Genetic markers in Andean Puya species (Bromeliaceae) with implications on plastome evolution and phylogeny

Lu Liu, Yu Qu Zhang, Liscely Tumi, Mery L. Suni, Mónica Arakaki, Kevin S. Burgess, Xue Jun Ge

Research output: Contribution to journalArticlepeer-review

Abstract

The Andean plant endemic Puya is a striking example of recent and rapid diversification from central Chile to the northern Andes, tracking mountain uplift. This study generated 12 complete plastomes representing nine Puya species and compared them to five published plastomes for their features, genomic evolution, and phylogeny. The total size of the Puya plastomes ranged from 159,542 to 159,839 bp with 37.3%–37.4% GC content. The Puya plastomes were highly conserved in organization and structure with a typical quadripartite genome structure. Each of the 17 consensus plastomes harbored 133 genes, including 87 protein-coding genes, 38 tRNA (transfer RNA) genes, and eight rRNA (ribosomal RNA) genes; we found 69–78 tandem repeats, 45–60 SSRs (simple sequence repeats), and 8–22 repeat structures among 13 species. Four protein-coding genes were identified under positive site-specific selection in Puya. The complete plastomes and hypervariable regions collectively provided pronounced species discrimination in Puya and a practical tool for future phylogenetic studies. The reconstructed phylogeny and estimated divergence time for the lineage suggest that the diversification of Puya is related to Andean orogeny and Pleistocene climatic oscillations. This study provides plastome resources for species delimitation and novel phylogenetic and biogeographic studies.

Original languageEnglish
Article numbere9159
JournalEcology and Evolution
Volume12
Issue number8
DOIs
StatePublished - Aug 2022
Externally publishedYes

Bibliographical note

Funding Information:
We are grateful to Prof. Asunción Cano for field assistance and species identification and to SERFOR—Ministry of Agriculture of Peru for issuing the Collection Permit Nos: 282‐2017, 140‐2017, 043‐2018, and 436‐2018. We also thank Yu‐Ying Zhou for assistance with the DNA experiment. This study was financially supported by the International Partnership Program of the Chinese Academy of Sciences (Grant No. 151853KYSB20190027) and the CAS President's International Fellowship Initiative (Grant No. 2022VBA0003).

Funding Information:
We are grateful to Prof. Asunción Cano for field assistance and species identification and to SERFOR—Ministry of Agriculture of Peru for issuing the Collection Permit Nos: 282-2017, 140-2017, 043-2018, and 436-2018. We also thank Yu-Ying Zhou for assistance with the DNA experiment. This study was financially supported by the International Partnership Program of the Chinese Academy of Sciences (Grant No. 151853KYSB20190027) and the CAS President's International Fellowship Initiative (Grant No. 2022VBA0003).

Publisher Copyright:
© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

Keywords

  • divergence time estimation
  • genome feature
  • hypervariable region
  • phylogenetic reconstruction
  • plastome
  • Puya

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