Plastomes of Seven <i>Coelogyne</i> s.l. (Arethuseae, Orchidaceae) Species: Comparative Analysis and Phylogenetic Relationships

Songkun Lin; Ruyi Li; Shuling Tang; Yuming Chen; Yin Yan; Xuyong Gao; Xiaokang Zhuo

doi:10.3390/horticulturae11020144

Horticulturae (Jan 2025)

Plastomes of Seven <i>Coelogyne</i> s.l. (Arethuseae, Orchidaceae) Species: Comparative Analysis and Phylogenetic Relationships

Songkun Lin,
Ruyi Li,
Shuling Tang,
Yuming Chen,
Yin Yan,
Xuyong Gao,
Xiaokang Zhuo

Affiliations

Songkun Lin: College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Ruyi Li: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Shuling Tang: Zhangzhou Institute of Technology, Zhangzhou 363000, China
Yuming Chen: College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Yin Yan: College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Xuyong Gao: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Xiaokang Zhuo: College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China

DOI: https://doi.org/10.3390/horticulturae11020144
Journal volume & issue: Vol. 11, no. 2
p. 144

Abstract

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The Coelogyne s.l. is one of the emblematic genera of the Asian orchids, with high horticultural and medicinal values. However, the phylogenetic relationships of the genus inferred from previous studies based on a limited number of DNA markers remain ambiguous. In this study, we newly sequenced and assembled the complete plastomes of seven Coelogyne species: C. bulleyia, C. fimbriata, C. flaccida, C. prolifera, C. tricallosa, C. uncata, and an unknown taxa, Coelogyne sp. The plastomes of Coelogyne exhibited a typical quadripartite structure, varying in length between 157,476 bp and 160,096 bp, accompanied by a GC content spanning from 37.3% to 37.5%. A total of 132 genes were annotated for each plastome, including 86 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Among these, 19 genes underwent duplication within the inverted repeat (IR) regions, and 18 genes exhibited the presence of introns. Additionally, we detected 54 to 69 simple sequence repeats (SSRs) and 30 to 49 long repeats. In terms of codon usage frequency, leucine (Leu) emerged with the highest frequency, while cysteine (Cys) exhibited the lowest occurrence. Furthermore, eight hypervariable regions (atpB-rbcL, psbK-psbI, rps8-rpl14, rps16-trnQUUG, psaC-ndhE, ndhF-rpl32, psbB-psbT, and ycf1) were identified. Phylogenetic analyses using complete plastomes and protein-coding genes indicated that Coelogyne s.l. was monophyletic. Moreover, the results robustly supported the division of Coelogyne s.l. into five clades. This study provides a comprehensive analysis of the structural variation and phylogenetic analysis of the Coelogyne s.l. based on plastome data. The findings offer significant insights into the plastid genomic characteristics and the phylogenetic relationships of Coelogyne s.l., contributing to a deeper understanding of its evolutionary history.

Published in Horticulturae

ISSN: 2311-7524 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Agriculture: Plant culture
Website: http://www.mdpi.com/journal/horticulturae

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