Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae
Abstract
:1. Introduction
2. Results
2.1. Chloroplast Genome Features of N. lappaceum
2.2. Characterization of SSRs and Repeat Sequences
2.3. Codon Usage Analysis and RNA Editing Sites Prediction
2.4. Comparative Genomes Analysis
2.5. Expansion and Contraction of IR Regions
2.6. Synonymous (Ks) and Non-Synonymous (Ka) Substitution Rate Analysis
2.7. Phylogenetic Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Material, DNA Extraction, and Sequencing
4.2. Chloroplast Genome Assembly and Annotation
4.3. Chloroplast Genome Analysis
4.4. Genome Comparison
4.5. Positive Selection Analysis of Protein Sequence
4.6. Phylogenetic Analysis
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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Genome Feature | Dimocarpus longan | Litchi chinensis | Pometia tomentosa | Sapindus mukorossi | Nephelium lappaceum | Dodonaea viscosa | Eurycorymbus cavaleriei | Koelreuteria paniculata | Xanthoceras sorbifolium |
---|---|---|---|---|---|---|---|---|---|
GenBank | MG214255 | KY635881 | MN106254 | KM454982 | MT936934 | KM454982 | MF155892 | MG813997 | KY859413 |
Size (bp) | 160,833 | 162,524 | 160,818 | 160,481 | 161,321 | 159,375 | 158,777 | 163,258 | 161,231 |
LSC (bp) | 85,707 | 85,750 | 85,666 | 85,650 | 86,068 | 872,014 | 86,940 | 90,236 | 85,299 |
SSC (bp) | 18,270 | 16,568 | 18,360 | 18,873 | 18,153 | 17,972 | 17,991 | 18,268 | 18,692 |
IR (bp) | 28,428 | 30,103 | 28,396 | 27,979 | 28,550 | 27,099 | 26,923 | 27,377 | 28,620 |
Total genes | 132 | 132 | 133 | 135 | 132 | 135 (2 Pseudogene) | 137 | 133 (3 Pseudogene) | 132 |
Protein genes | 87 | 87 | 88 | 88 | 87 | 88 | 89 | 85 | 86 |
tRNA genes | 37 | 37 | 37 | 39 | 37 | 37 | 40 | 37 | 38 |
rRNA genes | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 |
GC (%) | 37.79% | 37.80% | 37.87% | 37.66% | 37.77% | 37.86% | 37.92% | 37.30% | 37.69% |
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Dong, F.; Lin, Z.; Lin, J.; Ming, R.; Zhang, W. Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae. Plants 2021, 10, 283. https://doi.org/10.3390/plants10020283
Dong F, Lin Z, Lin J, Ming R, Zhang W. Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae. Plants. 2021; 10(2):283. https://doi.org/10.3390/plants10020283
Chicago/Turabian StyleDong, Fei, Zhicong Lin, Jing Lin, Ray Ming, and Wenping Zhang. 2021. "Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae" Plants 10, no. 2: 283. https://doi.org/10.3390/plants10020283