Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants

doi:10.1111/jse.12708

J Syst Evol ›› 2022, Vol. 60 ›› Issue (4): 773-788.DOI: 10.1111/jse.12708

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Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants

Jia-Yu Xue^1,2,3 , Shan-Shan Dong⁴ , Ming-Qiang Wang¹ , Tian-Qiang Song⁵ , Guang-Can Zhou^1,6, Zhen Li³ , Yves Van de Peer^2,3,7, Zhu-Qing Shao⁵ , Wei Wang⁸ , Min Chen¹ , Yan-Mei Zhang¹ , Xiao-Qin Sun¹ , Hong-Feng Chen⁹ , Yong-Xia Zhang¹⁰, Shou-Zhou Zhang⁴ , Fei Chen¹¹, Liang-Sheng Zhang¹¹, Cymon Cox¹², Yang Liu^4* , Qiang Wang^5*, and Yue-Yu Hang^1*

¹ Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
² College of Horticulture, Nanjing Agricultural University, Nanjing 210093, China
³ Department of Plant Biotechnology and Bioinformatics, VIB‐UGent Center for Plant Systems Biology, Ghent University, Ghent 9052, Belgium
⁴ Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
⁵ State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210046, China
⁶College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze 274015, Shandong, China
⁷ Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
⁸ State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
⁹ South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
¹⁰College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, Guangdong, China
¹¹ State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
¹²Centro de Ciências do Mar, Universidade do Algarve, Faro 8005‐319, Portuga

^*Authors for correspondence. Yang Liu. E‐mail: yang.liu0508@gmail.com; Qiang Wang. E‐mail: wangq@nju.edu.cn; Yue‐Yu Hang. E‐mail: hangyueyu@cnbg.net

Received:2020-03-15 Accepted:2020-11-16 Online:2020-11-20 Published:2022-07-01

Abstract

Abstract:

The early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypotheses regarding overall angiosperm phylogeny, but mitochondrial genomes have been largely ignored as a relevant source of information. Here we sequenced mitochondrial genomes from 18 angiosperms to fill taxon-sampling gaps in Austrobaileyales, magnoliids, Chloranthales, Ceratophyllales, and major lineages of eudicots and monocots. We assembled a data matrix of 38 mitochondrial genes from 107 taxa to assess how well mitochondrial genomic data address current uncertainties in angiosperm relationships. Although we recovered conflicting phylogenies based on different data sets and analytical methods, we also observed congruence regarding deep relationships of several major angiosperm lineages: Chloranthales were always inferred to be the sister group of Ceratophyllales, Austrobaileyales to mesangiosperms, and the unplaced Dilleniales was consistently resolved as the sister to superasterids. Substitutional saturation, GC compositional heterogeneity, and codon-usage bias are possible reasons for the noise/conflict that may impact phylogenetic reconstruction; and angiosperm mitochondrial genes may not be substantially affected by these factors. The third codon positions of the mitochondrial genes appear to contain more parsimony-informative sites than the first and second codon positions, and therefore produced better resolved phylogenetic relationships with generally strong support. The relationships among these major lineages remain incompletely resolved, perhaps as a result of the rapidity of early radiations. Nevertheless, data from mitochondrial genomes provide additional evidence and alternative hypotheses for exploring the early evolution and diversification of the angiosperms.

Key words: early angiosperm radiation, incongruence, mitochondrial genome, phylogenomics, systematic error

Jia-Yu Xue, Shan-Shan Dong, Ming-Qiang Wang, Tian-Qiang Song, Guang-Can Zhou, Zhen Li, Yves Van de Peer, Zhu-Qing Shao, Wei Wang, Min Chen, Yan-Mei Zhang, Xiao-Qin Sun, Hong-Feng Chen, Yong-Xia Zhang, Shou-Zhou Zhang, Fei Chen, Liang-Sheng Zhang, Cymon Cox, Yang Liu, Qiang Wang, and Yue-Yu Hang. Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants[J]. J Syst Evol, 2022, 60(4): 773-788.

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Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants

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