Characteristics and Phylogenetic Analysis of the Complete Plastomes of Anthogonium gracile and Eleorchis japonica (Epidendroideae, Orchidaceae)
文献类型： 外文期刊
作者： Gao, Xuyong 1 ; Chen, Yuming 1 ; Xu, Xiaowei 3 ; Chen, Hongjiang 4 ; Xing, Bingcong 5 ; Pan, Jianli 6 ; Li, Minghe 1 ; Zhou, Zhuang 2 ;
作者机构： 1.Fujian Agr & Forestry Univ, Coll Landscape Architecture, Key Lab Natl Forestry & Grassland Adm Orchid Conse, Fuzhou 350002, Peoples R China
2.Zhejiang Acad Agr Sci, Zhejiang Inst Subtrop Crops, Wenzhou 325005, Peoples R China
3.Wenzhou Forestry Technol Promot & Wildlife Protect, Wenzhou 325000, Peoples R China
4.Zhejiang Pharmaceut Univ, Coll Chinese Med, Ningbo 315500, Peoples R China
5.Zhejiang A&F Univ, Natl Key Lab Dev & Utilizat Forest Food Resources, Hangzhou 311300, Peoples R China
6.Tonglu Bishui Ecol Agr Dev Co Ltd, Hangzhou 311519, Peoples R China
关键词： Arethusinae; Anthogonium gracile; Eleorchis japonica; plastid genome; phylogenetic analysis
期刊名称：HORTICULTURAE （ 影响因子：3.0； 五年影响因子：3.2 ）
ISSN：
年卷期： 2025 年 11 卷 6 期
页码：
收录情况： SCI
摘要： Phylogenetic relationships within the subtribe Arethusinae (Arethuseae: Epidendroideae: Orchidaceae) remain unresolved, with particular uncertainty surrounding the phylogenetic positions of Anthogonium gracile and Eleorchis japonica. The monophyly of this subtribe remains contentious, making it one of the challenging taxa in Orchidaceae phylogenetics. In this study, we sequenced and analyzed the complete plastome sequences of A. gracile and E. japonica for the first time, aiming to elucidate their plastome characteristics and phylogenetic relationships. Both plastomes exhibited a conserved quadripartite structure, with 158,358 bp in A. gracile and 152,432 bp in E. japonica, and GC contents of 37.1% and 37.3%, respectively. Comparative analyses revealed strong structural conservation, but notable gene losses: E. japonica lacked seven ndh genes (ndhC/D/F/G/H/I/K), whereas A. gracile retained a complete ndh gene set. Repetitive sequence analysis identified an abundance of simple sequence repeats (68 and 77), tandem repeats (43 and 30), and long repeats (35 and 40). Codon usage displayed a bias toward the A/U termination, with leucine and isoleucine being the most frequent. Selection pressure analysis indicated that 68 protein-coding genes underwent purifying selection (Ka/Ks < 1), suggesting evolutionary conservation of plastome protein-coding genes. Nucleotide diversity analysis highlighted six hypervariable regions (rps8-rpl14, rps16-trnQ(UUG), psbB-psbT, trnT(UGU)-trnL(UAA), trnF(GAA)-ndhJ, and ycf1), suggesting their potential as molecular markers. Phylogenomic reconstruction, using complete plastome sequences, (ML, MP, and BI) indicated that Arethusinae was non-monophyletic. A. gracile formed a sister relationship with Mengzia foliosa and E. japonica, whereas Arundina graminifolia exhibited a sister relationship with Coelogyninae members. These results shed new light on the plastome characteristics and phylogenetic relationships of Arethusinae.
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