ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Bioinformatics
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1675536
This article is part of the Research TopicMulti-omics and Computational Biology in Horticultural Plants: From Genotype to Phenotype, Volume IIIView all 15 articles
Comparative Chloroplast Genomics of Rutaceae: Structural Divergence, Adaptive Evolution, and Phylogenomic Implications
Provisionally accepted
Yichao Chen1Ningge Liu2Hong Wang1Huifeng Luo3Zhiliang Xie1Hongao Yu1Yaojun Chang1Bosheng Zheng1Xinchen Zheng1Jun Sheng2Yajie Jiang2Shuzhe Ye2Yonggang Hua4
Haijie Ma2*
Fei Li1*- 1Wenzhou Vocational College of Science and Technology, Wenzhou, China
- 2Zhejiang Agriculture and Forestry University, Hangzhou, China
- 3Institute of Horticulture, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
- 4Hangzhou Agricultural Technology Extension Center, Hangzhou, China
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The study of chloroplast genome evolutionary dynamics provides critical insights into plant adaptive evolution and phylogenetic relationships. This research conducted a systematic comparative analysis of chloroplast genomes across 35 species within the Rutaceae family. All genomes displayed the typical quadripartite structure, with sizes ranging from 155 to 161 kb, GC contents between 38.17% and 38.83%, and gene counts varying from 122 to 144. Structural conservation was high across species,, with variations mainly localized at the boundaries of inverted repeat (IR) regions. AT-rich mononucleotide simple sequence repeats (SSRs) were dominant and primarily distributed in non-coding regions. Collinearity analysis revealed high sequence conservation alongside lineage-specific rearrangements. Relative synonymous codon usage (RSCU) analysis revealed significant heterogeneity among species, with values ranging from 0.386 to 1.797. ENC-GC3s, GC3-GC12, and PR2 analyses indicated a marked deviation from neutral evolution. Selection pressure analysis indicated strong purifying selection (Ka/Ks < 0.2) acting on photosynthetic system genes, while certain genes (e.g., matK, rpl20) exhibited signals of positive selection, highlighting adaptive evolutionary features in specific genomic regions. Phylogenetic reconstruction placed Murraya paniculata within a clade containing other Murraya species, closely related to Citrus and Clausena, reflecting morphological and biogeographic patterns. This study provides a molecular framework for taxonomic revision in Rutaceae and enhances understanding of chloroplast genome evolution in the family.
Keywords: Chloroplast genome, Murraya paniculata, Rutaceae, Comparative genomics, adaptive evolution, phylogeny, Selection pressure
Received: 29 Jul 2025; Accepted: 28 Aug 2025.
Copyright: © 2025 Chen, Liu, Wang, Luo, Xie, Yu, Chang, Zheng, Zheng, Sheng, Jiang, Ye, Hua, Ma 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:
Haijie Ma, Zhejiang Agriculture and Forestry University, Hangzhou, China
Fei Li, Wenzhou Vocational College of Science and Technology, Wenzhou, China
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