The GC content of three ITS regions among clades.

This is the first study to systematically evaluate rRNA secondary structures of Hedysareae with an emphasis on Hedysarum. ITS2 and 5.8S regions of the genus shared a common secondary structure with a four-fingered central loop, whereas ITS1 possessed five distinct structures. The secondary structural features of the two regions provided advantageous data for clades, species groups, and closely related species. Hemi-CBCs were mostly observed in the reconstruction of species groups, and Nsts, mostly between closely related species. The investigations showed that ITS1 varied more than ITS2 in length, GC content, and most of the diversity indices within the tribe. Maximum likelihood analyses of the synchronized sequence-structure tree of ITS1 were performed. The accuracy and phylogenetic signals of ITS1 were higher than ITS2. The similar GC content, and no CBC, in both spacers, fortified the close relationship of CEGO and H. sections Stracheya and Hedysarum clades in the synchronized sequence-structure tree topology of ITS1. In both regions, no inter-generic CBCs were detected inside the CEGO clade and the inter-sectional level of Hedysarum. But, in the ITS2 region, a CBC was detected between H. section Multicaulia, and Taverniera versus H. sections Hedysarum, and Stracheya. The lowest inter-sectional genetic distance and structural features were found between H. sect. Hedysarum and H. sect. Stracheya clades in the ITS2 region.

本研究首次系统评价了岩黄耆族（Hedysareae）的核糖体RNA（rRNA）二级结构，研究重点聚焦岩黄耆属（Hedysarum）。该属的内转录间隔区2（ITS2）与5.8S核糖体RNA（5.8S rRNA）区域共享一类以四指状中央环为典型特征的保守二级结构，而内转录间隔区1（ITS1）则存在五种不同的二级结构。上述两个区域的二级结构特征，可为演化支（clades）、物种群以及近缘物种的分类与系统发育分析提供有效依据。半保守碱基替换（Hemi-CBC）多出现于物种群的系统发育重建过程中，而核苷酸替换位点（Nsts）则多存在于近缘物种之间。研究表明，在岩黄耆族内，ITS1在序列长度、GC含量以及多数多样性指数方面的变异程度均高于ITS2。本研究对ITS1序列构建同步序列-结构系统发育树并开展最大似然法（maximum likelihood）分析，结果显示ITS1的分析准确率与系统发育信号均优于ITS2。在ITS1的同步序列-结构系统发育树拓扑结构中，CEGO类群与岩黄耆属斯特拉彻亚组（H. sect. Stracheya）、岩黄耆亚组（H. sect. Hedysarum）演化支间的近缘关系，因两个间隔区GC含量相近且未检测到保守碱基替换（CBC）而得到进一步强化。在这两个区域中，CEGO演化支内部以及岩黄耆属的亚组分类水平上，均未检测到属间保守碱基替换。但在ITS2区域中，多茎亚组（H. sect. Multicaulia）与Taverniera类群，分别与岩黄耆亚组、斯特拉彻亚组之间检测到了保守碱基替换。在ITS2区域中，岩黄耆亚组与斯特拉彻亚组演化支之间的种间遗传距离与结构特征差异均为最小。