Characteristics and Phylogenetic Analysis of the Complete Plastomes of <i>Anthogonium gracile</i> and <i>Eleorchis japonica</i> (Epidendroideae, Orchidaceae)
Phylogenetic relationships within the subtribe Arethusinae (Arethuseae: Epidendroideae: Orchidaceae) remain unresolved, with particular uncertainty surrounding the phylogenetic positions of <i>Anthogonium gracile</i> and <i>Eleorchis japonica</i>. The monophyly of this subtri...
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2025-06-01
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| author | Xuyong Gao Yuming Chen Xiaowei Xu Hongjiang Chen Bingcong Xing Jianli Pan Minghe Li Zhuang Zhou |
| author_facet | Xuyong Gao Yuming Chen Xiaowei Xu Hongjiang Chen Bingcong Xing Jianli Pan Minghe Li Zhuang Zhou |
| author_sort | Xuyong Gao |
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| description | Phylogenetic relationships within the subtribe Arethusinae (Arethuseae: Epidendroideae: Orchidaceae) remain unresolved, with particular uncertainty surrounding the phylogenetic positions of <i>Anthogonium gracile</i> and <i>Eleorchis japonica</i>. 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 <i>A. gracile</i> and <i>E. japonica</i> 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 <i>A. gracile</i> and 152,432 bp in <i>E. japonica</i>, and GC contents of 37.1% and 37.3%, respectively. Comparative analyses revealed strong structural conservation, but notable gene losses: <i>E. japonica</i> lacked seven <i>ndh</i> genes (<i>ndhC/D/F/G/H/I/K</i>), whereas <i>A. gracile</i> retained a complete <i>ndh</i> 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 (<i>rps8</i>-<i>rpl14</i>, <i>rps16-trnQ<sup>UUG</sup></i>, <i>psbB</i>-<i>psbT</i>, <i>trnT<sup>UGU</sup></i>-<i>trnL<sup>UAA</sup></i>, <i>trnF<sup>GAA</sup></i>-<i>ndhJ</i>, and <i>ycf1</i>), suggesting their potential as molecular markers. Phylogenomic reconstruction, using complete plastome sequences, (ML, MP, and BI) indicated that Arethusinae was non-monophyletic. <i>A. gracile</i> formed a sister relationship with <i>Mengzia foliosa</i> and <i>E. japonica</i>, whereas <i>Arundina graminifolia</i> exhibited a sister relationship with Coelogyninae members. These results shed new light on the plastome characteristics and phylogenetic relationships of Arethusinae. |
| format | Article |
| id | doaj-art-3eccf393fc834fc0abfc323d0d211dc1 |
| institution | Kabale University |
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| publishDate | 2025-06-01 |
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| spelling | doaj-art-3eccf393fc834fc0abfc323d0d211dc12025-08-20T03:27:18ZengMDPI AGHorticulturae2311-75242025-06-0111669810.3390/horticulturae11060698Characteristics and Phylogenetic Analysis of the Complete Plastomes of <i>Anthogonium gracile</i> and <i>Eleorchis japonica</i> (Epidendroideae, Orchidaceae)Xuyong Gao0Yuming Chen1Xiaowei Xu2Hongjiang Chen3Bingcong Xing4Jianli Pan5Minghe Li6Zhuang Zhou7Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaWenzhou Forestry Technology Promotion and Wildlife Protection and Management Station, Wenzhou 325000, ChinaCollege of Chinese Medicine, Zhejiang Pharmaceutical University, Ningbo 315500, ChinaNational Key Laboratory for Development and Utilization of Forest Food Resources, Zhejiang A&F University, Hangzhou 311300, ChinaTonglu Bishui Ecological Agriculture Development Co., Ltd., Hangzhou 311519, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaZhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, ChinaPhylogenetic relationships within the subtribe Arethusinae (Arethuseae: Epidendroideae: Orchidaceae) remain unresolved, with particular uncertainty surrounding the phylogenetic positions of <i>Anthogonium gracile</i> and <i>Eleorchis japonica</i>. 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 <i>A. gracile</i> and <i>E. japonica</i> 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 <i>A. gracile</i> and 152,432 bp in <i>E. japonica</i>, and GC contents of 37.1% and 37.3%, respectively. Comparative analyses revealed strong structural conservation, but notable gene losses: <i>E. japonica</i> lacked seven <i>ndh</i> genes (<i>ndhC/D/F/G/H/I/K</i>), whereas <i>A. gracile</i> retained a complete <i>ndh</i> 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 (<i>rps8</i>-<i>rpl14</i>, <i>rps16-trnQ<sup>UUG</sup></i>, <i>psbB</i>-<i>psbT</i>, <i>trnT<sup>UGU</sup></i>-<i>trnL<sup>UAA</sup></i>, <i>trnF<sup>GAA</sup></i>-<i>ndhJ</i>, and <i>ycf1</i>), suggesting their potential as molecular markers. Phylogenomic reconstruction, using complete plastome sequences, (ML, MP, and BI) indicated that Arethusinae was non-monophyletic. <i>A. gracile</i> formed a sister relationship with <i>Mengzia foliosa</i> and <i>E. japonica</i>, whereas <i>Arundina graminifolia</i> exhibited a sister relationship with Coelogyninae members. These results shed new light on the plastome characteristics and phylogenetic relationships of Arethusinae.https://www.mdpi.com/2311-7524/11/6/698Arethusinae<i>Anthogonium gracile</i><i>Eleorchis japonica</i>plastid genomephylogenetic analysis |
| spellingShingle | Xuyong Gao Yuming Chen Xiaowei Xu Hongjiang Chen Bingcong Xing Jianli Pan Minghe Li Zhuang Zhou Characteristics and Phylogenetic Analysis of the Complete Plastomes of <i>Anthogonium gracile</i> and <i>Eleorchis japonica</i> (Epidendroideae, Orchidaceae) Horticulturae Arethusinae <i>Anthogonium gracile</i> <i>Eleorchis japonica</i> plastid genome phylogenetic analysis |
| title | Characteristics and Phylogenetic Analysis of the Complete Plastomes of <i>Anthogonium gracile</i> and <i>Eleorchis japonica</i> (Epidendroideae, Orchidaceae) |
| title_full | Characteristics and Phylogenetic Analysis of the Complete Plastomes of <i>Anthogonium gracile</i> and <i>Eleorchis japonica</i> (Epidendroideae, Orchidaceae) |
| title_fullStr | Characteristics and Phylogenetic Analysis of the Complete Plastomes of <i>Anthogonium gracile</i> and <i>Eleorchis japonica</i> (Epidendroideae, Orchidaceae) |
| title_full_unstemmed | Characteristics and Phylogenetic Analysis of the Complete Plastomes of <i>Anthogonium gracile</i> and <i>Eleorchis japonica</i> (Epidendroideae, Orchidaceae) |
| title_short | Characteristics and Phylogenetic Analysis of the Complete Plastomes of <i>Anthogonium gracile</i> and <i>Eleorchis japonica</i> (Epidendroideae, Orchidaceae) |
| title_sort | characteristics and phylogenetic analysis of the complete plastomes of i anthogonium gracile i and i eleorchis japonica i epidendroideae orchidaceae |
| topic | Arethusinae <i>Anthogonium gracile</i> <i>Eleorchis japonica</i> plastid genome phylogenetic analysis |
| url | https://www.mdpi.com/2311-7524/11/6/698 |
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