Chloroplast genome of an extremely endangered conifer Thuja sutchuenensis Franch. gene organization, comparative and phylogenetic analysis

Tao Yu, Bing Hong Huang, Yuyang Zhang, Pei Chun Liao, Jun Qing Li

Research output: Contribution to journalArticle

2 Citations (Scopus)


Thuja sutchuenensis is a critically endangered tertiary relict species of Cupressaceae from southwestern China. We sequenced the complete chloroplast (cp) genome of T. sutchuenensis, showing the genome content of 129,776 bp, 118 unique genes including 82 unique protein-coding genes, 32 tRNA genes, and 4 rRNA genes. The genome structures, gene order, and GC content are similar to other typical gymnosperm cp genomes. Thirty-eight simple sequence repeats were identified in the T. sutchuenensis cp genome. We also found an apparent inversion between trnT and psbK between genera Thuja and Thujopsis. In addition, positive selection signals were detected in seven genes with high Ka/Ks ratios. The reconstructed phylogeny based on locally collinear blocks of cp genomes among 21 gymnosperms species is similar to previous inferences. We also inferred a Late-Miocene divergence between T. sutchuenensis and T. standishii, according to the dating of ~ 11.05 Mya by cp genomes. These results will be helpful for future studies of Cupressaceae phylogeny as well as studies in population genetics, systematics, and cp genetic engineering.

Original languageEnglish
Pages (from-to)409-418
Number of pages10
JournalPhysiology and Molecular Biology of Plants
Issue number3
Publication statusPublished - 2020 Mar 1



  • Chloroplast genome
  • Non-synonymous substitution
  • Phylogenomics
  • Sequence divergence
  • Thuja sutchuenensis

ASJC Scopus subject areas

  • Physiology
  • Molecular Biology
  • Plant Science

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