Wang Xia, Guo Lei, Ding Lulu, Medina Leopoldo, Wang Ruihong, Li Pan
Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China.
Real Jardín Botánico, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
Front Plant Sci. 2024 Sep 3;15:1439206. doi: 10.3389/fpls.2024.1439206. eCollection 2024.
L., a genus of the Scrophulariaceae, is a group of important medicinal plants used for eliminating heat and detoxifying. East Asia has an abundance of potentially medicinal species, and it serves as a secondary diversity center of the genus. However, the genomic resources available for germplasm identification and pharmaceutical exploration of East Asian are insufficient, hindering its commercial and industrial development. Additionally, the interspecific relationships of most East Asian species remain unclear.
In this study, we sequenced the leaves of 25 East Asian species of the genus , assembled and annotated the complete chloroplast genomes, and subsequently performed comparative and phylogenetic analyses on these genomes.
The conserved plastome length of these 25 species ranged from 151,582 bp to 153,239 bp, containing a total of 132 coding genes, including 18 duplicated genes and 114 unique genes. Through genome alignment of these 25 species, 38-53 repeated sequences and 7 shared SSRs were identified, along with regions with high nucleotide polymorphism (Pi), which could potentially serve as molecular markers for species identification. The genome structure, gene content, and arrangement showed conservation, while variations were observed in the IR boundary regions and IGS. Phylogenetic inferences based on whole plastomes or on coding sequences (CDS) only yielded congruent results. We categorized the 25 East Asian species into six distinct clades and further explored their interspecies relationships using morphological characteristics, such as flower color, the relative position of stamens and corolla, and plant height. This could lay a genetic basis for future resource development of in East Asia.
地黄属玄参科，是一类重要的药用植物，具有清热凉血、解毒之功效。东亚地区拥有丰富的潜在药用物种，是地黄属的次生多样性中心。然而，目前可用于东亚地黄种质鉴定和药物开发的基因组资源不足，阻碍了其商业和产业发展。此外，大多数东亚地黄物种的种间关系仍不明确。
在本研究中，我们对25种东亚地黄属植物的叶片进行了测序，组装并注释了完整的叶绿体基因组，随后对这些基因组进行了比较和系统发育分析。
这25个物种的叶绿体基因组长度保守，范围在151,582 bp至153,239 bp之间，共包含132个编码基因，其中包括18个重复基因和114个独特基因。通过对这25个物种的基因组比对，鉴定出38 - 53个重复序列和7个共享的简单序列重复（SSR），以及具有高核苷酸多态性（Pi）的区域，这些区域有可能作为物种鉴定的分子标记。基因组结构、基因含量和排列显示出保守性，但在反向重复序列（IR）边界区域和间隔序列（IGS）中观察到了变异。基于整个叶绿体基因组或仅基于编码序列（CDS）的系统发育推断得出了一致的结果。我们将这25种东亚地黄物种分为六个不同的进化枝，并利用花的颜色、雄蕊和花冠的相对位置以及株高等形态特征进一步探索了它们的种间关系。这可为东亚地黄未来的资源开发奠定遗传基础。
