ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Bioinformatics
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1649951
This article is part of the Research TopicEvolutionary Dynamics, Functional Variation and Application of Plant Organellar GenomeView all 29 articles
Assembly and Comparative Analysis of the First Complete Mitochondrial Genome of Citrus medica (Rutaceae)
Provisionally accepted
- Foshan University, Foshan, China
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Citrus medica, a phylogenetically pivotal progenitor of contemporary citrus cultivars, holds significant economic value due to its medicinal compounds and its role in breeding stress-resistant hybrids. The essential functions of organellar genomes in plant adaptation and metabolic regulation necessitate the characterization of their architecture to elucidate the genomic basis for these traits. However, the absence of a complete mitochondrial genome has hindered investigations into inter-organellar interactions and diversification mechanisms within this key species. To address this gap, we used hybrid Illumina-Nanopore sequencing to produce the first mitochondrial genome (553,930 bp, GC content of 45.04%), annotating 65 genes (36 protein-coding genes, 25 tRNAs, and four rRNAs). Comparative analysis revealed 44 homologous fragments (totaling 41,479 bp) transferred from the chloroplast genome, including two 6,767 bp segments containing 11 genes (rps7 and 10 tRNAs), with nine tRNA genes being either pseudogenized or lost from the chloroplast genome. The mitogenome includes 633 repetitive sequences (386 dispersed, 215 simple sequence repeats, 32 tandem), with inverted repeats exceeding 11 kb potentially facilitating recombination. Additionally, we predicted 600 RNA editing sites (predominantly C-to-U) in 34 protein-coding genes, affecting amino acid hydrophobicity in 38.83% of these sites. Phylogenetic reconstruction using 19 mitochondrial genomes positioned C. medica closest to C. unshiu. Synteny analysis highlighted significant structural divergence among Rutaceae mitochondrial genomes, with nucleotide diversity (Pi) indicating 15 polymorphic genes. This study establishes a foundational mitogenomic resource for C. medica, demonstrating significant acquisition of chloroplast-derived sequences and dynamic genome architecture, thus advancing the understanding of organellar evolution in citrus and supporting the breeding of stress-resistant cultivars.
Keywords: Citrus medica, organelle, Mitochondrial Genome, Chloroplast genome, Systematic evolution
Received: 19 Jun 2025; Accepted: 05 Sep 2025.
Copyright: © 2025 Wu, Liu, Liao, Liu, Xie, Zheng, Hong, Chen and Li. 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: Tao Li, Foshan University, Foshan, China
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