Structural Reorganization in Two Alfalfa Mitochondrial Genome Assemblies and Mitochondrial Evolution in Medicago Species
Abstract
:1. Introduction
2. Results
2.1. Sequencing and Assembly
2.2. Characteristics of the Mitogenomes of Zhongmu No.1 and Zhongmu No.4
2.3. Validation of Isoforms
2.4. Evolution of the Mitochondrial Genomes of Zhongmu No.1 and Zhongmu No.4
2.5. Evolutionary Analysis of the Medicago Accessions
3. Discussion
3.1. Mitochondrial Genome Sequencing Strategies
3.2. Validation of Isoforms
3.3. Genomic Differences in Zhongmu No.1 and Zhongmu No.4
3.4. Population Evolution Analysis
4. Materials and Methods
4.1. Taxon Sampling, DNA Extraction, and Sequencing
4.2. Mitochondrion Assembly and Annotation
4.3. Validation of Isoforms
4.4. Collinearity Analysis
4.5. SNP Calling
4.6. Population Evolution Analysis
4.7. Assembly of the cox1 and rrn18s Genes
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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O7 | Reads | O8 | Reads | O9 | Reads | F6 | Reads | F8 | Reads |
---|---|---|---|---|---|---|---|---|---|
O1−, O7− | 28 | O3−, O8+ | 24 | / | / | F1−, F6− | 195 | / | / |
O7−, O2− | 31 | O8+, O6− | 38 | / | / | F5−, F6− | 240 | / | / |
O6−, −O7 | 25 | O5−, O8+ | 40 | / | / | F6−, F1− | 222 | / | / |
O7−, O4− | 28 | O8+, O1− | 8 | / | / | F6−, F7− | 216 | / | / |
O1−, O7−, O2- | 0 | O3−, O8+, O6− | 3 | O2−, O9+, O3− | 28 | F1−, F6−, F1− | 84 | F7−, F8−, F2− | 27 |
O1−, O7−, O4- | 1 | O3−, O8+, O1− | 1 | O4−, O9+, O5− | 39 | F6−, F1−, F6− | 0 | F4−, F8+, F3− | 77 |
O6−, O7−, O2- | 0 | O5−, O8+, O6− | 1 | O2−, O9+, O5− | 0 | F5−, F6−, F1− | 97 | F7−, F8−, F4+ | 290 |
O6−, O7−, O4- | 0 | O5−, O8+, O1− | 0 | O4−, O9+, O3− | 0 | F5−, F6−, F7− | 108 | F2+, F8+, F3− | 292 |
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He, X.; Zhang, X.; Deng, Y.; Yang, R.; Yu, L.-X.; Jia, S.; Zhang, T. Structural Reorganization in Two Alfalfa Mitochondrial Genome Assemblies and Mitochondrial Evolution in Medicago Species. Int. J. Mol. Sci. 2023, 24, 17334. https://doi.org/10.3390/ijms242417334
He X, Zhang X, Deng Y, Yang R, Yu L-X, Jia S, Zhang T. Structural Reorganization in Two Alfalfa Mitochondrial Genome Assemblies and Mitochondrial Evolution in Medicago Species. International Journal of Molecular Sciences. 2023; 24(24):17334. https://doi.org/10.3390/ijms242417334
Chicago/Turabian StyleHe, Xiaofan, Xiaopeng Zhang, Yantian Deng, Rui Yang, Long-Xi Yu, Shangang Jia, and Tiejun Zhang. 2023. "Structural Reorganization in Two Alfalfa Mitochondrial Genome Assemblies and Mitochondrial Evolution in Medicago Species" International Journal of Molecular Sciences 24, no. 24: 17334. https://doi.org/10.3390/ijms242417334