Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea.
Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Korea.
PLoS One. 2022 Oct 5;17(10):e0275590. doi: 10.1371/journal.pone.0275590. eCollection 2022.
Euonymus hamiltonianus and its relatives (Celastraceae family) are used for ornamental and medicinal purposes. However, species identification in Euonymus is difficult due to their morphological diversity. Using plastid genome (plastome) data, we attempt to reveal phylogenetic relationship among Euonymus species and develop useful markers for molecular identification. We assembled the plastome and nuclear ribosomal DNA (nrDNA) sequences from five Euonymus lines collected from South Korea: three Euonymus hamiltonianus accessions, E. europaeus, and E. japonicus. We conducted an in-depth comparative analysis using ten plastomes, including other publicly available plastome data for this genus. The genome structures, gene contents, and gene orders were similar in all Euonymus plastomes in this study. Analysis of nucleotide diversity revealed six divergence hotspots in their plastomes. We identified 339 single nucleotide polymorphisms and 293 insertion or deletions among the four E. hamiltonianus plastomes, pointing to abundant diversity even within the same species. Among 77 commonly shared genes, 9 and 33 were identified as conserved genes in the genus Euonymus and E. hamiltonianus, respectively. Phylogenetic analysis based on plastome and nrDNA sequences revealed the overall consensus and relationships between plastomes and nrDNAs. Finally, we developed six barcoding markers and successfully applied them to 31 E. hamiltonianus lines collected from South Korea. Our findings provide the molecular basis for the classification and molecular taxonomic criteria for the genus Euonymus (at least in Korea), which should aid in more objective classification within this genus. Moreover, the newly developed markers will be useful for understanding the species delimitation of E. hamiltonianus and closely related species.
美实卫矛及其近缘种（卫矛科）被广泛用于观赏和药用。然而，由于其形态多样性，美实卫矛属种的鉴定较为困难。本研究利用质体基因组（质体组）数据，旨在揭示美实卫矛属种间的系统发育关系，并开发用于分子鉴定的有用标记。我们从韩国采集的 5 条美实卫矛属植物（3 个美实卫矛种、欧洲卫矛和日本卫矛）中组装了质体基因组和核核糖体 DNA（nrDNA）序列。我们利用包括该属其他已公开的质体组数据在内的 10 个质体组进行了深入的比较分析。在所研究的美实卫矛属植物的所有质体基因组中，基因组结构、基因含量和基因顺序都很相似。核苷酸多样性分析揭示了其质体基因组中的 6 个分化热点。我们在 4 个美实卫矛种的质体基因组中鉴定了 339 个单核苷酸多态性和 293 个插入/缺失，这表明即使在同一物种内也存在丰富的多样性。在 77 个共同共享的基因中，分别有 9 个和 33 个被鉴定为美实卫矛属和美实卫矛种的保守基因。基于质体组和 nrDNA 序列的系统发育分析显示了整体共识以及质体组和 nrDNA 之间的关系。最后，我们开发了 6 个条形码标记，并成功应用于从韩国采集的 31 个美实卫矛种。本研究为美实卫矛属（至少在韩国）的分类和分子分类标准提供了分子基础，这将有助于该属内更客观的分类。此外，新开发的标记将有助于理解美实卫矛及其近缘种的物种界限。
