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Plastid phylogenomic insights into relationships, divergence, and evolution of Apiales

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Abstract

Main conclusion

Members of Apiales are monophyletic and radiated in the Late Cretaceous. Fruit morphologies are critical for Apiales evolution and negative selection and mutation pressure play important roles in environmental adaptation.

Abstract

Apiales include many foods, spices, medicinal, and ornamental plants, but the phylogenetic relationships, origin and divergence, and adaptive evolution remain poorly understood. Here, we reconstructed Apiales phylogeny based on 72 plastid genes from 280 species plastid genomes representing six of seven families of this order. Highly supported phylogenetic relationships were detected, which revealed that each family of Apiales is monophyletic and confirmed that Pennanticeae is a member of Apiales. Genera Centella and Dickinsia are members of Apiaceae, and the genus Hydrocotyle previously classified into Apiaceae is confirmed to belong to Araliaceae. Besides, coalescent phylogenetic analysis and gene trees cluster revealed ten genes that can be used for distinguishing species among families of Apiales. Molecular dating suggested that the Apiales originated during the mid-Cretaceous (109.51 Ma), with the families’ radiation occurring in the Late Cretaceous. Apiaceae species exhibit higher differentiation compared to other families. Ancestral trait reconstruction suggested that fruit morphological evolution may be related to shifts in plant types (herbaceous or woody), which in turn is related to the distribution areas and species numbers. Codon bias and positive selection analyses suggest that negative selection and mutation pressure may play important roles in environmental adaptation of Apiales members. Our results improve the phylogenetic framework of Apiales and provide insights into the origin, divergence, and adaptive evolution of this order and its members.

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Data availability

All data generated or analyzed during this study are included in this published article and in its online supplemental material.

Abbreviations

BEB:

Bayesian empirical bayes

CUB:

Codon usage bias

HPD:

Highest posterior density

PCG:

Protein-coding gene

PSSs:

Positively selected amino acid sites

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (Grant Nos. 32100180, 32070221, and 32170209), the China Postdoctoral Science Foundation (2020M683303), and the Fundamental Research Funds for the Central Universities (2021SCU12097, SCU2022D003).

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  1. Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People’s Republic of China

    Deng-Feng Xie, Ting Ren, Bo-Ni Song, Song-Dong Zhou & Xing-Jin He

  2. Sichuan Academy of Forestry, Chengdu, 610081, Sichuan, People’s Republic of China

    Chuan Xie

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Xie, DF., Xie, C., Ren, T. et al. Plastid phylogenomic insights into relationships, divergence, and evolution of Apiales. Planta 256, 117 (2022). https://doi.org/10.1007/s00425-022-04031-w

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