Complete mitogenome assembly of Lilium amoenum E. H. Wilson ex Sealy revealed its multiple chromosomal configurations, genome evolution, phylogenetic implications, and RNA-editing.
- 1Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
- 2Yunnan Yunhua United Development Co., Ltd., Kunming, Yunnan, 650599, China. [email protected].
- 3Yunnan Agricultural University, Kunming, Yunnan, 650201, China. [email protected].
Abstract
Background
Lilium amoenum E. H. Wilson ex Sealy is a wild lily species endemic to Yunnan, China, and is of considerable ornamental and scientific interest owing to its solitary, pendulous, fragrant, rose-purple flowers. Although the chloroplast genome of this species has been reported, its mitogenome has not yet been characterized. To address this gap, we employed a hybrid sequencing strategy combining Illumina short-read and Nanopore long-read data to assemble and annotate, for the first time, the complete mitogenome of L. amoenum.Result
The mitogenome of L. amoenum exhibits a distinctive multichromosomal architecture comprising 13 circular chromosomes and one linear chromosome, with a total length of 789,335 bp and an overall GC content of 45.11%. In total, 55 genes were annotated, including 37 protein-coding genes (PCGs), 3 rRNA genes, and 15 tRNA genes. We also identified 171 simple sequence repeats (SSRs), eight tandem repeats, and 509 dispersed repeats. Homology analysis detected 14 plastid-derived fragments totaling 4,723 bp, representing 0.60% of the mitogenome. Collinearity analysis revealed extensive genomic rearrangements between L. amoenum and its close relatives, indicating substantial structural divergence during mitogenome evolution. Phylogenetic analysis based on the mitogenomes of 26 species showed that L. amoenum clusters with other members of Lilium, consistent with the APG IV classification system. In addition, 493 C-to-U RNA editing sites in the coding regions of mitochondrial PCGs were predicted. Lastly, we successfully validated five randomly selected RNA editing sites.Conclusion
This study provides the first complete mitogenome of L. amoenum, revealing its unique multi-chromosomal configuration. Moreover, it offers a valuable genomic resource for breeding, species identification, germplasm conservation, and phylogenetic studies within Lilium species.
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BibTeX
@article{guo2026complete,
title = {{Complete mitogenome assembly of Lilium amoenum E. H. Wilson ex Sealy revealed its multiple chromosomal configurations, genome evolution, phylogenetic implications, and RNA-editing.}},
author = {Yanbing Guo and Ziwei Li and Shengyue Yi and Shuxian Li and Wenyi Dong and Hongzhi Wu},
journal = {BMC plant biology},
year = {2026},
month = aug,
doi = {10.1186/s12870-026-09675-4},
url = {https://europepmc.org/article/MED/42967990},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Complete mitogenome assembly of Lilium amoenum E. H. Wilson ex Sealy revealed its multiple chromosomal configurations, genome evolution, phylogenetic implications, and RNA-editing.
AU - Yanbing Guo
AU - Ziwei Li
AU - Shengyue Yi
AU - Shuxian Li
AU - Wenyi Dong
AU - Hongzhi Wu
PY - 2026
DA - 2026/08/05
JO - BMC plant biology
DO - 10.1186/s12870-026-09675-4
UR - https://europepmc.org/article/MED/42967990
AB - Background Lilium amoenum E. H. Wilson ex Sealy is a wild lily species endemic to Yunnan, China, and is of considerable ornamental and scientific interest owing to its solitary, pendulous, fragrant, rose-purple flowers. Although the chloroplast genome of this species has been reported, its mitogenome has not yet been characterized. To address this gap, we employed a hybrid sequencing strategy combining Illumina short-read and Nanopore long-read data to assemble and annotate, for the first time, the complete mitogenome of L. amoenum.Result The mitogenome of L. amoenum exhibits a distinctive multichromosomal architecture comprising 13 circular chromosomes and one linear chromosome, with a total length of 789,335 bp and an overall GC content of 45.11%. In total, 55 genes were annotated, including 37 protein-coding genes (PCGs), 3 rRNA genes, and 15 tRNA genes. We also identified 171 simple sequence repeats (SSRs), eight tandem repeats, and 509 dispersed repeats. Homology analysis detected 14 plastid-derived fragments totaling 4,723 bp, representing 0.60% of the mitogenome. Collinearity analysis revealed extensive genomic rearrangements between L. amoenum and its close relatives, indicating substantial structural divergence during mitogenome evolution. Phylogenetic analysis based on the mitogenomes of 26 species showed that L. amoenum clusters with other members of Lilium, consistent with the APG IV classification system. In addition, 493 C-to-U RNA editing sites in the coding regions of mitochondrial PCGs were predicted. Lastly, we successfully validated five randomly selected RNA editing sites.Conclusion This study provides the first complete mitogenome of L. amoenum, revealing its unique multi-chromosomal configuration. Moreover, it offers a valuable genomic resource for breeding, species identification, germplasm conservation, and phylogenetic studies within Lilium species.
SN - 1471-2229
ER -