College of Pharmacy, Dali University, Dali, 671000, China.
Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, 671000, China.
Sci Rep. 2024 Jun 17;14(1):13945. doi: 10.1038/s41598-024-64896-7.
Veronica anagallis-aquatica L. and Veronica undulata Wall. are widely used ethnomedicinal plants in China. The two species have different clinical efficacies, while their extremely similar morphology and unclear interspecific relationship make it difficult to accurately identify them, leading to increased instances of mixed usage. This article reports on the complete chloroplast genomes sequence of these two species and their related Veronica species to conduct a comparative genomics analysis and phylogenetic construction. The results showed that the chloroplast (cp) genomes of Veronica exhibited typical circular quadripartite structures, with total lengths of 149,386 to 152,319 base pairs (bp), and GC content of 37.9 to 38.1%, and the number of genes was between 129-134. The total number of simple sequence repeats (SSRs) in V. anagallis-aquatica and V. undulata is 37 and 36, while V. arvensis had the highest total number of 56, predominantly characterized by A/T single bases. The vast majority of long repeat sequence types are forward repeats and palindromic repeats. Selective Ka/Ks values showed that three genes were under positive selection. Sequence differences often occur in the non-coding regions of the large single-copy region (LSC) and small single-copy region (SSC), with the lowest sequence variation in the inverted repeat regions (IR). Seven highly variable regions (trnT-GGU-psbD, rps8-rpl16, trnQ-UUG, trnN-GUU-ndhF, petL, ycf3, and ycf1) were detected, which may be potential molecular markers for identifying V. anagallis-aquatica and V. undulata. The phylogenetic tree indicates that there is a close genetic relationship between the genera Veronica and Neopicrorhiza, and V. anagallis-aquatica and V. undulata are sister groups. The molecular clock analysis results indicate that the divergence time of Veronica may occur at ∼ 9.09 Ma, and the divergence time of these two species occurs at ∼ 0.48 Ma. It is speculated that climate change may be the cause of Veronica species diversity and promote the radiation of the genus. The chloroplast genome data of nine Veronica specie provides important insights into the characteristics and evolution of the chloroplast genome of this genus, as well as the phylogenetic relationships of the genus Veronica.
水苦荬和皱叶碎米荠是中国广泛应用于民间医学的两种植物。这两种植物具有不同的临床功效，但它们形态极其相似，种间关系不明确，难以准确识别，导致混合使用的情况增加。本文报道了这两种植物及其相关的婆婆纳属植物的完整叶绿体基因组序列，进行了比较基因组分析和系统发育构建。结果表明，婆婆纳属植物的叶绿体基因组呈典型的圆形四分体结构，总长度为 149386 到 152319 碱基对（bp），GC 含量为 37.9%到 38.1%，基因数量在 129 到 134 之间。水苦荬和皱叶碎米荠的简单序列重复（SSR）总数分别为 37 和 36，而婆婆纳属植物的 SSR 总数最高，为 56，主要以 A/T 单碱基为主。绝大多数长重复序列类型为正向重复和回文重复。选择的 Ka/Ks 值表明，有三个基因受到正选择。序列差异经常发生在大片段单拷贝区（LSC）和小片段单拷贝区（SSC）的非编码区，而反向重复区（IR）的序列变异最低。检测到七个高度可变区（trnT-GGU-psbD、rps8-rpl16、trnQ-UUG、trnN-GUU-ndhF、petL、ycf3 和 ycf1），它们可能是鉴定水苦荬和皱叶碎米荠的潜在分子标记。系统发育树表明，婆婆纳属和列当属之间存在密切的遗传关系，水苦荬和皱叶碎米荠是姐妹群。分子钟分析结果表明，婆婆纳属的分化时间约为 9.09Ma，而这两个种的分化时间约为 0.48Ma。推测气候变化可能是婆婆纳属物种多样性的原因，并促进了该属的辐射。九个婆婆纳属植物的叶绿体基因组数据为该属叶绿体基因组的特征和进化以及婆婆纳属的系统发育关系提供了重要的见解。
