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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| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-06-01
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| Series: | Horticulturae |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2311-7524/11/6/698 |
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| Summary: | 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. |
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| ISSN: | 2311-7524 |