Chinese Journal OF Rice Science >
Assembly, Codon Usage Bias, and Phylogenetic Analysis of Chloroplast Genome of Oryza meyeriana
Received date: 2024-06-19
Revised date: 2024-07-12
Online published: 2025-11-19
【Objective】 Oryza meyeriana, which is shade-tolerant and retains many primitive traits, is the only xerophytic type of wild rice in the genus Oryza. This study aims to enrich the genetic foundation of O. meyeriana and provide reference for vector construction of its superior genes. 【Methods】 The chloroplast genome of Yunnan O. meyeriana was sequenced using second-generation sequencing technology, followed by assembly and annotation. Codon usage bias and phylogenetic relationships were analyzed with RStudio and MEGA. 【Results】 The results showed that the total length of the chloroplast genome was 135,937 bp, with a GC content of 39.0%. The average effective number of codons(ENC) value was 48.09, indicating weak codon usage bias. ENC-plot, PR2-plot, and neutral plot analyses revealed that selection pressure plays a major role in shaping the chloroplast codon usage bias in Oryza meyeriana, and that this bias mainly regulates genes involved in self-replication and the photosynthetic system. A total of 16 optimal codons were identified, among which 14 ended with A/U and 2 ended with G/C. Phylogenetic analysis based on the chloroplast genome showed that Oryza meyeriana is closely related to O. brachyantha.【Conclusion】 This study enriches our understanding of the genomic composition and genetic information of Oryza meyeriana. The findings provide a basis for mining favorable genes related to photosynthesis and for investigating the evolution of wild rice species.
Key words： Yunnan Oryza meyeriana; chloroplast genome; codon usage bias; phylogeny
LI Rongxin, WANG Bo, XIAO Suqin, YIN Fuyou, ZHANG Jianhong, ZHONG Qiaofang, CHEN Ling, LI Jinlu, YANG Hesheng, CHENG Zaiquan, LIU Li . Assembly, Codon Usage Bias, and Phylogenetic Analysis of Chloroplast Genome of Oryza meyeriana[J]. Chinese Journal OF Rice Science, 2025 , 39(6) : 801 -812 . DOI: 10.16819/j.1001-7216.2025.240612
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