Background

Persicaria maackiana (Regel) is a potential medicinal plant that exerts anti-diabetic effects. However, the lack of genomic information on P. maackiana hinders research at the molecular level.

Objective

Herein, we aimed to construct a draft genome assembly and obtain comprehensive genomic information on P. maackiana using high-throughput sequencing tools PacBio Sequel II and Illumina.

Methods

Persicaria maackiana samples from three natural populations in Gaecheon, Gichi, and Uiryeong reservoirs in South Korea were used to generate genomic DNA libraries, perform genome de novo assembly, gene ontology analysis, phylogenetic tree analysis, genotyping, and identify microsatellite markers.

Results

The assembled P. maackiana genome yielded 32,179 contigs. Assessment of assembly integrity revealed 1503 (93.12%) complete Benchmarking Universal Single-Copy Orthologs. A total of 64,712 protein-coding genes were predicted and annotated successfully in the protein database. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs, 13,778 genes were annotated into 18 categories. Genes that activated AMPK were identified in the KEGG pathway. A total of 316,992 microsatellite loci were identified, and primers targeting the flanking regions were developed for 292,059 microsatellite loci. Of these, 150 primer sets were randomly selected for amplification, and 30 of these primer sets were identified as polymorphic. These primers amplified 3–9 alleles. The mean observed and expected heterozygosity were 0.189 and 0.593, respectively. Polymorphism information content values of the markers were 0.361–0.754.

Conclusion

Collectively, our study provides a valuable resource for future comparative genomics, phylogeny, and population studies of P. maackiana.

中文翻译：

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使用 Illumina 和 PacBio 测序对韩国 Persicaria maackiana（蓼科）进行基因组组装和微卫星标记开发

背景

Persicaria maackiana (Regel) 是一种具有抗糖尿病作用的潜在药用植物。然而， P. maackiana基因组信息的缺乏阻碍了分子水平的研究。

客观的

在此，我们的目标是使用高通量测序工具 PacBio Sequel II 和 Illumina构建基因组草图并获得P. maackiana的全面基因组信息。

方法

来自韩国盖川、吉知和宜宁水库三个自然种群的Persicaria maackiana样本被用来生成基因组 DNA 文库，进行基因组从头组装、基因本体分析、系统发育树分析、基因分型和鉴定微卫星标记。

结果

组装的P. maackiana基因组产生了 32,179 个重叠群。组装完整性评估显示 1503 个（93.12%）完整的基准通用单拷贝直向同源物。蛋白质数据库中总共成功预测并注释了64,712个蛋白质编码基因。在京都基因和基因组百科全书 (KEGG) 直向同源物中，13,778 个基因被注释为 18 个类别。 KEGG 通路中鉴定出了激活 AMPK 的基因。总共鉴定了 316,992 个微卫星位点，并针对 292,059 个微卫星位点开发了针对侧翼区域的引物。其中，随机选择150对引物进行扩增，其中30对引物被鉴定为多态性。这些引物扩增了 3-9 个等位基因。观察到的平均杂合度和预期杂合度分别为 0.189 和 0.593。标记多态性信息含量值为0.361~0.754。

结论

总的来说，我们的研究为未来P. maackiana的比较基因组学、系统发育和种群研究提供了宝贵的资源。