Table1_Comparative plastome analyses and evolutionary relationships of 25 East Asian species within the medicinal plant genus Scrophularia (Scrophulariaceae).docx

BackgroudScrophularia 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 Scrophularia 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 Scrophularia are insufficient, hindering its commercial and industrial development. Additionally, the interspecific relationships of most East Asian Scrophularia species remain unclear.
MethodsIn this study, we sequenced the leaves of 25 East Asian species of the genus Scrophularia, assembled and annotated the complete chloroplast genomes, and subsequently performed comparative and phylogenetic analyses on these genomes.
Results and discussionThe 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 Scrophularia 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 Scrophularia in East Asia.

### 背景
玄参属（Scrophularia L.）隶属于玄参科（Scrophulariaceae），是一类兼具重要药用价值的植物类群，可清热解毒。东亚地区拥有大量具备药用潜力的玄参属物种，是该属的第二大多样性分布中心。然而，当前可用于东亚玄参属种质鉴定与药学开发的基因组资源仍较为匮乏，制约了其商业化与产业化发展。此外，多数东亚玄参属物种的种间亲缘关系仍不明确。
### 方法
本研究对25种东亚玄参属植物的叶片进行测序，组装并注释了完整叶绿体基因组（chloroplast genome），随后对这些基因组开展比较基因组学与系统发育分析。
### 结果与讨论
这25个物种的保守质体基因组长度介于151,582 bp至153,239 bp之间，共包含132个编码基因，其中18个为重复基因，114个为独特基因。通过对这25个物种的基因组进行序列比对，共鉴定出38至53条重复序列与7个共享的简单序列重复（SSR，Simple Sequence Repeat）位点，同时发现了多个核苷酸多态性（Pi，Nucleotide Polymorphism）较高的区域，这些序列可潜在作为物种鉴定的分子标记。该类群的基因组结构、基因组成与基因排布均较为保守，但在反向重复（IR，Inverted Repeat）边界区域与基因间区（IGS，Intergenic Spacer）存在变异。基于完整质体基因组或仅基于编码序列（CDS，Coding Sequence）构建的系统发育推论结果一致。本研究将25种东亚玄参属植物划分为6个独立的演化支（clade），并结合花色、雄蕊与花冠的相对位置、株高等形态特征进一步解析了其种间亲缘关系。本研究可为未来东亚地区玄参属植物的资源开发奠定遗传基础。