Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea.
Genes Genomics. 2024 Feb;46(2):187-202. doi: 10.1007/s13258-023-01479-2. Epub 2024 Jan 19.
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.
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.
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.
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.
Collectively, our study provides a valuable resource for future comparative genomics, phylogeny, and population studies of P. maackiana.
大花蓼（Persicaria maackiana（Regel））是一种具有降血糖作用的潜在药用植物。然而，由于缺乏大花蓼的基因组信息，限制了其在分子水平上的研究。
本研究旨在利用 PacBio Sequel II 和 Illumina 高通量测序工具构建大花蓼的基因组草图，并获得其全面的基因组信息。
从韩国加川、基池和丽水水库的三个自然种群中采集大花蓼样本，用于生成基因组 DNA 文库，进行基因组从头组装、基因本体论分析、系统发育树分析、基因分型和微卫星标记鉴定。
组装的大花蓼基因组得到 32179 个 contigs。组装完整性评估显示，有 1503 个（93.12%）完整的 Benchmarking Universal Single-Copy Orthologs。在蛋白质数据库中成功预测并注释了 64712 个蛋白质编码基因。在京都基因与基因组百科全书（KEGG）直系同源物中，有 13778 个基因被注释到 18 个类别中。KEGG 途径中鉴定出激活 AMPK 的基因。共鉴定出 316992 个微卫星位点，并为 292059 个微卫星位点设计了侧翼区域的引物。其中，随机选择了 150 对引物进行扩增，其中 30 对引物被鉴定为多态性。这些引物扩增出 3-9 个等位基因。观察到的和预期的杂合度分别为 0.189 和 0.593。标记的多态信息含量值为 0.361-0.754。
综上所述，本研究为大花蓼的比较基因组学、系统发育和群体研究提供了有价值的资源。
