Complete Chloroplast Genome Analysis of Casearia kurzii: Gene Loss at IR Boundaries and Monophyletic Evolution within Casearia

Casearia kurzii is a near-threatened medicinal plant in Salicacea. C. kurzii has important medicinal values. However, the similarity in morphological characters of casearia species and the controversial phylogenetic relationships within the genus have led to misidentification and hindered clinical application studies. To improve molecular methods for distinguishing casearia species, we report the complete chloroplast genome of C. kurzii obtained by high-throughput Illumina sequencing. It was also analyzed in comparison with 14 other closely related species. The results showed that the chloroplast genome of C. kurzii was 157,998 bp long and presented a typical tetrad structure with unique features: (1) absence of rpl22 and ycf1 genes at the IR boundary, and (2) presence of 60 exclusively mononucleotide SSRs. Ten highly variable regions were identified as potential molecular markers for species identification. Phylogenetic analysis strongly supported the monophyletic grouping of C. kurzii with C. velutina and C. glomerata (100% bootstrap support), with an estimated divergence time of 15.8 Mya (95% HPD: 5.2-28.9 Mya). In conclusion, This study not only reports the first complete chloroplast genome sequence and structural features of C. kurzii but also provides insights into the evolutionary history of Casearia. The identified molecular markers and unique genomics features present valuable tools for conservation genetics research and germplasm resource management of C. kurzii,establishing a foundation for investigating the species’ adaptive evolutionary mechanisms. Supporting data inclond: 1. Figures_raw_data；2. Analysis_data；3. Phylogenetic_data three parts，and a data documentation file is named README.txt云南脚骨脆（Casearia kurzii）是隶属于杨柳科（Salicaceae）的近危药用植物，具有重要的药用价值。然而，脚骨脆属（Casearia）物种间形态性状相似，且该属内系统发育关系存在争议，这导致了物种鉴定错误，同时阻碍了其临床应用研究。为优化脚骨脆属物种的分子鉴定方法，本研究通过高通量Illumina测序技术，获得了云南脚骨脆的完整叶绿体基因组，并将其与另外14个近缘物种的叶绿体基因组进行了比较分析。 研究结果显示，云南脚骨脆的叶绿体基因组全长为157998 bp（碱基对），呈现典型的四分体结构，并具备两项独特特征：其一，反向重复区（IR）边界处缺失rpl22与ycf1基因；其二，含有60个专属的单核苷酸型简单序列重复（SSRs，Simple Sequence Repeats）。本研究共鉴定出10个高变区域，可作为物种鉴定的潜在分子标记。系统发育分析强烈支持云南脚骨脆与绒毛脚骨脆（C. velutina）、球花脚骨脆（C. glomerata）聚为单系群，自展支持率为100%，估计的分化时间为15.8百万年前（Mya），95%最高后验密度（HPD）区间为5.2-28.9 Mya。 综上，本研究不仅首次报道了云南脚骨脆的完整叶绿体基因组序列及其结构特征，同时也为揭示脚骨脆属的演化历史提供了新的视角。本研究鉴定得到的分子标记与独特的基因组特征，可为云南脚骨脆的保护遗传学研究及种质资源管理提供宝贵的工具，同时为解析该物种的适应性演化机制奠定了基础。 本研究附带的支撑数据包括：1. 原始图片数据（Figures_raw_data）；2. 分析数据（Analysis_data）；3. 系统发育分析数据（Phylogenetic_data）三类，此外还有一份名为README.txt的数据说明文件。