Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae s.l. (Dipsacales) Plastomes
Abstract
:1. Introduction
2. Results
2.1. Plastome Organization
2.2. Elevated Substitution Rates in the Plastomes of the Subfamily Valerianoideae
2.3. Structural Evolution of Plastid-Encoded accD Gene in Caprifoliaceae s.l. Plastomes
2.4. Length Variation in the Valeriana accD Gene
2.5. Correlation between Structural Change and Substitution Rates in the Plastid-Encoded clpP Gene
3. Discussion
4. Materials and Methods
4.1. Genome Sequencing, Assembly, and Annotation
4.2. Comparative Analyses
4.3. Estimation of Substitution Rates
4.4. Survey of Variability in the Plastid-Encoded accD Gene
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Taxon | Dipsacoideae | Valerianoideae | |||
---|---|---|---|---|---|
Dipsacus japonicus | Scabiosa comosa | Fedia cornucopiae | Valeriana fauriei | Valerianella locusta | |
Size (bp) | 160,243 | 159,651 | 152,196 | 155,302 | 149,809 |
LSC length (bp) | 87,066 | 87,477 | 82,960 | 85,541 | 82,103 |
SSC length (bp) | 17,850 | 18,716 | 15,862 | 15,159 | 15,796 |
IR length (bp) | 27,664 | 26,729 | 26,687 | 27,301 | 25,955 |
Number of protein-coding genes | 78 (6) | 78 (7) | 79 (4) | 79 (4) | 79 (4) |
Number of tRNA genes | 29 (8) | 30 (7) | 30 (7) | 30 (7) | 30 (7) |
Number of rRNA genes | 4 (4) | 4 (4) | 4 (4) | 4 (4) | 4 (4) |
Number of introns | 21 (5) | 20 (5) | 21 (5) | 21 (5) | 19 (5) |
GC content (%) | 38.8 | 38.7 | 38.2 | 38.4 | 38.1 |
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Park, S.; Jun, M.; Park, S.; Park, S. Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae s.l. (Dipsacales) Plastomes. Int. J. Mol. Sci. 2021, 22, 10485. https://doi.org/10.3390/ijms221910485
Park S, Jun M, Park S, Park S. Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae s.l. (Dipsacales) Plastomes. International Journal of Molecular Sciences. 2021; 22(19):10485. https://doi.org/10.3390/ijms221910485
Chicago/Turabian StylePark, Seongjun, Minji Jun, Sunmi Park, and SeonJoo Park. 2021. "Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae s.l. (Dipsacales) Plastomes" International Journal of Molecular Sciences 22, no. 19: 10485. https://doi.org/10.3390/ijms221910485