Background Gardenia jasminoides 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. Methods In this study, one wild and one cultivated gardenia materials were resequenced using IlluminaHiSeq sequencing platform and the data were evaluated to understand the genomic characteristics of G. jasminoides. Results 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 G. jasminoides was further explored, which provided basic data for molecular breeding and genetic diversity of G. jasminoides in the future.

中文翻译：

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药用植物栀子的全基因组重测序分析

【背景】 栀子是一种中药用植物，具有较高的药用价值和经济价值，具有丰富的遗传多样性，但对其遗传多样性的研究还远远不够。方法本研究利用IlluminaHiSeq测序平台对1份野生栀子材料和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。结果经过数据分析，结果显示11.77G的干净数据，Q30达到了90.96%。样本与参考基因组平均比对率为96.08%，平均覆盖深度为15X，基因组覆盖率为85.93%。鉴定了FD和YP1的SNP，并分别开发了3,087,176和3,241,416个SNP。另外，SNP非同义突变、InDel突变、样本与参考基因组之间还检测到SV突变和CNV突变，并对DNA水平变异的基因进行KEGG、GO和COG数据库注释。进一步探究了茉莉花主要药用物质藏红花素和栀子生物合成途径中的结构基因变异，为今后茉莉花分子育种和遗传多样性提供基础数据。