Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510000, China.
Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
Int J Mol Sci. 2018 Mar 30;19(4):1037. doi: 10.3390/ijms19041037.
(), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of lags far behind largely due to the scarcity of genomic data. In this study, one complete chloroplast (cp) genome of was generated via the genome skimming approach and compared to another available cp genome comprehensively at the genome scale. We found that the structure of the cp genome in was highly consistent with genome size variation which might result from DNA repeat variations in the two cp genomes. Heterogeneous sequence divergence patterns were revealed in different regions of the cp genomes, with most (59 out of 75) of the detected SNPs (single nucleotide polymorphisms) located in the gene regions, whereas most (50 out of 80) of the indels (insertions/deletions) were distributed in the intergenic spacers. In addition, we also found that all the 40 putative coding-region-located SNPs were synonymous mutations. A total of 71 polymorphic cpDNA fragments were further identified, among which 20 loci were selected as potential molecular markers for subsequent population genetics studies of . Moreover, eight polymorphic cpSSR loci were also developed. The sister relationship between and in Garryales was also confirmed based on the cp phylogenomic analyses. Overall, this study will shed new light on the conservation genomics of this endangered plant in the future.
杜仲（Eucommia ulmoides）是杜仲科唯一一种具有重要药用和工业价值的物种，是中国特有的第三纪孑遗植物。然而，由于基因组数据的稀缺，杜仲的种群遗传学研究远远落后。在本研究中，通过基因组扫掠方法生成了一个完整的杜仲叶绿体（cp）基因组，并与另一个可用的杜仲 cp 基因组进行了全面的基因组比较。我们发现，杜仲 cp 基因组的结构与基因组大小的变化高度一致，这可能是由于两个杜仲 cp 基因组中的 DNA 重复变异所致。不同区域的异质序列分化模式在杜仲 cp 基因组中得到揭示，大多数（75 个中的 59 个）检测到的单核苷酸多态性（SNP）位于基因区域，而大多数（80 个中的 50 个）插入/缺失（indels）分布在基因间区。此外，我们还发现所有 40 个假定的编码区定位 SNP 均为同义突变。进一步鉴定出 71 个多态性 cpDNA 片段，其中 20 个位点被选为随后进行杜仲种群遗传学研究的潜在分子标记。此外，还开发了 8 个多态性 cpSSR 位点。基于 cp 系统发育分析，还证实了杜仲与 Garryales 中麻柳树的姐妹关系。总的来说，这项研究将为未来这种濒危植物的保护基因组学提供新的见解。
