四角(Vitaceae)以其观赏性而闻名,药用,和生态意义。然而,四角叶绿体基因组的结构和变异特征及其对系统发育关系的影响仍未得到充分研究。这项研究利用生物信息学方法来组装和注释10个Tetrastigma物种的叶绿体基因组,并将其与五个先前测序的物种进行比较。这项研究分析了基因组成,简单的序列重复,和密码子使用模式,显示出较高的A/T含量,在五个物种和几个首选密码子中唯一鉴定的五核苷酸重复。此外,对15个四角物种的叶绿体基因组进行了比较分析,检查它们的结构差异并识别多态性热点(rps16,rps16-trnQ,trnS,trnD,psbc-trnS-psbz,accD-psaI,psbE-petL-petG,等。)适用于DNA标记开发。此外,系统发育和选择压力分析是基于这15个四角物种的叶绿体基因组进行的,验证和阐明Tetrastigma内的属内关系。Futhermore,正选择的几个基因,比如atpF和accD,被确认,对四角自适应进化的启示。利用40种藤本植物,估计了四角的发散时间,阐明Tetrastigma相对于其他属的进化关系。分析揭示了上新世和上新世的四角不同的差异,在始新世之前可能有古代分歧事件。此外,家族级选择性压力分析确定了将四角与其他属区分开来的关键特征,显示出较高程度的净化选择。这项研究丰富了Tetrastigma的叶绿体基因组数据,并为物种鉴定提供了新的见解,系统发育分析,和适应性进化,增强我们对这些物种的遗传多样性和进化史的理解。
Tetrastigma (Vitaceae) is known for its ornamental, medicinal, and ecological significance. However, the structural and variational characteristics of the Tetrastigma chloroplast genome and their impact on phylogenetic relationships remain underexplored. This study utilized bioinformatics methods to assemble and annotate the chloroplast genomes of 10 Tetrastigma species and compare them with five previously sequenced species. This study analyzed gene composition, simple sequence repeats, and codon usage patterns, revealing a high A/T content, uniquely identified pentanucleotide repeats in five species and several preferred codons. In addition, comparative analyses were conducted of the chloroplast genomes of 15 Tetrastigma species, examining their structural differences and identifying polymorphic hotspots (rps16, rps16-trnQ, trnS, trnD, psbC-trnS-psbZ, accD-psaI, psbE-petL-petG, etc.) suitable for DNA marker development. Furthermore, phylogenetic and selective pressure analyses were performed based on the chloroplast genomes of these 15 Tetrastigma species, validating and elucidating intra-genus relationships within Tetrastigma. Futhermore, several genes under positive selection, such as atpF and accD, were identified, shedding light on the adaptive evolution of Tetrastigma. Utilizing 40 Vitaceae species, the divergence time of Tetrastigma was estimated, clarifying the evolutionary relationships within Tetrastigma relative to other genera. The analysis revealed diverse divergences of Tetrastigma in the Miocene and Pliocene, with possible ancient divergence events before the Eocene. Furthermore, family-level selective pressure analysis identified key features distinguishing Tetrastigma from other genera, showing a higher degree of purifying selection. This research enriches the chloroplast genome data for Tetrastigma and offers new insights into species identification, phylogenetic analysis, and adaptive evolution, enhancing our understanding of the genetic diversity and evolutionary history of these species.