ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1555104
This article is part of the Research TopicEvolutionary Adaptations of Plant Genes: A Comprehensive Study of Phylogenomics, Epigenetic Changes, and Protein DynamicsView all 7 articles
Characterization of the complete chloroplast genome and comparative analysis of the phylogeny and codon usage bias of three Yunnan wild rice species
Provisionally accepted
Rongxin Li
Bo WangSuqin XiaoLing ChenFuyou YinJinlu LiCong JiangDunyu ZhangQiaofang ZhongYun Zhang
Jiaxin XingZaiquan Cheng*
Liu Li*- Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kuming, Yunnan Province, China
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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.
Keywords: Yunnan wild rice species, Chloroplast genome, phylogeny, codon usage bias, Photosynthetic system
Received: 03 Jan 2025; Accepted: 18 Jun 2025.
Copyright: © 2025 Li, Wang, Xiao, Chen, Yin, Li, Jiang, Zhang, Zhong, Zhang, Xing, Cheng and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Zaiquan Cheng, Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kuming, Yunnan Province, China
Liu Li, Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kuming, Yunnan Province, China
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