Complete plastomes of 17 species of maples (Sapindaceae: Acer): comparative analyses and phylogenomic implications

Abstract

The genus Acer, commonly known as maple, is a large plant lineage that comprises many economically and ecologically important species. However, because of low interspecific morphological variations and scarcity of molecular data, it is challenging to estimate the enigmatic phylogeny of Acer, limiting further utilization and conservation of maples. In this study, we generated complete plastomes of 17 species of maples representing 10 major sections of Acer and conducted comprehensively comparative genomic and phylogenomic analyses in Acer. The 17 plastomes are perfectly conserved in linear gene order and range narrowly in length of 155–157 kb with four constituent parts (LSC, SSC, IRa and IRb), whereas three IR types (amplum-, flabellatum- and yangbiense-like) are observed and the IR borders variation resulted in remarkable gene content divergence (132–134). In addition, there are apparently heterogeneous sequence divergences across the cp genome and 20 noncoding loci with fast evolutionary rates are further identified as potential molecular markers for subsequent studies on Acer. Furthermore, whole plastome sequences obtained the highest phylogenetic resolution and provided strong support for most backbone nodes of Acer among the seven analyzed data sets (LSC, SSC, IRs, coding, noncoding, 20-markers and whole-cp-genome), highlighting the significance of increasing informative sites in resolving intractable phylogenetic relationships of Acer. The section Negundo diverged firstly in Acer and close relationships among sects. Arguta, Ginnala, Macrantha, Oblonga, Pentaphylla, Platanoidea and Trifoliata were uncovered. Interspecific relationships within species-rich sects. Macrantha, Palmata and Platanoidea are also clearly resolved by plastid phylogenomics.

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Acknowledgements

We would like to thank Xun Gong, Jian Liu, Renchao Zhou, Xinxin Zhu, Yifei Li and Yongxiang Kang for their kind help in samples collection.

Funding

This work is supported by the National Natural Science Foundation of China (31600173), Xinglin Talent Funding of Guangzhou University of Chinese Medicine (A1-AFD018181Z3949) and the Excellent Doctor Fund of Zhongkai University of Agriculture and Engineering (KA180581235).

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W-CW and X–ZZ conceived and designed the experiments, W-CW performed the experiments, W-CW, S-YC and X-ZZ analyzed the data, S-YC and X-ZZ contributed reagents/materials/analysis tools, and W-CW and X-ZZ wrote the paper. All authors reviewed and approved the final manuscript.

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Correspondence to Xianzhi Zhang.

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Online Resource 1.

The list of 30 taxa and accession numbers of the chloroplast genome sequences used in phylogenetic analysis. (PDF 215 kb)

Online Resource 2.

The seven alignments, i.e., LSC, SSC, IRs, coding, noncoding, 20-markers and whole-cp-genome data sets used in phylogenetic analysis. (NEX 18190 kb)

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Information on Electronic Supplementary Material

Online Resource 1. The list of 30 taxa and accession numbers of the chloroplast genome sequences used in phylogenetic analysis.

Online Resource 2. The seven alignments, i.e., LSC, SSC, IRs, coding, noncoding, 20-markers and whole-cp-genome data sets used in phylogenetic analysis.

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Wang, W., Chen, S. & Zhang, X. Complete plastomes of 17 species of maples (Sapindaceae: Acer): comparative analyses and phylogenomic implications. Plant Syst Evol 306, 61 (2020). https://doi.org/10.1007/s00606-020-01690-8

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Keywords

  • Acer
  • Chloroplast genome
  • Comparative genomics
  • Divergent IR borders
  • Mutation hotspots
  • Phylogenomics