Evolution and structural variations in chloroplast tRNAs in gymnosperms
Autor: | Tong Zhou, Jiu-Xia Wang, Zhong-Hu Li, Min-Feng Fang, Jian-Ni Liu, Yu-He Zhao, Yan Li |
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Rok vydání: | 2021 |
Předmět: |
Chloroplasts
Evolution Conservation Molecular Sequence Variation QH426-470 environment and public health Genome Chloroplast tRNA Phylogenetic relationship Gymnosperm RNA Transfer Molecular evolution Genetics Transversion Ecosystem Phylogeny biology Phylogenetic tree food and beverages biology.organism_classification Chloroplast Cycadopsida Evolutionary biology Transfer RNA Minimum free energy TP248.13-248.65 Research Article Biotechnology |
Zdroj: | BMC Genomics BMC Genomics, Vol 22, Iss 1, Pp 1-20 (2021) |
ISSN: | 1471-2164 |
Popis: | 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. |
Databáze: | OpenAIRE |
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