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Analysis of chloroplast genome characteristics and codon usage bias in 14 species of Annonaceae

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Abstract

For the study of species evolution, chloroplast gene expression, and transformation, the chloroplast genome is an invaluable resource. Codon usage bias (CUB) analysis is a tool that is utilized to improve gene expression and investigate evolutionary connections in genetic transformation. In this study, we analysed chloroplast genome differences, codon usage patterns and the sources of variation on CUB in 14 Annonaceae species using bioinformatics tools. The study showed that there was a significant variation in both gene sizes and numbers between the 14 species, but conservation was still maintained. It’s worth noting that there were noticeable differences in the IR/SC sector boundary and the types of SSRs among the 14 species. The mono-nucleotide repeat type was the most common, with A/T repeats being more prevalent than G/C repeats. Among the different types of repeats, forward and palindromic repeats were the most abundant, followed by reverse repeats, and complement repeats were relatively rare. Codon composition analysis revealed that all 14 species had a frequency of GC lower than 50%. Additionally, it was observed that the proteins in-coding sequences of chloroplast genes tend to end with A/T at the third codon position. Among these species, 21 codons exhibited bias (RSCU > 1), and there were 8 high-frequency (HF) codons and 5 optimal codons that were identical across the species. According to the ENC-plot and Neutrality plot analysis, natural selection had less impact on the CUB of A. muricate and A. reticulata. Based on the PR2-plot, it was evident that base G had a higher frequency than C, and T had a higher frequency A. The correspondence analysis (COA) revealed that codon usage patterns different in Annonaceae.

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Acknowledgements

We would like to thank the anonymous reviewers for their valuable comments on the manuscript.

Funding

This research was funded by the project of Yuanmou Rural Revitalization Science and Technology Innovation Demonstration County, Grant number 202304BT090025, and the Revitalization of the Chuxiong industry technology leader training program.

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Author contribution X. H. and Y. L. were the designers and performers of the research, analyzed the data, and wrote the writing-original draft of the paper; F. M. was involved in the design and analysis of the results of the experiment, provided the analytical tools, and guided the writing; Y. D. collected and organized of the data, reviewed the draft manuscript, and approved the final manuscript; M. S. curated and analyzed data, produced figures and charts, and guided the writing of the manuscript; S. Y. was involved in the analysis of results, wrote and reviewed the draft manuscript, and approved the final manuscript; H. L. was the conceptualizers and leaders of the project, and guided the study design, data analysis, writing, review and editing. All authors edited the manuscript and approve its submission in the current form.

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Correspondence to Haigang Liu.

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Hu, X., Li, Y., Meng, F. et al. Analysis of chloroplast genome characteristics and codon usage bias in 14 species of Annonaceae. Funct Integr Genomics 24, 109 (2024). https://doi.org/10.1007/s10142-024-01389-w

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  • DOI: https://doi.org/10.1007/s10142-024-01389-w

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