eclipta alba: Antioxidants and antidiabetic activities
  Nur Nahar Sohe, John Sushma Nannepaga, Wan Amir Nizam Wan Ahmad, Norizah Mhd. Sarbon, Mannur Ismail Shaik
  Pharmacological Research - Natural Products.2026; 10: 100483.     CrossRef
• Construction of a Single File Reference Transcriptome Database for Deodeok (Codonopsis lanceolata) and Sseumbagwi (Ixeridium dentata)
  Tae-Ho Lee, Yun-Ho Oh, Ji-Nam Kang, Si-Myung Lee
  Korean Journal of Breeding Science.2023; 55(4): 321.     CrossRef
• Unraveling the secrets of Eclipta alba (L.) Hassk.: a comprehensive study of morpho-anatomy and DNA barcoding
  D. K. Wahyuni, B. F. Yoku, S. R. Mukarromah, P. R. Purnama, M. Ilham, G. A. Rakashiwi, D. T. Indriati, Junairiah, S. Wacharasindhu, S. Prasongsuk, S. Subramaniam, H. Purnobasuki
  Brazilian Journal of Biology.2023;[Epub]     CrossRef
• Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F1 hybrid combinations
  Hyun-Seung Park, Won Kyung Lee, Sang-Choon Lee, Hyun Oh Lee, Ho Jun Joh, Jee Young Park, Sunggil Kim, Kihwan Song, Tae-Jin Yang
  Scientific Reports.2021;[Epub]     CrossRef
• Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers
  Tao Zhou, Jian Wang, Yun Jia, Wenli Li, Fusheng Xu, Xumei Wang
  International Journal of Molecular Sciences.2018; 19(7): 1962.     CrossRef