Novel Perspectives on Chloroplast tRNA Genomic and Structural Variations Imply the Evolution of Papilionoideae (Fabaceae)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Taxon Sampling and Annotation of pttRNAs
2.2. Comprehensive Identification of Sequence and Structural Variations
2.3. Overall Evaluation of the Substitution Frequencies
3. Results
3.1. Gene Content and Size of pttRNAs in Papilionoideae
3.2. Remarkable Variations in Conserved Sequences between IRLC and Non-IRLC Clade pttRNAs
3.3. Intron Analyses Revealed Substantial Inter-Lineage Structural Disparities and Informative Indels
3.4. Atypical Structures Identified in Papilionoideae pttRNAs
3.5. Hyper-Variable Patterns of Nucleotide Substitutions in pttRNAs at the Inter-Lineage Level
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Isotype | IRLC (156) | Non-IRLC (109) | Isotype | IRLC (156) | Non-IRLC (109) | ||||
---|---|---|---|---|---|---|---|---|---|
Anticodon | Length/nt (Mean ± SD) | Anticodon | Length/nt (Mean ± SD) | Anticodon | Length/nt (Mean ± SD) | Anticodon | Length/nt (Mean ± SD) | ||
Ala | UGC (155) *△ | 73.0 ± 0.0 | UGC (109) △ | 73.0 ± 0.0 | Met | CAU (156) | 73.0 ± 0.0 | CAU (109) | 73.0 ± 0.1 |
Cys | GCA (156) | 70.9 ± 0.7 | GCA (109) | 71.0 ± 0.0 | Asn | GUU (156) | 73.0 ± 0.0 | GUU (109) | 73.0 ± 0.0 |
Asp | GUC (156) | 74.0 ± 0.0 | GUC (109) | 74.0 ± 0.0 | Pro | UGG (156) | 74.0 ± 0.0 | UGG (109) | 74.0 ± 0.0 |
Glu | UUC (156) | 73.0 ± 0.0 | UUC (109) | 73.0 ± 0.0 | Gln | UUG (156) | 72.0 ± 0.1 | UUG (109) | 72.0 ± 0.0 |
Phe | GAA (156) | 73.0 ± 0.0 | GAA (109) | 73.0 ± 0.0 | Arg | ACG (156) | 74.0 ± 0.0 | ACG (109) | 74.0 ± 0.0 |
fMet | CAU (156) | 74.0 ± 0.0 | CAU (109) | 74.0 ± 0.0 | UCU (156) | 72.0 ± 0.0 | UCU (109) | 72.0 ± 0.0 | |
Gly | GCC (156) | 71.0 ± 0.0 | GCC (109) | 71.1 ± 0.0 | Ser | GCU (156) | 87.0 ± 0.0 | GCU (109) | 87.0 ± 0.0 |
UCC (156) △ | 72.0 ± 0.0 | UCC (109) △ | 72.0 ± 0.0 | GGA (156) | 88.0 ± 0.0 | GGA (109) | 88.7 ± 1.3 | ||
His | GUG (156) | 74.0 ± 0.0 | GUG (107) * | 74.0 ± 0.0 | UGA (156) | 90.2 ± 1.8 | UGA (109) | 92.8 ± 0.5 | |
Ile | CAU (154) * | 74.0 ± 0.0 | CAU (109) | 74.0 ± 0.0 | Thr | GGU (156) | 72.6 ± 0.9 | GGU (109) | 72.0 ± 0.2 |
GAU (155) *△ | 72.0 ± 0.0 | GAU (109) △ | 72.0 ± 0.0 | UGU (155) * | 73.0 ± 0.0 | UGU (109) | 73.0 ± 0.0 | ||
Lys | UUU (156) △ | 72.0 ± 0.0 | UUU (109) △ | 72.0 ± 0.0 | Val | GAC (155) * | 72.0 ± 0.0 | GAC (109) | 72.0 ± 0.0 |
Leu | CAA (156) | 81.1 ± 0.6 | CAA (109) | 81.0 ± 0.0 | UAC (156) △ | 75.6 ± 0.5 | UAC (109) △ | 76.0 ± 0.2 | |
UAA (156) △ | 87.0 ± 0.0 | UAA (109) △ | 87.0 ± 0.1 | Trp | CCA (156) | 74.0 ± 0.0 | CCA (109) | 74.0 ± 0.0 | |
UAG (156) | 80.0 ± 0.0 | UAG (109) | 80.0 ± 0.1 | Tyr | GUA (156) | 84.0 ± 0.0 | GUA (109) | 84.0 ± 0.2 |
tRNA Type | Length (bp) | GC Content (%) | ||
---|---|---|---|---|
IRLC | Non-IRLC | IRLC | Non-IRLC | |
trnA-UGC | 808.40 ± 7.05 | 800.70 ± 10.20 | 48.62 ± 0.62 | 50.82 ± 0.47 |
trnG-UCC | 684.23 ± 15.39 | 707.19 ± 16.79 | 29.70 ± 0.52 | 29.87 ± 0.68 |
trnI-GAU | 751.72 ± 85.21 | 950.18 ± 8.35 | 47.42 ± 0.64 | 48.35 ± 0.47 |
trnK-UUU | 2490.79 ± 52.03 | 2568.51 ± 38.06 | 31.53 ± 0.55 | 31.54 ± 0.60 |
trnL-UAA | 445.29 ± 84.34 | 524.69 ± 24.80 | 33.29 ± 1.37 | 33.57 ± 0.77 |
trnV-UAC | 579.45 ± 9.42 | 593.15 ± 8.31 | 31.41 ± 1.30 | 33.45 ± 0.98 |
Location of Atypical Structures | Isoacceptor tRNA | Average Minimal free Energy (kcal/mol) | ||
---|---|---|---|---|
Total | IRLC | Non-IRLC | ||
AC-arm | trnR-ACG | –26.80 | –26.81 | –26.80 |
trnT-UGU | –28.58 | –28.41 | –28.83 | |
ANC-loop | trnL-UAA | –26.54 | –26.88 | –26.05 |
trnV-UAC | –25.33 | –25.46 | –25.15 | |
V-region | trnL-CAA | –24.18 | –24.22 | –24.12 |
trnS-GCU | –28.80 | –28.84 | –28.73 | |
trnS-GGA | –30.47 | –29.85 | –31.35 | |
trnS-UGA | –33.02 | –31.28 | –35.51 | |
trnY-GUA | –29.35 | –29.46 | –29.21 | |
Ψ-arm | trnC-GCA | –24.31 | –24.10 | –24.60 |
Isoacceptor tRNA | IRLC | Non-IRLC | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Total Size | ti | ti Ratio | tv | ti Ratio | ti/tv | Total Size | ti | ti Ratio | tv | ti Ratio | ti/tv | |
trnA-UGC | 11,315 | 0 | 0.00% | 1 | 0.01% | 0.00 | 7957 | 0 | 0.00% | 0 | 0.00% | / |
trnC-GCA | 11,067 | 170 | 1.54% | 35 | 0.32% | 4.86 | 7739 | 58 | 0.75% | 9 | 0.12% | 6.44 |
trnD-GUC | 11,544 | 115 | 1.00% | 0 | 0.00% | / | 8066 | 35 | 0.43% | 0 | 0.00% | / |
trnE-UUC | 11,388 | 29 | 0.25% | 11 | 0.10% | 2.64 | 7957 | 114 | 1.43% | 5 | 0.06% | 22.80 |
trnF-GAA | 11,388 | 167 | 1.47% | 20 | 0.18% | 8.35 | 7957 | 24 | 0.30% | 0 | 0.00% | / |
trnfM-CAU | 11,544 | 130 | 1.13% | 61 | 0.53% | 2.13 | 8066 | 55 | 0.68% | 1 | 0.01% | 55.00 |
trnG-GCC | 11,076 | 127 | 1.15% | 27 | 0.24% | 4.70 | 7739 | 31 | 0.40% | 1 | 0.01% | 31.00 |
trnG-UCC | 11,160 | 50 | 0.45% | 0 | 0.00% | / | 7848 | 26 | 0.33% | 0 | 0.00% | / |
trnH-GUG | 11,544 | 109 | 0.94% | 17 | 0.15% | 6.41 | 7909 | 17 | 0.21% | 3 | 0.04% | 5.67 |
trnI-CAU | 11,396 | 51 | 0.45% | 16 | 0.14% | 3.19 | 8066 | 0 | 0.00% | 1 | 0.01% | 0.00 |
trnI-GAU | 11,160 | 44 | 0.39% | 16 | 0.14% | 2.75 | 7848 | 1 | 0.01% | 0 | 0.00% | / |
trnK-UUU | 11,232 | 10 | 0.09% | 0 | 0.00% | / | 7848 | 20 | 0.25% | 3 | 0.04% | 6.67 |
trnL-CAA | 12,650 | 83 | 0.66% | 31 | 0.25% | 2.68 | 8829 | 3 | 0.03% | 2 | 0.02% | 1.50 |
trnL-UAA | 13,572 | 13 | 0.10% | 16 | 0.12% | 0.81 | 9483 | 63 | 0.66% | 58 | 0.61% | 1.09 |
trnL-UAG | 12,480 | 51 | 0.41% | 0 | 0.00% | / | 8722 | 31 | 0.36% | 5 | 0.06% | 6.20 |
trnM-CAU | 11,388 | 31 | 0.27% | 2 | 0.02% | 15.50 | 7958 | 10 | 0.13% | 20 | 0.25% | 0.50 |
trnN-GUU | 11,388 | 105 | 0.92% | 0 | 0.00% | / | 7957 | 11 | 0.14% | 0 | 0.00% | / |
trnP-UGG | 11,544 | 59 | 0.51% | 1 | 0.01% | 59.00 | 8066 | 13 | 0.16% | 0 | 0.00% | / |
trnQ-UUG | 11,233 | 225 | 2.00% | 65 | 0.58% | 3.46 | 7848 | 32 | 0.41% | 37 | 0.47% | 0.86 |
trnR-ACG | 11,544 | 5 | 0.04% | 2 | 0.02% | 2.50 | 8066 | 0 | 0.00% | 0 | 0.00% | / |
trnR-UCU | 11,232 | 71 | 0.63% | 49 | 0.44% | 1.45 | 7848 | 6 | 0.08% | 7 | 0.09% | 0.86 |
trnS-GCU | 13,572 | 25 | 0.18% | 121 | 0.89% | 0.21 | 9483 | 20 | 0.21% | 8 | 0.08% | 2.50 |
trnS-GGA | 13,728 | 87 | 0.63% | 75 | 0.55% | 1.16 | 9672 | 71 | 0.73% | 21 | 0.22% | 3.38 |
trnS-UGA | 14,075 | 113 | 0.80% | 63 | 0.45% | 1.79 | 10,117 | 87 | 0.86% | 93 | 0.92% | 0.94 |
trnT-GGU | 11,329 | 159 | 1.40% | 3 | 0.03% | 53.00 | 7850 | 35 | 0.45% | 1 | 0.01% | 35.00 |
trnT-UGU | 11,315 | 74 | 0.65% | 18 | 0.16% | 4.11 | 7957 | 44 | 0.55% | 5 | 0.06% | 8.80 |
trnV-GAC | 11,160 | 219 | 1.96% | 25 | 0.22% | 8.76 | 7848 | 39 | 0.50% | 8 | 0.10% | 4.88 |
trnV-UAC | 11,794 | 15 | 0.13% | 8 | 0.07% | 1.88 | 8282 | 63 | 0.76% | 9 | 0.11% | 7.00 |
trnW-CCA | 11,544 | 22 | 0.19% | 0 | 0.00% | / | 8066 | 47 | 0.58% | 0 | 0.00% | / |
trnY-GUA | 13,104 | 76 | 0.58% | 2 | 0.02% | 38.00 | 9158 | 35 | 0.38% | 2 | 0.02% | 17.50 |
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Han, S.; Zhang, S.; Peng, H.; Ge, W.; Yang, J.; Wu, H.; Dai, C.; Zhu, B.; Kan, X. Novel Perspectives on Chloroplast tRNA Genomic and Structural Variations Imply the Evolution of Papilionoideae (Fabaceae). Horticulturae 2024, 10, 932. https://doi.org/10.3390/horticulturae10090932
Han S, Zhang S, Peng H, Ge W, Yang J, Wu H, Dai C, Zhu B, Kan X. Novel Perspectives on Chloroplast tRNA Genomic and Structural Variations Imply the Evolution of Papilionoideae (Fabaceae). Horticulturae. 2024; 10(9):932. https://doi.org/10.3390/horticulturae10090932
Chicago/Turabian StyleHan, Shiyun, Sijia Zhang, Hui Peng, Wen Ge, Jianke Yang, Huaqin Wu, Chenwei Dai, Bo Zhu, and Xianzhao Kan. 2024. "Novel Perspectives on Chloroplast tRNA Genomic and Structural Variations Imply the Evolution of Papilionoideae (Fabaceae)" Horticulturae 10, no. 9: 932. https://doi.org/10.3390/horticulturae10090932