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

文献类型： 外文期刊

作者： Hu, Xiang 1 ; Li, Yaqi 2 ; Meng, Fuxuan 1 ; Duan, Yuanjie 1 ; Sun, Manying 1 ; Yang, Shiying 1 ; Liu, Haigang 1 ;

作者机构： 1.Yunnan Acad Agr Sci, Trop Ecoagr Res Inst, Yuanmou 651300, Yunnan, Peoples R China

2.Yunnan Acad Agr Sci, Trop & Subtrop Cash Crops Res Inst, Baoshan 678000, Yunnan, Peoples R China

关键词： Annonaceae; Chloroplast genome; Codon usage bias; Optimal codon; Natural selection

期刊名称：FUNCTIONAL & INTEGRATIVE GENOMICS （ 影响因子：2.9； 五年影响因子：3.3 ）

ISSN： 1438-793X

年卷期： 2024 年 24 卷 3 期

页码：

收录情况： SCI

摘要： 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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