State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Silviculture and Tree Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
Sci Rep. 2020 Jul 22;10(1):12188. doi: 10.1038/s41598-020-68092-1.
The rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa 'Margo Koster' and performed comparative analyses with sequences previously published for other species in the Rosaceae family. The chloroplast genome of Rosa 'Margo Koster', with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa 'Margo Koster' were verified and manually corrected by Sanger sequencing. Comparative genome analysis showed that the IR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. The phylogenetic analysis within the Rosa genus showed that Rosa 'Margo Koster' is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species.
玫瑰是最重要的观赏木本植物之一，因为其广泛的用途和高经济价值。在此，我们对微型玫瑰品种 Rosa 'Margo Koster' 的完整叶绿体基因组进行了测序，并与蔷薇科其他物种先前发表的序列进行了比较分析。Rosa 'Margo Koster' 的叶绿体基因组大小为 157,395 bp，具有被子植物叶绿体基因组的典型四部分圆形结构，共包含 81 个蛋白编码基因、30 个 tRNA 基因和 4 个 rRNA 基因。通过 Sanger 测序验证并手动校正了叶绿体基因组的连接区。比较基因组分析表明，IR 收缩和扩张事件导致了 rps19 和 ycf1 假基因。在蔷薇属内的系统发育分析表明，Rosa 'Margo Koster' 与 Rosa odorata 比与其他 Rosa 物种更接近。此外，我们鉴定和筛选了高度变异的序列和 cpSSR，并通过 Sanger 测序和毛细管电泳比较了它们区分玫瑰品种的能力。结果表明，15 个 cpSSR 是多态的，但在一组玫瑰品种中，它们的区分能力仅中等。然而，在 cpSSR 侧翼区发现了 150 多个单核苷酸变异 (SNV)，结果表明这些 SNV 具有更高的变异性和更强的玫瑰品种分析能力。这些发现表明，叶绿体基因组中的核苷酸突变可能是玫瑰品种鉴别和 DNA 分析的有效而强大的工具。蔷薇属叶绿体基因组序列中的这些分子标记将促进该物种的种群和系统发育研究及其他相关研究。
