Assembly of the Complete Mitochondrial Genome of Chinese Plum (Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Sampling and DNA Sequencing
2.2. Assembly and Annotation of Mitogenomes
2.3. Identification of Repeats and Repeat-Mediated Homologous Recombinations
2.4. RNA Extraction and Sequencing
2.5. Identification of RNA Editing Sites in Mitochondrial Protein-Coding Genes (PCGs)
3. Results
3.1. Characteristics of the P. salicina Mitogenome
3.2. Comparison of Mitochondrial Genomes in ROSACEAE
3.3. Repeats and Homologous Recombinations
3.4. Characteristics of RNA Editing Sites in Mitochondrial PCGs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Group of Genes | Name of Genes | |
---|---|---|
Core genes | ATP synthase | atp1, atp4, atp6 1, atp8, atp9 |
Cytochrome c biogenesis | ccmB, ccmC, ccmFc 2, ccmFn | |
Ubichinol cytochrome c reductase | cob | |
Cytochrome c oxidase | cox1, cox2, cox3 | |
Maturases | matR | |
Transport membrane protein | mttB | |
NADH dehydrogenase | nad1 2, nad2 2, nad3 (×2), nad4 2, nad4L, nad5 2, nad6 (×2), nad7 2, nad9 | |
Variable genes | Large subunit of ribosome | rpl5, rpl10, rpl16 |
Small subunit of ribosome | rps1, rps3 2, rps4, rps12, rps13, rps14 | |
Succinate dehydrogenase | sdh3 1, sdh4 | |
rRNA genes | Ribosomal RNAs | rrn5, rrn18, rrn26 |
tRNA genes | Transfer RNAs | trnY-GUA, trnW-CCA 3, trnS-UGA, trnS-GCU, trnQ-UUG, trnP-UGG, trnN-GUU, trnN-AUU 3, trnM-CAU (×3), trnK-UUU, trnH-GUG, trnG-GCC, trnF-GAA, trnE-UUC, trnD-GUC, trnC-GCA (×2) |
Species | Accession Number | Genome Size (bp) | GC Content (%) | Number of PCGs | Multicopy Genes | |
---|---|---|---|---|---|---|
Core Genes | Variable Genes | |||||
Rosa chinensis | CM009589.1 | 313,448 | 45.48 | 24 | 9 (1) | rps3 |
Fragaria orientalis | NC_057524.1 | 275,143 | 45.24 | 24 | 7 | |
Malus domestica | NC_018554.1 | 396,947 | 45.39 | 24 | 9 (1) | rps12 |
Malus hupehensis var. mengshanensis | KR534606.1 | 422,555 | 45.21 | 24 (2) | 9 (1) | atp8, cox2, rps3 |
Eriobotrya japonica | NC_045228.1 | 434,980 | 45.42 | 24 (1) | 10 | nad4 |
Pyrus betulifolia | NC_054332.1 | 469,928 | 45.28 | 24 (2) | 10 (2) | atp1, nad6, rps1, rps4 |
Sorbus aucuparia | NC_052880.1 | 384,977 | 45.39 | 24 (1) | 9 | matR |
Sorbus torminalis | NC_052879.1 | 386,758 | 45.31 | 24 | 9 | |
Prunus avium | MT975322.1 | 444,582 | 45.62 | 24 | 10 (1) | rps3 |
Prunus salicina | OK563724.1 | 508,035 | 45.43 | 24 (2) | 10 | nad3, nad6 |
Repeat | Length (bp) | Direction | Position | Reads Support Master Circle Conformation | Reads Support Alternative Conformation |
---|---|---|---|---|---|
R1 | 511 | + | 200803–201313 | 182 | 11 |
– | 419510–419000 | (94.30%) | (5.70%) | ||
R2 | 472 | + | 156450–156921 | 167 | 4 |
– | 410364–409893 | (96.67%) | (2.33%) | ||
R3 | 393 | + | 164678–165070 | 135 | 4 |
– | 345427–345035 | (97.12%) | (2.88%) | ||
R4 | 385 | + | 361588–361972 | 166 | 3 |
+ | 501441–501825 | (98.22%) | (1.78%) | ||
R5 | 299 | + | 280928–281226 | 163 | 4 |
– | 358365–358067 | (97.60%) | (2.40%) | ||
R6 | 294 | + | 123383–123676 | 149 | 5 |
– | 154864–154571 | (96.75%) | (3.25%) | ||
R7 | 195 | + | 215708–215902 | 176 | 5 |
+ | 303436–303630 | (97.24%) | (2.76%) | ||
R8 | 175 | + | 290959–291133 | 182 | 1 |
+ | 362216–362390 | (99.45%) | (0.55%) | ||
R9 | 111 | + | 89335–89445 | 171 | 1 |
– | 343225–343115 | (99.42%) | (0.58%) |
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Fang, B.; Li, J.; Zhao, Q.; Liang, Y.; Yu, J. Assembly of the Complete Mitochondrial Genome of Chinese Plum (Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites. Genes 2021, 12, 1970. https://doi.org/10.3390/genes12121970
Fang B, Li J, Zhao Q, Liang Y, Yu J. Assembly of the Complete Mitochondrial Genome of Chinese Plum (Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites. Genes. 2021; 12(12):1970. https://doi.org/10.3390/genes12121970
Chicago/Turabian StyleFang, Bo, Jingling Li, Qian Zhao, Yuping Liang, and Jie Yu. 2021. "Assembly of the Complete Mitochondrial Genome of Chinese Plum (Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites" Genes 12, no. 12: 1970. https://doi.org/10.3390/genes12121970