Abstract
BackgroundChloroplast 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.ResultsIn 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.ConclusionsThese findings provide novel insights into the molecular evolution and biological characteristics of chloroplast tRNAs in gymnosperms.
Highlights
IntroductionGymnosperms have important ecological and economic value, and they are the dominant species in forest ecosystems in the Northern Hemisphere
Chloroplast transfer RNAs can participate in various vital processes
TRNAAla was found to be missing in eight species, tRNAThr, tRNAGlu, tRNAPhe, and tRNALeu were missing in one species, tRNAVal was missing in two species, tRNALys was missing in 14 species, and tRNAGln was missing in five species
Summary
Gymnosperms have important ecological and economic value, and they are the dominant species in forest ecosystems in the Northern Hemisphere. Gymnosperms are the dominant species that form forest ecosystems in the Northern Hemisphere, which constitute 39% of the world’s forests, and they have great ecological and economic significance [1]. TRNAs are multifunctional molecules that are involved in multiple metabolic processes in cells in addition to their translation function, e.g., aminoacyl-tRNA is a biosynthetic precursor and amino acid donor for other macromolecules [9]. The secondary structures of tRNAs are mostly conserved and clover-shaped, where they have an amino acid receiving arm, D-arm, anticodon arm, D-loop (a loop coupled to the D-arm), anticodon loop (a loop coupled to the anticodon arm), and a TΨC loop (a loop coupled to the TΨC arm) [12]. The nucleotide sequence of a tRNA is hydrogen bonded to form a clover-shaped secondary structure, which folds into an inverted L-type tertiary structure [13]
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