ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Bioinformatics
Assembly and comparative analysis of the complete multichromosomal mitochondrial genome of an endangered orchid species, Calanthe sieboldii
Ting Ting Li 1
Jun Lu 1
Li Xiong 1
Guang Zhao 1
Fang Wu 2
Jun Yan 1
Ke Rui Huang 3
1. Hunan Provincial Demonstration Center of Forestry Seedling Breeding, Changsha, China
2. Hunan Edible Fungal Research Institute, Changsha, China
3. Hunan University of Arts and Science, Changde, China
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Abstract
Introduction: Plant mitochondrial genomes (mitogenomes) are known for their structural complexity, particularly within the Orchidaceae. To understand the evolutionary dynamics in the endangered genus Calanthe, this study provides the first complete mitogenome assembly for the endangered species Calanthe sieboldii, a species of horticultural and conservation importance. Methods: A hybrid sequencing approach combining Nanopore long reads and BGI short reads was used for denovo assembly. The genome was annotated, and we performed comparative analyses of repetitive sequences, interorganellar DNA transfer, codon usage, RNA editing, synteny, and phylogeny. Results: The 644,236 bp mitogenome exhibits a highly fragmented architecture, comprising 21 independent circular chromosomes ranging from 19.9 to 48.7 kb. We annotated 39 unique protein-coding genes, 23 tRNA genes, and 3 rRNA genes. The genome is characterized by a high density of repetitive sequences and a massive influx of chloroplast DNA, with mitochondrial–plastid sequences accounting for 12.72% of the total length. Comparative synteny analysis with other orchid species revealed an almost complete loss of gene order, highlighting extreme structural rearrangement. Despite this plasticity, core molecular features, such as codon usage and predicted RNA editing patterns, remain conserved. Phylogenetic analysis robustly placed C. sieboldii within the Orchidaceae. Discussion: This study decodes a complex multichromosomal mitogenome, reinforcing the paradigm of dynamic structural evolution in orchids and providing a vital genomic resource to support conservation efforts and evolutionary research on the Calanthe genus.
Summary
Keywords
Calanthe sieboldii, Mitogenomes, Orchidaceae, phylogenetic analysis, RNA Editing
Received
09 September 2025
Accepted
18 February 2026
Copyright
© 2026 Li, Lu, Xiong, Zhao, Wu, Yan and Huang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Jun Yan; Ke Rui Huang
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