. 2021 Oct 29;19(1):232.

doi: 10.1186/s12915-021-01166-2.

Plastid phylogenomic insights into relationships of all flowering plant families

Hong-Tao Li^#^{1

2}, Yang Luo^#³, Lu Gan^#^{1

2}, Peng-Fei Ma^#^{1

2}, Lian-Ming Gao^#^{2

3

4}, Jun-Bo Yang^#^{1

2}, Jie Cai^#¹, Matthew A Gitzendanner^{5

6}, Peter W Fritsch⁷, Ting Zhang¹, Jian-Jun Jin^{1

8}, Chun-Xia Zeng¹, Hong Wang^{2

3}, Wen-Bin Yu⁹, Rong Zhang¹, Michelle van der Bank¹⁰, Richard G Olmstead¹¹, Peter M Hollingsworth¹², Mark W Chase^{13

14}, Douglas E Soltis^{5

6}, Pamela S Soltis^{5

6

15}, Ting-Shuang Yi^{16

17}, De-Zhu Li^{18

19

20}

Affiliations

¹ Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
² Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
³ CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
⁴ Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China.
⁵ Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
⁶ Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.
⁷ Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76017, USA.
⁸ Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10025, USA.
⁹ Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
¹⁰ Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, Gauteng, 2006, South Africa.
¹¹ Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98195-5325, USA.
¹² Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, Scotland, UK.
¹³ Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, England, UK.
¹⁴ Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia.
¹⁵ Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
¹⁶ Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China. tingshuangyi@mail.kib.ac.cn.
¹⁷ Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China. tingshuangyi@mail.kib.ac.cn.
¹⁸ Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China. dzl@mail.kib.ac.cn.
¹⁹ Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China. dzl@mail.kib.ac.cn.
²⁰ CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China. dzl@mail.kib.ac.cn.

^# Contributed equally.

PMID: 34711223
PMCID: PMC8555322
DOI: 10.1186/s12915-021-01166-2

Plastid phylogenomic insights into relationships of all flowering plant families

Hong-Tao Li et al. BMC Biol. 2021.

. 2021 Oct 29;19(1):232.

doi: 10.1186/s12915-021-01166-2.

Authors

Affiliations

¹ Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
² Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
³ CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
⁴ Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China.
⁵ Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
⁶ Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.
⁷ Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76017, USA.
⁸ Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10025, USA.
⁹ Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
¹⁰ Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, Gauteng, 2006, South Africa.
¹¹ Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98195-5325, USA.
¹² Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, Scotland, UK.
¹³ Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, England, UK.
¹⁴ Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia.
¹⁵ Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
¹⁶ Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China. tingshuangyi@mail.kib.ac.cn.
¹⁷ Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China. tingshuangyi@mail.kib.ac.cn.
¹⁸ Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China. dzl@mail.kib.ac.cn.
¹⁹ Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China. dzl@mail.kib.ac.cn.
²⁰ CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China. dzl@mail.kib.ac.cn.

^# Contributed equally.

PMID: 34711223
PMCID: PMC8555322
DOI: 10.1186/s12915-021-01166-2

Abstract

Background: Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades.

Results: Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation.

Conclusions: We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.

Keywords: Interfamilial relationships; Mesangiospermae; PPA II; Plastome; Tree of life.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

**Fig. 1**
Relationships of 68 angiosperm orders in PPA II, based on maximum likelihood analysis of 80 plastid genes and 4782 samples. Bootstrap percentages less than 100 are shown. Twenty clades (labeled with roman numerals) are listed in Additional file 15: Table S2. Eight gymnosperm orders are included

**Fig. 2**
Relationships of 428 angiosperm families in PPA II, based on ML analysis of 80 plastid genes and 4782 samples. Bootstrap percentages less than 100 are shown. Five problematic families (Rafflesiaceae, Apodanthaceae, Balanophoraceae, Mitrastemonaceae, and Thismiaceae) are shown in dashed lines (see the “Results” section for details). Twenty clades (labeled with roman numerals) are listed in Additional file 15: Table S2

**Fig. 3**
Familial phylogenetic relationships in PPA II (left) versus APW (right) of Rosales (a), partial Brassicales (b), Commelinales (c), and Crossosomatales (d). All nodes in PPA II have 100 bootstrap percentages. Asterisks (*) represent the nodes with low BP in APW. The blue lines show different phylogenetic positions between PPA II and APW, and the green lines show increased support in PPA II

**Fig. 4**
Two contrasting topologies for the eight major lineages of angiosperms (Amborellales, Nymphaeales, Austrobaileyales, Ceratophyllales, Chloranthales, magnoliids, monocots, and eudicots) based on the plastid (left, light brown) [13] and nuclear (right) [–30, 34, 39] genome-scale datasets. Four recent studies with new nuclear genomes sequenced from different species of magnoliids (left, dark brown) [–38] also resolved the same topology as that of the plastid phylogeny. The asterisk indicates that this node was weakly supported

See this image and copyright information in PMC

References

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Plastid phylogenomic insights into relationships of all flowering plant families

Affiliations

Plastid phylogenomic insights into relationships of all flowering plant families

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources