De Novo Assembly of First Mitochondrial Genome in <i>Melicope pteleifolia</i> (Rutaceae): Resolving Inter-Organellar Gene Transfer Events Through Integrated Chloroplast Analysis
<i>Melicope pteleifolia</i> (Rutaceae) is a shrub or tree with high medicinal value. Although the physical features of <i>M. pteleifolia</i> are evident, the mitochondrial (mt) genome has yet to be investigated, and its evolutionary relationship within Rutaceae is unclear. Th...
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2025-06-01
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| author | Lijun Guo Wenwen Shi Yatao Luo Kai Gao Jingli Huang Hong Wei Pan Liang Longfei He Dong Xiao Jie Zhan Guangyu Zeng Aiqin Wang |
| author_facet | Lijun Guo Wenwen Shi Yatao Luo Kai Gao Jingli Huang Hong Wei Pan Liang Longfei He Dong Xiao Jie Zhan Guangyu Zeng Aiqin Wang |
| author_sort | Lijun Guo |
| collection | DOAJ |
| description | <i>Melicope pteleifolia</i> (Rutaceae) is a shrub or tree with high medicinal value. Although the physical features of <i>M. pteleifolia</i> are evident, the mitochondrial (mt) genome has yet to be investigated, and its evolutionary relationship within Rutaceae is unclear. The organelle genomes of <i>M. pteleifolia</i> were constructed using Nanopore and Illumina sequencing data. The circular mt genome is 780,107 base pairs (bp) long, with a GC content of 44.85%. It has 66 genes, consisting of 33 protein-coding genes (PCGs), 30 tRNA genes, and 3 rRNA genes. The length of the chloroplast (cp) genome was 158,987 bp, containing 88 PCGs, 37 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 507 and 353 repetitive sequences, respectively. RNA editing sites were abundant in <i>M. pteleifolia</i> organelle genomes, including 323 sites in mtDNA and 260 sites in cpDNA. Phylogenetic research using the cp and mt genomes of <i>M. pteleifolia</i> and nine additional species of the Rutaceae family precisely delineates its evolutionary and taxonomic position. Ka/Ks and nucleotide diversity indicated that the majority of the PCGs in the mitochondrial genome had experienced negative selection. These findings provided comprehensive information on the <i>M. pteleifolia</i> mitogenome for studying phylogenetic relationships in Rutaceae, with chloroplast-derived sequences providing critical evidence for inter-organellar genome evolution. |
| format | Article |
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| issn | 2311-7524 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
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| series | Horticulturae |
| spelling | doaj-art-c1ded0eb4339460db011d3623fcc6d3e2025-08-20T02:21:06ZengMDPI AGHorticulturae2311-75242025-06-0111662810.3390/horticulturae11060628De Novo Assembly of First Mitochondrial Genome in <i>Melicope pteleifolia</i> (Rutaceae): Resolving Inter-Organellar Gene Transfer Events Through Integrated Chloroplast AnalysisLijun Guo0Wenwen Shi1Yatao Luo2Kai Gao3Jingli Huang4Hong Wei5Pan Liang6Longfei He7Dong Xiao8Jie Zhan9Guangyu Zeng10Aiqin Wang11National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, ChinaNational Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, ChinaNational Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, ChinaNational Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, ChinaAgricultural and Animal Husbandry Industry Development Research Institute, Guangxi University, Nanning 530004, ChinaGuangxi State-Owned Sanmenjiang Forest Farm, Liuzhou 545001, ChinaGuangxi State-Owned Sanmenjiang Forest Farm, Liuzhou 545001, ChinaNational Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, ChinaNational Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, ChinaNational Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, ChinaGuangxi Forestry Science Research Institute, Nanning 530004, ChinaNational Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China<i>Melicope pteleifolia</i> (Rutaceae) is a shrub or tree with high medicinal value. Although the physical features of <i>M. pteleifolia</i> are evident, the mitochondrial (mt) genome has yet to be investigated, and its evolutionary relationship within Rutaceae is unclear. The organelle genomes of <i>M. pteleifolia</i> were constructed using Nanopore and Illumina sequencing data. The circular mt genome is 780,107 base pairs (bp) long, with a GC content of 44.85%. It has 66 genes, consisting of 33 protein-coding genes (PCGs), 30 tRNA genes, and 3 rRNA genes. The length of the chloroplast (cp) genome was 158,987 bp, containing 88 PCGs, 37 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 507 and 353 repetitive sequences, respectively. RNA editing sites were abundant in <i>M. pteleifolia</i> organelle genomes, including 323 sites in mtDNA and 260 sites in cpDNA. Phylogenetic research using the cp and mt genomes of <i>M. pteleifolia</i> and nine additional species of the Rutaceae family precisely delineates its evolutionary and taxonomic position. Ka/Ks and nucleotide diversity indicated that the majority of the PCGs in the mitochondrial genome had experienced negative selection. These findings provided comprehensive information on the <i>M. pteleifolia</i> mitogenome for studying phylogenetic relationships in Rutaceae, with chloroplast-derived sequences providing critical evidence for inter-organellar genome evolution.https://www.mdpi.com/2311-7524/11/6/628<i>Melicope pteleifolia</i>mitochondrial genomechloroplast genomeRNA editingphylogeny |
| spellingShingle | Lijun Guo Wenwen Shi Yatao Luo Kai Gao Jingli Huang Hong Wei Pan Liang Longfei He Dong Xiao Jie Zhan Guangyu Zeng Aiqin Wang De Novo Assembly of First Mitochondrial Genome in <i>Melicope pteleifolia</i> (Rutaceae): Resolving Inter-Organellar Gene Transfer Events Through Integrated Chloroplast Analysis Horticulturae <i>Melicope pteleifolia</i> mitochondrial genome chloroplast genome RNA editing phylogeny |
| title | De Novo Assembly of First Mitochondrial Genome in <i>Melicope pteleifolia</i> (Rutaceae): Resolving Inter-Organellar Gene Transfer Events Through Integrated Chloroplast Analysis |
| title_full | De Novo Assembly of First Mitochondrial Genome in <i>Melicope pteleifolia</i> (Rutaceae): Resolving Inter-Organellar Gene Transfer Events Through Integrated Chloroplast Analysis |
| title_fullStr | De Novo Assembly of First Mitochondrial Genome in <i>Melicope pteleifolia</i> (Rutaceae): Resolving Inter-Organellar Gene Transfer Events Through Integrated Chloroplast Analysis |
| title_full_unstemmed | De Novo Assembly of First Mitochondrial Genome in <i>Melicope pteleifolia</i> (Rutaceae): Resolving Inter-Organellar Gene Transfer Events Through Integrated Chloroplast Analysis |
| title_short | De Novo Assembly of First Mitochondrial Genome in <i>Melicope pteleifolia</i> (Rutaceae): Resolving Inter-Organellar Gene Transfer Events Through Integrated Chloroplast Analysis |
| title_sort | de novo assembly of first mitochondrial genome in i melicope pteleifolia i rutaceae resolving inter organellar gene transfer events through integrated chloroplast analysis |
| topic | <i>Melicope pteleifolia</i> mitochondrial genome chloroplast genome RNA editing phylogeny |
| url | https://www.mdpi.com/2311-7524/11/6/628 |
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