Table_6_Comparative Chloroplast Genomics of Dipsacales Species: Insights Into Sequence Variation, Adaptive Evolution, and Phylogenetic Relationships.XLSX

In general, the chloroplast genomes of angiosperms are considered to be highly conserved and affected little by adaptive evolution. In this study, we tested this hypothesis based on sequence differentiation and adaptive variation in the plastid genomes in the order Dipsacales. We sequenced the plastid genomes of one Adoxaceae species and six Caprifoliaceae species, and together with seven previously released Dipsacales chloroplasts, we determined the sequence variations, evolutionary divergence of the plastid genomes, and phylogeny of Dipsacales species. The chloroplast genomes of Adoxaceae species ranged in size from 157,074 bp (Sinadoxa corydalifolia) to 158,305 bp (Sambucus williamsii), and the plastid genomes of Caprifoliaceae varied from 154,732 bp (Lonicera fragrantissima var. lancifolia) to 156,874 bp (Weigela florida). The differences in the number of genes in Caprifoliaceae and Adoxaceae species were largely due to the expansion and contraction of inverted repeat regions. In addition, we found that the number of dispersed repeats (Adoxaceae = 37; Caprifoliaceae = 384) was much higher than that of tandem repeats (Adoxaceae = 34; Caprifoliaceae = 291) in Dipsacales species. Interestingly, we determined 19 genes with positive selection sites, including three genes encoding ATP protein subunits (atpA, atpB, and atpI), four genes for ribosome protein small subunits (rps3, rps7, rps14, and rps15), four genes for photosystem protein subunits (psaA, psaJ, psbC, and pabK), two genes for ribosome protein large subunits (rpl22 and rpl32), and the clpP, infA, matK, rbcL, ycf1, and ycf2 genes. These gene regions may have played key roles in the adaptation of Dipsacales to diverse environments. In addition, phylogenetic analysis based on the plastid genomes strongly supported the division of 14 Dipsacales species into two previously recognized sections. The diversification of Adoxaceae and Caprifoliaceae was dated to the late Cretaceous and Tertiary periods. The availability of these chloroplast genomes provides useful genetic information for studying taxonomy, phylogeny, and species evolution in Dipsacales.

总体而言，被子植物的叶绿体基因组被认为具有高度保守性，受适应性进化的影响甚微。在本研究中，我们基于Dipsacales科叶绿体基因组中的序列差异和适应性变异，对该假设进行了验证。我们对一种Adoxaceae科物种和六种Caprifoliaceae科物种的叶绿体基因组进行了测序，并结合先前发布的七个Dipsacales科叶绿体基因组，确定了序列变异、叶绿体基因组的进化分歧以及Dipsacales科物种的进化系统树。Adoxaceae科物种的叶绿体基因组大小介于157,074碱基对（Sinadoxa corydalifolia）至158,305碱基对（Sambucus williamsii）之间，而Caprifoliaceae科物种的叶绿体基因组大小介于154,732碱基对（Lonicera fragrantissima var. lancifolia）至156,874碱基对（Weigela florida）之间。Caprifoliaceae和Adoxaceae科物种中基因数量差异主要归因于反转重复区域的扩增和收缩。此外，我们发现Dipsacales科物种中散在重复序列的数量（Adoxaceae = 37；Caprifoliaceae = 384）远高于串联重复序列（Adoxaceae = 34；Caprifoliaceae = 291）。有趣的是，我们确定了19个具有正向选择位点的基因，包括三个编码ATP蛋白亚基的基因（atpA、atpB和atpI）、四个编码核糖体蛋白小亚基的基因（rps3、rps7、rps14和rps15）、四个编码光合系统蛋白亚基的基因（psaA、psaJ、psbC和pabK）、两个编码核糖体蛋白大亚基的基因（rpl22和rpl32）以及clpP、infA、matK、rbcL、ycf1和ycf2基因。这些基因区域可能在Dipsacales科适应多样化环境的过程中发挥了关键作用。此外，基于叶绿体基因组的系统发育分析强烈支持将14个Dipsacales科物种划分为先前已识别的两个类群。Adoxaceae和Caprifoliaceae科的多样性可以追溯到晚白垩纪和第三纪。这些叶绿体基因组的可用性为研究Dipsacales科的分类学、系统发育和物种进化提供了有价值的遗传信息。