Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus Arachis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genome Data
2.2. Detection of Duplicated Genes
2.3. Construction of Homologous Gene Quartets
2.4. Calculation of Ks and Ka
2.5. Gene Conversion Inference
2.6. Statistical Analysis of the Correlation between Conversion and Physical Location
2.7. Gene Ontology Analysis
3. Results
3.1. Genomic Homology
3.2. Homologous Gene Quartets
3.3. Gene Conversion between LCT-Related Duplicated Genes
3.4. Gene Conversion between PRT-Related Duplicated Genes
3.5. Conversion and Evolution
3.6. Conversion and Physical Position
3.7. Chromosome Rearrangements and Conversion
3.8. Gene Function Analysis
4. Discussion
4.1. Long-Lasting Extensive Conversions Affected the Evolution of Duplicated Genes in Peanut Genomes
4.2. Conversion Contributes to the Divergence of Genus Arachis Genomes
4.3. Donor Genes Are Preferred as Donors
4.4. Conversion and Genomic Rearrangements
4.5. Conversion and Function
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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Species | Quartet Patterns | Paralogues in Quartets | WCV-I a | WCV-II b | PCV c | Total | Conversion Rate (%) |
---|---|---|---|---|---|---|---|
A. duranensis | A1-B1-A2-B2 | 1871 | - | 4 | 216 | 220 | 11.8% |
A. ipaensis | - | 2 | 241 | 242 | 13.0% | ||
A. monticola A | Ama1-Amb1-Ama2-Amb2 | 99 | - | 2 | 11 | 13 | 13.1% |
A. monticola B | - | - | 14 | 14 | 14.1% | ||
A. hypogaea A (Shitouqi) | Aha1-Ahb1-Aha2-Ahb2 | 1314 | 3 | 3 | 121 | 126 | 9.6% |
A. hypogaea B (Shitouqi) | 3 | 2 | 112 | 115 | 8.8% | ||
A. hypogaea A (Tifrunner) | Aha1-Ahb1-Aha2-Ahb2 | 953 | 2 | 2 | 129 | 132 | 6.8% |
A. hypogaea B (Tifrunner) | 3 | 3 | 134 | 139 | 7.1% |
Orthologues | Converted Genes | Nonconverted Genes | p-Value (t-Test) | |
---|---|---|---|---|
A. duranensis–A. ipaensis | Pn | 0.055 | 0.023 | 9.48 × 10−14 |
Ps | 0.109 | 0.064 | 7.05 × 10−7 | |
Pn/Ps | 0.505 | 0.359 | 3.68 × 10−9 | |
A. monticola A–A. monticola B | Pn | 0.114 | 0.0380 | 1.40 × 10−3 |
Ps | 0.220 | 0.0846 | 3.60 × 10−3 | |
Pn/Ps | 0.523 | 0.449 | 1.30 × 10−3 | |
A. hypogaea A (Shitouqi)–A. hypogaea B (Shitouqi) | Pn | 0.0620 | 0.0483 | 2.10 × 10−3 |
Ps | 0.116 | 0.0900 | 9.00 × 10−3 | |
Pn/Ps | 0.534 | 0.537 | 4.98 × 10−5 | |
A. hypogaea A (Tifrunner)–A. hypogaea B (Tifrunner) | Pn | 0.0704 | 0.0340 | 4.01 × 10−5 |
Ps | 0.133 | 0.0753 | 4.10 × 10−5 | |
Pn/Ps | 0.529 | 0.452 | 9.33 × 10−7 |
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Shen, S.; Li, Y.; Wang, J.; Wei, C.; Wang, Z.; Ge, W.; Yuan, M.; Zhang, L.; Wang, L.; Sun, S.; et al. Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus Arachis. Genes 2021, 12, 1944. https://doi.org/10.3390/genes12121944
Shen S, Li Y, Wang J, Wei C, Wang Z, Ge W, Yuan M, Zhang L, Wang L, Sun S, et al. Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus Arachis. Genes. 2021; 12(12):1944. https://doi.org/10.3390/genes12121944
Chicago/Turabian StyleShen, Shaoqi, Yuxian Li, Jianyu Wang, Chendan Wei, Zhenyi Wang, Weina Ge, Min Yuan, Lan Zhang, Li Wang, Sangrong Sun, and et al. 2021. "Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus Arachis" Genes 12, no. 12: 1944. https://doi.org/10.3390/genes12121944