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Plastomes of Mimosoideae: structural and size variation, sequence divergence, and phylogenetic implication

Abstract

Plastomes of Fabaceae show both significant structural and size variation; however, most published plastomes are from subfamily Papilionoideae and only a few are from the other two subfamilies. In order to address the plastome structural and size variation of subfamily Mimosoideae, we integrated 11 newly sequenced plastomes from representing genera with three previously published ones. Each mimosoid plastome presented a typical quadripartite structure and contained 111 unique genes. Their inverted repeats (IRs) experienced multiple expansion/contraction; a ca. 13-kb IR expansion into small single copy (SSC) was detected in plastomes of a clade formed by tribe Ingeae and Acacia sensu stricto (s.s.), and a ca. 1.7-kb IR expansion into and a ca. 1.9-kb contraction out of large single copy (LSC) were found in Pithecellobium flexicaule and Acacia dealbata, respectively. Linear regression analysis showed decreased synonymous substitution rates of genes relocating from SSC into IR. A loss of both introns of clpP occurred in A. dealbata and Faidherbia albida, and a duplicated clpP copy was detected in A. dealbata. Furthermore, a 421-bp inversion that containing rps18 was found in A. dealbata. The size of mimosoid plastomes was found significantly affected by a IR-SC boundary shift, and also associated with repeat content. Plastome coding and noncoding regions with variable sequence divergence may supply valuable markers for molecular evolutionary and phylogenetic studies at different taxonomic levels. Plastid phylogenomics well resolved relationships among sampled mimosoid species.

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Acknowledgements

We would like to thank the Brisbane Botanic Garden and Kunming Botanic Garden for permission to sample fresh leaves, and Prof. Michelle van der Bank from University of Johannesburg for providing silica-gel-dried materials. This study was conducted in the Key Laboratory of the Southwest China Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences.

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Correspondence to De-Zhu Li or Ting-Shuang Yi.

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Funding

This study was funded by grants from the Ministry of Science and Technology of China, Basic Research Project (No. 2013FY112600), and the Talent Project of Yunnan Province (No. 2011CI042).

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

The newly sequenced plastomes have been submitted to GenBank with accession numbers KX852435–KX852445 (see Online Resource 1). The data matrix for phylogenetic reconstruction was deposited at the TreeBASE repository (http://purl.org/phylo/treebase/phylows/study/TB2:S20385).

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Communicated by Y. Tsumura

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Wang, YH., Qu, XJ., Chen, SY. et al. Plastomes of Mimosoideae: structural and size variation, sequence divergence, and phylogenetic implication. Tree Genetics & Genomes 13, 41 (2017). https://doi.org/10.1007/s11295-017-1124-1

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  • DOI: https://doi.org/10.1007/s11295-017-1124-1

Keywords

  • Plastome
  • IR expansion/contraction
  • Repeats
  • Mimosoideae
  • Sequence divergence
  • Phylogenomics