中国水稻科学2025，Vol.39Issue(6)：801-812,12.DOI:10.16819/j.1001-7216.2025.240612
野生稻叶绿体基因组组装与密码子偏好性分析及系统发育研究
Assembly,Codon Usage Bias,and Phylogenetic Analysis of Chloroplast Genome of Oryza meyeriana
摘要
Abstract
[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.关键词
云南疣粒野生稻/叶绿体基因组/密码子偏好性/系统发育Key words
Yunnan Oryza meyeriana/chloroplast genome/codon usage bias/phylogeny引用本文复制引用
李荣欣,程在全,刘丽,王波,肖素勤,殷富有,张建红,钟巧芳,陈玲,李金璐,杨和生..野生稻叶绿体基因组组装与密码子偏好性分析及系统发育研究[J].中国水稻科学,2025,39(6):801-812,12.基金项目
国家重点研发计划资助项目(2021YFD1200102-02) （2021YFD1200102-02）
云南省农业联合专项-重点项目(202301BD070001-149) （202301BD070001-149）
云南省种子种业联合实验室项目(202205AR070001-01) （202205AR070001-01）
云南省杨庆文专家工作站项目(202305AF150161). （202305AF150161）
