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Structural variation and evolution of chloroplast tRNAs in green algae

As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary charact...

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Autores principales: Qi, Fangbing, Zhao, Yajing, Zhao, Ningbo, Wang, Kai, Li, Zhonghu, Wang, Yingjuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8176911/
https://www.ncbi.nlm.nih.gov/pubmed/34131524
http://dx.doi.org/10.7717/peerj.11524
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author Qi, Fangbing
Zhao, Yajing
Zhao, Ningbo
Wang, Kai
Li, Zhonghu
Wang, Yingjuan
author_facet Qi, Fangbing
Zhao, Yajing
Zhao, Ningbo
Wang, Kai
Li, Zhonghu
Wang, Yingjuan
author_sort Qi, Fangbing
collection PubMed
description As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28–32, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23–27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anti-codon loop of the tRNA, but the analysis scored poorly and it is presumed that these introns are not functional. After multiple sequence alignment, the Ψ-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the replication loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. Based on the constructed phylogenetic tree, mutations were found to accompany the evolution of the Green algae chloroplast tRNA. Moreover, chloroplast tRNAs of Chlorophyceae are consistent with those of monocotyledons and gymnosperms in terms of evolutionary patterns, sharing a common multi-phylogenetic pattern and rooted in a rich common ancestor. Sequence alignment and systematic analysis of tRNA in chloroplast genome of Chlorophyceae, clarified the characteristics and rules of tRNA changes, which will promote the evolutionary relationship of tRNA and the origin and evolution of chloroplast.
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spelling pubmed-81769112021-06-14 Structural variation and evolution of chloroplast tRNAs in green algae Qi, Fangbing Zhao, Yajing Zhao, Ningbo Wang, Kai Li, Zhonghu Wang, Yingjuan PeerJ Bioinformatics As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28–32, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23–27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anti-codon loop of the tRNA, but the analysis scored poorly and it is presumed that these introns are not functional. After multiple sequence alignment, the Ψ-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the replication loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. Based on the constructed phylogenetic tree, mutations were found to accompany the evolution of the Green algae chloroplast tRNA. Moreover, chloroplast tRNAs of Chlorophyceae are consistent with those of monocotyledons and gymnosperms in terms of evolutionary patterns, sharing a common multi-phylogenetic pattern and rooted in a rich common ancestor. Sequence alignment and systematic analysis of tRNA in chloroplast genome of Chlorophyceae, clarified the characteristics and rules of tRNA changes, which will promote the evolutionary relationship of tRNA and the origin and evolution of chloroplast. PeerJ Inc. 2021-06-01 /pmc/articles/PMC8176911/ /pubmed/34131524 http://dx.doi.org/10.7717/peerj.11524 Text en ©2021 Qi et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Qi, Fangbing
Zhao, Yajing
Zhao, Ningbo
Wang, Kai
Li, Zhonghu
Wang, Yingjuan
Structural variation and evolution of chloroplast tRNAs in green algae
title Structural variation and evolution of chloroplast tRNAs in green algae
title_full Structural variation and evolution of chloroplast tRNAs in green algae
title_fullStr Structural variation and evolution of chloroplast tRNAs in green algae
title_full_unstemmed Structural variation and evolution of chloroplast tRNAs in green algae
title_short Structural variation and evolution of chloroplast tRNAs in green algae
title_sort structural variation and evolution of chloroplast trnas in green algae
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8176911/
https://www.ncbi.nlm.nih.gov/pubmed/34131524
http://dx.doi.org/10.7717/peerj.11524
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