Background Chloroplast transfer RNAs (tRNAs) can participate in various vital processes. Gymnosperms have important ecological and economic value, and they are the dominant species in forest ecosystems in the Northern Hemisphere. However, the evolution and structural changes in chloroplast tRNAs in gymnosperms remain largely unclear. Results In this study, we determined the nucleotide evolution, phylogenetic relationships, and structural variations in 1779 chloroplast tRNAs in gymnosperms. The numbers and types of tRNA genes present in the chloroplast genomes of different gymnosperms did not differ greatly, where the average number of tRNAs was 33 and the frequencies of occurrence for various types of tRNAs were generally consistent. Nearly half of the anticodons were absent. Molecular sequence variation analysis identified the conserved secondary structures of tRNAs. About a quarter of the tRNA genes were found to contain precoded 3′ CCA tails. A few tRNAs have undergone novel structural changes that are closely related to their minimum free energy, and these structural changes affect the stability of the tRNAs. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors. The transition rate was higher than the transversion rate in gymnosperm chloroplast tRNAs. More loss events than duplication events have occurred in gymnosperm chloroplast tRNAs during their evolutionary process. Conclusions These findings provide novel insights into the molecular evolution and biological characteristics of chloroplast tRNAs in gymnosperms.

The complete chloroplast genome from Cardiocrinum cathayanum (Liliaceae), an important herbaceous perennial species of the Liliaceae, is determined in this study. We characterized its whole plastid genome sequence using the Illumina sequencing platform. The whole plastid genome of C. cathayanum was a typical quadripartite circular molecule with 152,502 bp in length, comprised of a large single copy region of 82,517 bp, a small single copy region of 17,311 bp, and two inverted repeat regions of 26,337 bp. A total of 136 genes, 84 protein-coding genes, 38 tRNA, and 8 rRNA genes were identified. The GC content in the chloroplast genome, LSC region, SSC region, and IR region were 42.5, 34.9, 30.8, and 42.5%, respectively. Phylogenetic analysis suggested that C. cathayanum is more closely related with Allium cepa, Allium prattii, Amana edulis, and Erythronium sibiricum, these species were clustered into a clade with high bootstrap support. ARTICLE HISTORY

Paeonia rockii subsp. taibaishanica (Paeoniaceae), one of the tree peony species, is endemic to the Qinling Mountains in central China. In this study, we characterized its whole plastid genome sequence using the Illumina sequencing platform. The complete plastid genome size of P. rockii subsp. taibaishanica is 153,368 bp in length, including a large single copy (LSC) region of 85,030 bp, a small single copy (SSC) region of 17,042 bp, and a pair of inverted repeats (IRs) of 25,648 bp. The genome contains 131 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC contents in chloroplast genome, LSC region, SSC region, and IR region were 38.3%, 36.6%, 32.6%, and 43.1%, respectively. A total of 16 species are used to construct the phylogenetic tree of Paeoniaceae, the results showed that P. rockii subsp . taibaishanica is more closely related with congeneric Paeonia suffruticosa and Paeonia ostii , these species were clustered into a clade with high bootstrap support.