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. 2025 May 29:16:1590173.
doi: 10.3389/fpls.2025.1590173. eCollection 2025.

The complex DNA molecular combination with a linear and circular structure in Magnolia kwangsiensis mitochondrial genome

Qing Li  1   2 , Wentao Sheng  1   2
Affiliations

The complex DNA molecular combination with a linear and circular structure in Magnolia kwangsiensis mitochondrial genome

Qing Li et al. Front Plant Sci. .

Abstract

Background: Magnolia kwangsiensis is an endangered Magnoliaceae species, holding scientific, aesthetic, and economic value. But limited genetic research was reported. To better understand M. kwangsiensis genomics, we aimed to assemble and analyze its mitochondrial genome.

Results: M. kwangsiensis has a branched structure, composing a linear and circular molecular structure with 428,449 bp and 126,869 bp, and GC contents of 47.51% and 47.38%. The total genome size is 555,318 bp, with GC content of 47.47%. A total of 68 genes were annotated, comprising 40 protein-coding, 23 tRNA, three rRNA genes, and two pseudo-genes. And nad1, atp9, and nad6 exhibited the highest nucleotide diversity, while atp1 and nad5 exhibited the lowest. Relative synonymous codon usage (RSCU) analysis revealed 29 codons with RSCU values > 1, showing A/U preference for codons ending. Moreover, 211 simple sequence, 1101 dispersed, and 39 tandem repeats were checked. The mitochondrial genome of M. kwangsiensis and Magnolia figo showed relatively good synteny. And 32 homologous fragments were discriminated between its mitochondrial and chloroplast genome, with a total of 29,253 bp and an average 914 bp. Phylogenetic analysis indicated that M. kwangsiensis is the most closely related to Liriodendron tulipifera.

Conclusion: The information provided herein contributes genomic knowledge for the M. kwangsiensis breeding research.

Keywords: M. kwangsiensis; RSCU; branched structure; mitochondrial genome; repeat.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Mitochondrial genome map of Magnolia kwangsiensis. Note: Mitochondrial genome molecular 1 map in Magnolia kwangsiensis; Mitochondrial genome molecular 2 map in Magnolia kwangsiensis (Circle outside genes: Forward coding of genes; circle inside genes: Reverse coding of genes; Internal dark gray circle: GC content).
Figure 2
Figure 2
Statistical analysis of Magnolia kwangsiensis mitochondrial codon preference.
Figure 3
Figure 3
Line graph of gene Pi values in Magnolia kwangsiensis.
Figure 4
Figure 4
Repeat sequences of the Magnolia kwangsiensis mitochondrial genome. (A) The distribution of repetitive sequences; (B) SSR distribution; (C) dispersed repeat length distribution; (D) SSR type composition.
Figure 5
Figure 5
Colinear analysis between Magnolia kwangsiensis and Magnoliaceae plants.
Figure 6
Figure 6
Homologous sequence analysis of chloroplast and mitochondrion in Magnolia kwangsiensis.
Figure 7
Figure 7
Mitochondrial genome sequence similarity comparison ring map of six Magnoliaceae species.
Figure 8
Figure 8
Phylogenetic tree of Magnolia kwangsiensis constructed using mitochondrial genomes of 29 representative plants.
Figure 9
Figure 9
Prediction of RNA editing sites in Magnolia kwangsiensis.
Figure 10
Figure 10
Box plot of Ka/Ks ratio for 39 PCGs of Magnolia kwangsiensis in Magnoliaceae family.
See this image and copyright information in PMC

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