Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae)
Abstract
:1. Introduction
2. Result
2.1. The Plastome Characters of Vanda
2.2. Repeated Analysis
2.3. Codon Usage Bias
2.4. Plastome Sequence Divergence and DNA Marker Investigation
2.5. Phylogenetic Analyses and Character Reconstruction
3. Discussion
3.1. The Plastome Characteristics and Structural Evolution
3.2. The Barcoding Investigation and Phylogenetic Analyses
4. Materials and Methods
4.1. Sampling and Sequencing
4.2. Assembly and Annotation
4.3. Sequence and Structure Divergence Analyses
4.4. Repetitive Sequence and Codon Usage Analyses
4.5. Phylogenetic Analyses and Measurement of Divergence Variables
4.6. Character Reconstruction of Ndh Gene Status in Vanda
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Taxa | Length (bp) | GC Content (%) | Gene Numbers | ||||||
---|---|---|---|---|---|---|---|---|---|
Plastome | LSC | IR | SSC | Total | CDS | tRNA | rRNA | ||
V. alpina | 149,273 | 85,819 | 25,860 | 11,734 | 36.7 | 120 | 74 | 38 | 8 |
V. ampullaceum | 146,340 | 85,436 | 24,523 | 11,858 | 36.5 | 120 | 74 | 38 | 8 |
V. brunnea | 149,216 | 85,783 | 25,860 | 11,713 | 36.7 | 120 | 74 | 38 | 8 |
V. coelestis | 148,073 | 85,105 | 25,772 | 11,424 | 36.8 | 120 | 74 | 38 | 8 |
V. coerulea | 149,268 | 85,982 | 25,787 | 11,712 | 36.6 | 120 | 74 | 38 | 8 |
V. coerulescens | 149,410 | 85,954 | 25,965 | 11,526 | 36.7 | 120 | 74 | 38 | 8 |
V. concolor | 149,474 | 85,678 | 25,897 | 12,002 | 36.6 | 120 | 74 | 38 | 8 |
V. cristata | 146,993 | 83,927 | 25,772 | 11,522 | 36.7 | 120 | 74 | 38 | 8 |
V. falcata | 146,497 | 83,808 | 25,457 | 11,775 | 36.6 | 120 | 74 | 38 | 8 |
V. pumila | 149,273 | 85,819 | 25,860 | 11,734 | 36.7 | 120 | 74 | 38 | 8 |
V. richardsiana | 146,498 | 83,809 | 25,457 | 11,775 | 36.6 | 120 | 74 | 38 | 8 |
V. subconcolor | 149,490 | 85,691 | 25,912 | 11,975 | 36.6 | 120 | 74 | 38 | 8 |
V. xichangensis | 146,681 | 83,920 | 25,505 | 11,751 | 36.6 | 120 | 74 | 38 | 8 |
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Lei, W.; Zhou, P.; Pei, Z.; Liu, Y.; Luo, Y.; Xiang, X. Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae). Int. J. Mol. Sci. 2024, 25, 9538. https://doi.org/10.3390/ijms25179538
Lei W, Zhou P, Pei Z, Liu Y, Luo Y, Xiang X. Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae). International Journal of Molecular Sciences. 2024; 25(17):9538. https://doi.org/10.3390/ijms25179538
Chicago/Turabian StyleLei, Wanshun, Peng Zhou, Zelong Pei, Yizhen Liu, Yan Luo, and Xiaoguo Xiang. 2024. "Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae)" International Journal of Molecular Sciences 25, no. 17: 9538. https://doi.org/10.3390/ijms25179538