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Comparative transcriptome analysis and identification of candidate adaptive evolution genes of Miscanthus lutarioriparius and Miscanthus sacchariflorus

Abstract

Miscanthus species are perennial C4 grasses that are considered promising energy crops because of their high biomass yields, excellent adaptability and low management costs. Miscanthus lutarioriparius and Miscanthus sacchariflorus are closely related subspecies that are distributed in different habitats. However, there are only a few reports on the mechanisms by which Miscanthus adapts to different environments. Here, comparative transcriptomic and morphological analyses were used to study the evolutionary adaptation of M. lutarioriparius and M. sacchariflorus to different habitats. In total, among 7586 identified orthologs, 2060 orthologs involved in phenylpropanoid biosynthesis and plant hormones were differentially expressed between the two species. Through an analysis of the Ka/Ks ratios of the orthologs, we estimated that the divergence time between the two species was approximately 4.37 Mya. In addition, 37 candidate positively selected orthologs (PSGs) that played important roles in the adaptation of these species to different habitats were identified. Then, the expression levels of 20 PSGs in response to flooding and drought stress were analyzed, and the analysis revealed significant changes in their expression levels. These results facilitate our understanding of the evolutionary adaptation to habitats and the speciation of M. lutarioriparius and M. sacchariflorus. We hypothesise that lignin synthesis genes are the main cause of the morphological differences between the two species. In summary, the plant nonspecific phospholipase C gene family and the receptor-like protein kinase gene family played important roles in the evolution of these two species.

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Availability of data and material

The sequencing raw data from 6 RNA-Seq libraries were deposited on the Sequence Read Archive from NCBI under SRA accession: SRP158951 and SRP190160. Data are available here:

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Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (No. 31571740), Anhui University of Science and Technology launched a research fund to attract talents (No:13200389).

Funding

This work was financially supported by the National Natural Science Foundation of China (No. 31571740), and the Anhui University of Science and Technology launched a research fund to attract talents (13200389).

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Jia Wang performed and analyzed the experiments, and wrote the manuscript; Jianyong Zhu and Jiajing Sheng contributed experiments materials and provided assistance to the experiments. Ying Diao and Zhongli Hu offered scientific advice, guided the experiments and revised the manuscript. All authors read and approved the final manuscript revision.

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Correspondence to Ying Diao.

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Wang, J., Sheng, J., Zhu, J. et al. Comparative transcriptome analysis and identification of candidate adaptive evolution genes of Miscanthus lutarioriparius and Miscanthus sacchariflorus. Physiol Mol Biol Plants 27, 1499–1512 (2021). https://doi.org/10.1007/s12298-021-01030-1

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Keywords

  • Transcriptome
  • Ortholog
  • Evolutionary adaptation
  • Miscanthus lutarioriparius
  • Miscanthus sacchariflorus