Fujian Academy of Forestry Sciences, Fuzhou, Fujian, China.
College of Landscape and Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
PeerJ. 2023 Sep 18;11:e16056. doi: 10.7717/peerj.16056. eCollection 2023.
is a species of Chinese medicinal plant, which has high medicinal and economic value and rich genetic diversity, but the study on its genetic diversity is far not enough.
In this study, one wild and one cultivated gardenia materials were resequenced using HiSeq sequencing platform and the data were evaluated to understand the genomic characteristics of s.
After data analysis, the results showed that clean data of 11.77G, Q30 reached 90.96%. The average comparison rate between the sample and reference genome was 96.08%, the average coverage depth was 15X, and the genome coverage was 85.93%. The SNPs of FD and YP1 were identified, and 3,087,176 and 3,241,416 SNPs were developed, respectively. In addition, SNP non-synonymous mutation, InDel mutation, SV mutation and CNV mutation were also detected between the sample and the reference genome, and KEGG, GO and COG database annotations were made for genes with DNA level variation. The structural gene variation in the biosynthetic pathway of crocin and gardenia, the main medicinal substance of was further explored, which provided basic data for molecular breeding and genetic diversity of s in the future.
栀子是一种中药材，具有很高的药用和经济价值，遗传多样性丰富，但对其遗传多样性的研究还远远不够。
本研究利用 HiSeq 测序平台对 1 份野生栀子和 1 份栽培栀子材料进行重测序，并对数据进行评估，以了解栀子的基因组特征。
数据分析后，结果表明 clean data 为 11.77G，Q30 达到 90.96%。样本与参考基因组的平均比对率为 96.08%，平均覆盖深度为 15X，基因组覆盖度为 85.93%。鉴定出 FD 和 YP1 的 SNPs，分别开发了 3087176 个和 3241416 个 SNPs。此外，还检测到样本与参考基因组之间的 SNP 非同义突变、InDel 突变、SV 突变和 CNV 突变，并对具有 DNA 水平变异的基因进行了 KEGG、GO 和 COG 数据库注释。进一步探讨了栀子中藏红花酸和栀子主要药用物质生物合成途径的结构基因变异，为栀子今后的分子育种和遗传多样性提供了基础数据。
