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Article

Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants

by
Ting-Ting Zhang
1,
Yang Yang
1,
Xiao-Yu Song
1,
Xin-Yu Gao
1,
Xian-Liang Zhang
2,
Jun-Jie Zhao
2,
Ke-Hai Zhou
2,
Chang-Bao Zhao
2,
Wei Li
2,
Dai-Gang Yang
2,
Xiong-Feng Ma
2,3,* and
Zhong-Hu Li
1,*
1
Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
2
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
3
School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
*
Authors to whom correspondence should be addressed.
Genes 2021, 12(6), 822; https://doi.org/10.3390/genes12060822
Submission received: 29 March 2021 / Revised: 16 May 2021 / Accepted: 24 May 2021 / Published: 27 May 2021
(This article belongs to the Special Issue Gene Expression and Modification in Plant Organelles)
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Abstract

Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as “bridges” in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of Gossypium L. contained introns, and cp tRNAIle contained the anti-codon (C-A-U), which was generally the anti-codon of tRNAMet. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family.
Keywords: cotton; chloroplast tRNA; evolution; phylogenetic relationship; structural variation cotton; chloroplast tRNA; evolution; phylogenetic relationship; structural variation

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MDPI and ACS Style

Zhang, T.-T.; Yang, Y.; Song, X.-Y.; Gao, X.-Y.; Zhang, X.-L.; Zhao, J.-J.; Zhou, K.-H.; Zhao, C.-B.; Li, W.; Yang, D.-G.; et al. Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants. Genes 2021, 12, 822. https://doi.org/10.3390/genes12060822

AMA Style

Zhang T-T, Yang Y, Song X-Y, Gao X-Y, Zhang X-L, Zhao J-J, Zhou K-H, Zhao C-B, Li W, Yang D-G, et al. Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants. Genes. 2021; 12(6):822. https://doi.org/10.3390/genes12060822

Chicago/Turabian Style

Zhang, Ting-Ting, Yang Yang, Xiao-Yu Song, Xin-Yu Gao, Xian-Liang Zhang, Jun-Jie Zhao, Ke-Hai Zhou, Chang-Bao Zhao, Wei Li, Dai-Gang Yang, and et al. 2021. "Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants" Genes 12, no. 6: 822. https://doi.org/10.3390/genes12060822

APA Style

Zhang, T.-T., Yang, Y., Song, X.-Y., Gao, X.-Y., Zhang, X.-L., Zhao, J.-J., Zhou, K.-H., Zhao, C.-B., Li, W., Yang, D.-G., Ma, X.-F., & Li, Z.-H. (2021). Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants. Genes, 12(6), 822. https://doi.org/10.3390/genes12060822

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