Dating Whole Genome Duplication in Ceratopteris thalictroides and Potential Adaptive Values of Retained Gene Duplicates
Abstract
:1. Introduction
2. Results
2.1. Chromosome Counting
2.2. Benchmarking Universal Single Copy Orthologs (BUSCO) Analysis
2.3. Identification of Pairs of Paralogous and WGD Events Estimated on the Basis of Ks Age Distributions
2.4. Functional Classifications of Retained Duplicates after WGD Events Revealed That Retained Genes Are Biased Rather Than Random
2.5. Dating the WGD Event in C. thalictroides Using Ks Distribution Peaks and Absolute Dating
2.6. Phylogenomic Analysis of MADS-box Family Genes
3. Discussion
3.1. Inferring WGD from Ks Age Distribution
3.2. Absolute Dating of the WGD Event in C. thalictroides
3.3. WGDs Contribute to Evolutionary Success and Potential Adaptation of Ceratopteris
4. Materials and Methods
4.1. Chromosome Counting
4.2. Data Collection
4.3. BUSCO Analysis
4.4. Evaluation of WGD candidates on the Basis of Ks Age Distribution
4.5. Absolute Dating
4.6. Functional Enrichment
4.7. Identification of the MADS-box Gene Family in C. thalictroides
4.8. Phylogenetic Analysis
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
WGD | Whole-genome duplication |
KT | Cretaceous–Tertiary |
PETM | Paleocene-Eocene Thermal Maximum |
Ks | synonymous substitutions per synonymous site |
BUSCO | Benchmarking Universal Single Copy Orthologs |
EST | expressed sequence tag |
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Species | Total Reads (Clean) | Number of Contigs | Total Number of Unigenes | N50 (bp) | Mean Length (bp) |
---|---|---|---|---|---|
Triploid a | 35,528,634 | 69,929 | 60,823 | 787 | 576.00 |
Diploid b | 31,741,082 | 74,728 | 83,202 | 1610 | 912.26 |
Goniophlebium niponicumb | 38,786,214 | 54,152 | 58,494 | 1663 | 951.92 |
Woodwardia proliferab | 40,967,322 | 69,931 | 74,564 | 1557 | 859.72 |
Dennstaedtia pilosellab | 45,618,446 | 84,813 | 89,185 | 1582 | 831.56 |
Cheilanthes chusanab | 51,851,066 | 49,449 | 52,782 | 1727 | 1012.63 |
Acrostichum aureumb | 43,422,574 | 46,189 | 50,594 | 1729 | 1043.2 |
Osmolindsaea odoratab | 46,808,646 | 113,778 | 130,549 | 1521 | 845.96 |
Alsophila podophyllab | 48,768,608 | 66,254 | 72,404 | 1580 | 904.62 |
Species | BUSCO Notation Assessment Results |
---|---|
Diploid | C: 63.7% [S:39.7%, D:24%], F:5.9%, M: 30.4%, n: 1440 |
Triploid | C: 34.3% [S:30.5%, D:3.8%], F:12.2%, M: 53.5%, n: 1440 |
No. of Duplicates | No. of Components | Bayesian Information Criterion | Mixture Means (Ks) | Variance (Ks) | Proportion |
---|---|---|---|---|---|
Diploid | |||||
8364 | 7 | 5998.011 | 0.128 | 0.0004 | 0.091 |
8364 | 7 | 5998.011 | 0.238 | 0.0048 | 0.074 |
8364 | 7 | 5998.011 | 0.499 | 0.0248 | 0.079 |
8364 | 7 | 5998.011 | 1.148 | 0.0461 | 0.278 |
8364 | 7 | 5998.011 | 1.526 | 0.1619 | 0.265 |
8364 | 7 | 5998.011 | 2.989 | 0.6015 | 0.176 |
8364 | 7 | 5998.011 | 4.561 | 0.0790 | 0.036 |
Triploid | |||||
3088 | 5 | 3380.834 | 0.154 | 0.0016 | 0.075 |
3088 | 5 | 3380.834 | 0.338 | 0.0135 | 0.066 |
3088 | 5 | 3380.834 | 1.199 | 0.1591 | 0.464 |
3088 | 5 | 3380.834 | 2.268 | 0.5133 | 0.282 |
3088 | 5 | 3380.834 | 4.019 | 0.2962 | 0.112 |
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Zhang, R.; Wang, F.-G.; Zhang, J.; Shang, H.; Liu, L.; Wang, H.; Zhao, G.-H.; Shen, H.; Yan, Y.-H. Dating Whole Genome Duplication in Ceratopteris thalictroides and Potential Adaptive Values of Retained Gene Duplicates. Int. J. Mol. Sci. 2019, 20, 1926. https://doi.org/10.3390/ijms20081926
Zhang R, Wang F-G, Zhang J, Shang H, Liu L, Wang H, Zhao G-H, Shen H, Yan Y-H. Dating Whole Genome Duplication in Ceratopteris thalictroides and Potential Adaptive Values of Retained Gene Duplicates. International Journal of Molecular Sciences. 2019; 20(8):1926. https://doi.org/10.3390/ijms20081926
Chicago/Turabian StyleZhang, Rui, Fa-Guo Wang, Jiao Zhang, Hui Shang, Li Liu, Hao Wang, Guo-Hua Zhao, Hui Shen, and Yue-Hong Yan. 2019. "Dating Whole Genome Duplication in Ceratopteris thalictroides and Potential Adaptive Values of Retained Gene Duplicates" International Journal of Molecular Sciences 20, no. 8: 1926. https://doi.org/10.3390/ijms20081926
APA StyleZhang, R., Wang, F. -G., Zhang, J., Shang, H., Liu, L., Wang, H., Zhao, G. -H., Shen, H., & Yan, Y. -H. (2019). Dating Whole Genome Duplication in Ceratopteris thalictroides and Potential Adaptive Values of Retained Gene Duplicates. International Journal of Molecular Sciences, 20(8), 1926. https://doi.org/10.3390/ijms20081926