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Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants

(2020) MOLECULAR BIOLOGY AND EVOLUTION. 37(8). p.2394-2413
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Abstract
For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K–pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein–protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein–protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.
Keywords
Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, whole-genome duplication, gene expression, methylation, gene balance, subgenome dominance, DNA METHYLATION, FUNCTIONAL DIVERGENCE, ARABIDOPSIS-THALIANA, SUBGENOME DOMINANCE, DOSAGE-SENSITIVITY, METABOLIC NETWORK, PROVIDES INSIGHTS, EVOLUTION, ANNOTATION, IMPACT

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MLA
Shi, Tao, et al. “Distinct Expression and Methylation Patterns for Genes with Different Fates Following a Single Whole-Genome Duplication in Flowering Plants.” MOLECULAR BIOLOGY AND EVOLUTION, vol. 37, no. 8, 2020, pp. 2394–413, doi:10.1093/molbev/msaa105.
APA
Shi, T., Rahmani, R. S., Gugger, P. F., Wang, M., Li, H., Zhang, Y., … Chen, J. (2020). Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants. MOLECULAR BIOLOGY AND EVOLUTION, 37(8), 2394–2413. https://doi.org/10.1093/molbev/msaa105
Chicago author-date
Shi, Tao, Razgar Seyed Rahmani, Paul F. Gugger, Muhua Wang, Hui Li, Yue Zhang, Zhizhong Li, et al. 2020. “Distinct Expression and Methylation Patterns for Genes with Different Fates Following a Single Whole-Genome Duplication in Flowering Plants.” MOLECULAR BIOLOGY AND EVOLUTION 37 (8): 2394–2413. https://doi.org/10.1093/molbev/msaa105.
Chicago author-date (all authors)
Shi, Tao, Razgar Seyed Rahmani, Paul F. Gugger, Muhua Wang, Hui Li, Yue Zhang, Zhizhong Li, Qingfeng Wang, Yves Van de Peer, Kathleen Marchal, and Jinming Chen. 2020. “Distinct Expression and Methylation Patterns for Genes with Different Fates Following a Single Whole-Genome Duplication in Flowering Plants.” MOLECULAR BIOLOGY AND EVOLUTION 37 (8): 2394–2413. doi:10.1093/molbev/msaa105.
Vancouver
1.
Shi T, Rahmani RS, Gugger PF, Wang M, Li H, Zhang Y, et al. Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants. MOLECULAR BIOLOGY AND EVOLUTION. 2020;37(8):2394–413.
IEEE
[1]
T. Shi et al., “Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants,” MOLECULAR BIOLOGY AND EVOLUTION, vol. 37, no. 8, pp. 2394–2413, 2020.
@article{8660644,
  abstract     = {For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K–pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein–protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein–protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.},
  author       = {Shi, Tao and Rahmani, Razgar Seyed and Gugger, Paul F. and Wang, Muhua and Li, Hui and Zhang, Yue and Li, Zhizhong and Wang, Qingfeng and Van de Peer, Yves and Marchal, Kathleen and Chen, Jinming},
  issn         = {0737-4038},
  journal      = {MOLECULAR BIOLOGY AND EVOLUTION},
  keywords     = {Genetics,Ecology,Evolution,Behavior and Systematics,Molecular Biology,whole-genome duplication,gene expression,methylation,gene balance,subgenome dominance,DNA METHYLATION,FUNCTIONAL DIVERGENCE,ARABIDOPSIS-THALIANA,SUBGENOME DOMINANCE,DOSAGE-SENSITIVITY,METABOLIC NETWORK,PROVIDES INSIGHTS,EVOLUTION,ANNOTATION,IMPACT},
  language     = {eng},
  number       = {8},
  pages        = {2394--2413},
  title        = {Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants},
  url          = {http://dx.doi.org/10.1093/molbev/msaa105},
  volume       = {37},
  year         = {2020},
}

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