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Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence

Yue Zhang, Xingyu Yang, Yves Van de Peer (UGent) , Jinming Chen, Kathleen Marchal (UGent) and Tao Shi
(2022) PLANT JOURNAL. 112(3). p.830-846
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Abstract
Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contribution of the two key mechanisms to the evolution of gene function is largely unclear. Here, we studied AS in two closely related lotus plants, Nelumbo lutea, N. nucifera, and the outgroup Arabidopsis thaliana, for both single-copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs, and that the origin of lineage-specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single-copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue-dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms from local, small-scale duplicated, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contribute to creating the diversity of gene function during the evolution of lotus.
Keywords
Alternative splicing, Co-expression network, Functional divergence, Gene duplication, Nelumbo

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Citation

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MLA
Zhang, Yue, et al. “Evolution of Isoform‐level Gene Expression Patterns across Tissues during Lotus Species Divergence.” PLANT JOURNAL, vol. 112, no. 3, 2022, pp. 830–46, doi:10.1111/tpj.15984.
APA
Zhang, Y., Yang, X., Van de Peer, Y., Chen, J., Marchal, K., & Shi, T. (2022). Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence. PLANT JOURNAL, 112(3), 830–846. https://doi.org/10.1111/tpj.15984
Chicago author-date
Zhang, Yue, Xingyu Yang, Yves Van de Peer, Jinming Chen, Kathleen Marchal, and Tao Shi. 2022. “Evolution of Isoform‐level Gene Expression Patterns across Tissues during Lotus Species Divergence.” PLANT JOURNAL 112 (3): 830–46. https://doi.org/10.1111/tpj.15984.
Chicago author-date (all authors)
Zhang, Yue, Xingyu Yang, Yves Van de Peer, Jinming Chen, Kathleen Marchal, and Tao Shi. 2022. “Evolution of Isoform‐level Gene Expression Patterns across Tissues during Lotus Species Divergence.” PLANT JOURNAL 112 (3): 830–846. doi:10.1111/tpj.15984.
Vancouver
1.
Zhang Y, Yang X, Van de Peer Y, Chen J, Marchal K, Shi T. Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence. PLANT JOURNAL. 2022;112(3):830–46.
IEEE
[1]
Y. Zhang, X. Yang, Y. Van de Peer, J. Chen, K. Marchal, and T. Shi, “Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence,” PLANT JOURNAL, vol. 112, no. 3, pp. 830–846, 2022.
@article{8768857,
  abstract     = {{Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contribution of the two key mechanisms to the evolution of gene function is largely unclear. Here, we studied AS in two closely related lotus plants, Nelumbo lutea, N. nucifera, and the outgroup Arabidopsis thaliana, for both single-copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs, and that the origin of lineage-specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single-copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue-dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms from local, small-scale duplicated, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contribute to creating the diversity of gene function during the evolution of lotus.}},
  author       = {{Zhang, Yue and Yang, Xingyu and Van de Peer, Yves and Chen, Jinming and Marchal, Kathleen and Shi, Tao}},
  issn         = {{0960-7412}},
  journal      = {{PLANT JOURNAL}},
  keywords     = {{Alternative splicing,Co-expression network,Functional divergence,Gene duplication,Nelumbo}},
  language     = {{eng}},
  number       = {{3}},
  pages        = {{830--846}},
  title        = {{Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence}},
  url          = {{http://doi.org/10.1111/tpj.15984}},
  volume       = {{112}},
  year         = {{2022}},
}
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