Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human
Abstract
:1. Introduction
2. Materials and Methods
2.1. Acquisition of DNA Sequences
2.2. Sequence Alignment and Phylogenetic Analysis
2.3. Determination of Consensus Amino-Acid Sequences and Genetic Distance Analysis
2.4. Computation of Amino-Acid Conservation, Diversity, and Nucleotide Substitution Rate
2.5. Estimation of Gene Divergence Times
2.6. Statistical Analysis
3. Results
3.1. Intraspecies Variation of Nucleotide Diversity in the Peptide-Binding Region of Classical MHC Class I Genes
3.2. High Amino-Acid Sequence Diversity in the PBR of Pigs and Cattle MHC Class I Genes
3.3. Increased Nonsynonymous Substitutions in MHC Class I PBR in Artiodactyl Species than in Primates
3.4. Phylogenetics Analysis
3.5. Intraspecies Conservation of the Genetic Diversity Level for Peptide-Binding Pockets A and E
3.6. Presence of Conserved Sites in the Epitope-Binding Region of MHC Class I Genes across Different Species
3.7. Divergence Time of MHC Class I Genes between Artiodactyls and Primate Lineages
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sequence Differences (%) a | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
BoLA | HLA | Patr | SLA | ||||||||||
1 | 2 | 3 | A | B | C | A | B | C | 1 | 2 | 3 | ||
BoLA-1 | |||||||||||||
BoLA-2 | non-PBR b | 9.94 | |||||||||||
PBR c | 18.43 | ||||||||||||
BoLA-3 | non-PBR | 12.57 | 11.02 | ||||||||||
PBR | 22.04 | 17.25 | |||||||||||
HLA-A | non-PBR | 27.66 | 25.84 | 29.94 | |||||||||
PBR | 25.10 | 23.69 | 26.72 | ||||||||||
HLA-B | non-PBR | 24.86 | 23.04 | 26.28 | 13.79 | ||||||||
PBR | 22.40 | 23.06 | 25.46 | 18.16 | |||||||||
HLA-C | non-PBR | 29.02 | 27.01 | 29.99 | 17.45 | 12.47 | |||||||
PBR | 23.75 | 21.92 | 23.55 | 17.34 | 13.77 | ||||||||
Patr-A | non-PBR | 26.20 | 24.39 | 28.62 | 4.26 | 12.83 | 16.86 | ||||||
PBR | 24.69 | 23.16 | 26.29 | 9.84 | 19.09 | 17.41 | |||||||
Patr-B | non-PBR | 24.24 | 22.27 | 25.62 | 12.97 | 3.99 | 11.68 | 11.83 | |||||
PBR | 22.70 | 23.26 | 25.63 | 17.34 | 12.51 | 13.86 | 17.90 | ||||||
Patr-C | non-PBR | 29.26 | 27.21 | 30.18 | 17.27 | 12.22 | 5.32 | 16.77 | 11.56 | ||||
PBR | 24.66 | 22.98 | 24.60 | 18.57 | 15.47 | 7.93 | 17.96 | 15.38 | |||||
SLA-1 | non-PBR | 21.18 | 21.05 | 23.80 | 28.47 | 27.27 | 29.72 | 27.22 | 27.44 | 29.67 | |||
PBR | 26.28 | 24.62 | 27.02 | 26.69 | 26.73 | 25.50 | 26.30 | 26.62 | 26.15 | ||||
SLA-2 | non-PBR | 22.46 | 21.64 | 24.14 | 29.29 | 27.28 | 30.17 | 28.00 | 27.44 | 30.13 | 5.66 | ||
PBR | 25.87 | 24.61 | 26.83 | 26.90 | 26.12 | 25.29 | 26.56 | 26.12 | 26.07 | 15.34 | |||
SLA-3 | non-PBR | 21.57 | 21.12 | 23.60 | 29.17 | 27.78 | 29.82 | 27.82 | 27.92 | 29.81 | 4.59 | 6.38 | |
PBR | 25.29 | 24.31 | 26.43 | 26.74 | 25.70 | 24.92 | 26.05 | 25.55 | 25.24 | 17.68 | 17.18 |
Shannon Diversity Index (H) | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Region | BoLA | HLA | Patr | SLA | |||||||||
1 * | 2 * | 3 * | A * | B * | C * | A * | B *,** | C | 1 * | 2 * | 3 * | ||
PBR a | Entire region | 0.30 | 0.35 | 0.33 | 0.21 | 0.25 | 0.15 | 0.15 | 0.28 | 0.14 | 0.36 | 0.37 | 0.30 |
α1 domain | 0.31 | 0.4 | 0.34 | 0.21 | 0.3 | 0.13 | 0.15 | 0.37 | 0.12 | 0.44 | 0.44 | 0.31 | |
α2 domain | 0.33 | 0.34 | 0.35 | 0.23 | 0.22 | 0.18 | 0.16 | 0.21 | 0.16 | 0.33 | 0.34 | 0.3 | |
Non-PBR b | 0.06 | 0.10 | 0.13 | 0.10 | 0.08 | 0.08 | 0.03 | 0.05 | 0.10 | 0.07 | 0.05 | 0.08 |
Species | Locus | No. of Variable Sites (%) a | No. of Synonymous Sites (%) b (A) | No. of Nonsynonymous Sites (%) b (B) | (A)/(B) Ratio | Ka/Ks Ratio | |
---|---|---|---|---|---|---|---|
α1 Domain | α2 Domain | ||||||
Human | HLA-A | 71 (13.00) | 12 (2.20) | 43 (7.88) | 0.28 | 1.74 | 1.57 |
HLA-B | 83 (15.20) | 17 (3.11) | 45 (8.24) | 0.38 | 1.40 | 1.20 | |
HLA-C | 58 (10.62) | 13 (2.38) | 31 (5.68) | 0.42 | 0.75 | 1.18 | |
Mean | 70.67 (12.94) | 14.00 (2.56) | 39.67 (7.26) | 0.36 | 1.30 | 1.32 | |
Chimpanzee | Patr-A | 54 (9.89) | 16 (2.93) | 27 (4.95) | 0.59 | 0.89 | 1.12 |
Patr-B | 100 (18.32) | 22 (4.03) | 58 (10.62) | 0.38 | 1.08 | 1.21 | |
Patr-C | 52 (9.52) | 10 (1.83) | 30 (5.49) | 0.33 | 0.70 | 1.71 | |
Mean | 68.67 (12.58) | 16.00 (2.93) | 38.33 (7.02) | 0.44 | 0.89 | 1.35 | |
Cattle | BoLA-1 | 128 (23.44) | 30 (5.49) | 59 (10.81) | 0.51 | 0.63 | 1.63 |
BoLA-2 | 124 (22.71) | 23 (4.21) | 55 (10.07) | 0.42 | 1.05 | 1.65 | |
BoLA-3 | 119 (21.79) | 26 (4.76) | 60 (10.99) | 0.43 | 1.80 | 1.18 | |
Mean | 123.67 (22.65) | 26.33 (4.82) | 58.00 (10.62) | 0.45 | 1.16 | 1.49 | |
Pig | SLA-1 | 125 (22.89) | 17 (3.11) | 56 (10.26) | 0.30 | 1.54 | 1.66 |
SLA-2 | 135 (24.73%) | 29 (5.31%) | 59 (10.81%) | 0.49 | 1.16 | 1.86 | |
SLA-3 | 105 (19.23%) | 15 (2.75%) | 71 (13.00%) | 0.21 | 2.27 | 1.49 | |
Mean | 121.67 (22.28%) | 20.33 (3.72%) | 62.00 (11.3%) | 0.34 | 1.66 | 1.67 | |
Sheep | Ovar-N c | 142 (26.01) | 26 (4.76) | 61 (11.17) | 0.43 | 1.41 | 1.93 |
Shannon Diversity Index (H) | ||||||
---|---|---|---|---|---|---|
Locus | Peptide-Binding Pockets a | |||||
A | B | C | D | E * | F | |
SLA-1 | 0.65 | 1.12 | 1.48 | 1.01 | 1.59 | 0.74 |
SLA-2 | 0.58 | 1.18 | 1.55 | 1.16 | 1.75 | 0.88 |
SLA-3 | 0.38 | 0.63 | 0.96 | 0.68 | 1.3 | 0.66 |
Mean | 0.54 | 0.98 | 1.33 | 0.95 | 1.55 | 0.76 |
BoLA-1 | 0.39 | 0.72 | 1.15 | 1.55 | 1.75 | 0.7 |
BoLA-2 | 0.72 | 1.34 | 1.2 | 1.65 | 1.89 | 0.66 |
BoLA-3 | 0.69 | 0.98 | 1.23 | 1.28 | 1.7 | 0.85 |
Mean | 0.6 | 1.01 | 1.19 | 1.49 | 1.78 | 0.74 |
Patr-A | 0.37 | 0.66 | 0.91 | 0.9 | 1.12 | 0.28 |
Patr-B | 0.41 | 1.05 | 0.92 | 0.84 | 1.49 | 0.8 |
Patr-C | 0.44 | 0.42 | 0.55 | 0.86 | 1.36 | 0.48 |
Mean | 0.41 | 0.71 | 0.79 | 0.87 | 1.32 | 0.46 |
HLA-A | 0.47 | 0.58 | 0.78 | 0.78 | 1.38 | 0.47 |
HLA-B | 0.45 | 1.07 | 0.97 | 0.64 | 1.08 | 0.88 |
HLA-C | 0.2 | 0.47 | 0.64 | 0.81 | 1.01 | 0.57 |
Mean | 0.37 | 0.71 | 0.8 | 0.74 | 1.15 | 0.64 |
Ovar-N | 0.89 | 1.13 | 1.19 | 1.24 | 1.81 | 0.88 |
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Youk, S.; Kang, M.; Ahn, B.; Koo, Y.; Park, C. Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human. Genes 2024, 15, 7. https://doi.org/10.3390/genes15010007
Youk S, Kang M, Ahn B, Koo Y, Park C. Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human. Genes. 2024; 15(1):7. https://doi.org/10.3390/genes15010007
Chicago/Turabian StyleYouk, Seungyeon, Mingue Kang, Byeongyong Ahn, Yangmo Koo, and Chankyu Park. 2024. "Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human" Genes 15, no. 1: 7. https://doi.org/10.3390/genes15010007
APA StyleYouk, S., Kang, M., Ahn, B., Koo, Y., & Park, C. (2024). Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human. Genes, 15(1), 7. https://doi.org/10.3390/genes15010007