Open AccessChloroplast genome of an extremely endangered conifer Thuja sutchuenensis Franch.: gene organization, comparative and phylogenetic analysis
Author(s) -
Tao Yu,
Bing Huang,
Yuyang Zhang,
Pei Chun Liao,
Jun Qing Li
Publication year - 2020
Publication title -
physiology and molecular biology of plants/physiology and molecular biology of plants
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.754
H-Index - 35
eISSN - 0971-5894
pISSN - 0974-0430
DOI - 10.1007/s12298-019-00736-7
Subject(s) - biology , genome , cupressaceae , gymnosperm , chloroplast dna , nuclear gene , phylogenetics , phylogenetic tree , evolutionary biology , gc content , gene , genetics , botany , pollen
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.