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Characterization of the complete chloroplast genome and comparative analysis of the phylogeny and codon usage bias of three Yunnan wild rice species

文献类型： 外文期刊

作者： Li, Rongxin 1 ; Wang, Bo 1 ; Xiao, Suqin 1 ; Chen, Ling 1 ; Yin, Fuyou 1 ; Li, Jinlu 1 ; Jiang, Cong 1 ; Zhang, Dunyu 1 ; Zhong, Qiaofang 1 ; Zhang, Yun 1 ; Xing, Jiaxin 1 ; Cheng, Zaiquan 1 ; Liu, Li 1 ;

作者机构： 1.Yunnan Acad Agr Sci, Biotechnol & Germplasm Resources Inst, Kunming, Peoples R China

2.Yunnan Univ, Sch Agr, Kunming, Peoples R China

3.Yunnan Acad Agr Sci, Yunnan Prov Key Lab Agr Biotechnol, Kunming, Peoples R China

关键词： Yunnan wild rice species; chloroplast genome; phylogeny; codon usage bias; mutation pressure; natural selection

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：4.8； 五年影响因子：5.7 ）

ISSN： 1664-462X

年卷期： 2025 年 16 卷

页码：

收录情况： SCI

摘要： Background Wild rice species with a rich genetic diversity, wide adaptability, and high photosynthetic rates provide a valuable genetic reservoir for rice breeding.Methods In this study, the chloroplast (cp) genomes of three Yunnan wild rice species, namely Oryza rufipogon, Oryza officinalis, and Oryza granulata, were sequenced using second-generation sequencing technology, followed by assembly and annotation. Phylogeny and codon usage bias were analyzed using MEGA and RStudio.Results The total lengths of the cp genomes of the three species ranged from 134,556 to 135,937 bp, with a GC content of 39.0%. The large single-copy region of Oryza granulata was 2000 bp longer than that of the other two species. In total, 133 genes were identified in the cp genome, including domestication genes psbZ, ycf68, and lhba. Phylogenetic analysis showed that Oryza rufipogon is distinct from the Indian Oryza nivara, Oryza officinalis evolved from Oryza australiensis, and Oryza granulata shared a closer relationship with Oryza brachyantha. The average effective number of codons of the three species was above 45, indicating weak codon usage bias.Conclusion Analysis of the ENC, PR2, and neutrality plots revealed that natural selection played a significant role in the chloroplast codon usage bias of the three species, mainly regulating genes involved in self-replication and photosynthesis. Fourteen optimal codons were identified, with 13 ending in A/U and one ending in C. These results are crucial for mining favorable genes related to photosynthesis and investigating the evolution of wild rice species. Overall, this study provides valuable information on the genomic composition and genetics of three Yunnan wild rice species.

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