| 孙雅楠,陈泉,栗辉,石美琳.柑橘轮斑病菌线粒体基因组密码子使用偏好性分析[J].中国南方果树,2026,55(1): |
| 柑橘轮斑病菌线粒体基因组密码子使用偏好性分析 |
| Analysis of codon usage bias in the mitochondrial genome of Pseudofabraea citricarpar |
| 投稿时间：2024-11-08 修订日期：2025-03-30 |
| DOI：10.13938/j.issn.1007-1431.20240547 |
| 中文关键词: 柑橘轮斑病菌 密码子偏好性 线粒体基因组 自然选择 |
| 英文关键词:Pseudofabraea citricarpar Codon bias Mitochondrial genome Natural selection |
| 基金项目:重庆市教育委员会科学技术研究项目（KJ202301289858551、KJ2024012118654128）；重庆市现代山地特色高效农业产业技术体系创新团队专项（CQMAITS20240507） |
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| 中文摘要: |
| 【目的】了解柑橘轮斑病菌的线粒体基因组密码子使用特点及其形成的原因，为理解其遗传进化和致病机制提供新的视角。【方法】利用Phylosuite V1.2.3、CodonW1.4.2、RSCU、EMBOSS等在线软件对筛选出的柑橘轮斑病菌的线粒体基因组14个CDS序列进行密码子偏好性分析，筛选最优密码子。【结果】柑橘轮斑病菌线粒体基因组密码子GC含量整体偏低，平均值为29.42%，GC含量呈现GC2（34.13%）>GC1（33.65%）>GC3（19.85%）趋势；CAI值范围在0.108~0.173之间，平均为0.142<1，表明其对密码子的使用具有一定程度的偏好性，但这种偏好性不强；GC1与GC3s、ENC存在极显著负相关关系（P<0.01），GC2与GC，GC3与GC3s、ENC，GC3s与ENC，CBI与FOP间均存在极显著正相关关系（P<0.01）。RSCU分析鉴定出UUA、AUA、AAU等26个高频密码子（RSCU值>1），且全部以碱基A/U结尾。中性绘图分析、ENC-plot绘图分析结果均表明，在柑橘轮斑病菌的线粒体基因组密码子偏好性的形成过程中受基因突变和自然选择的双重作用，但以自然选择为主。筛选出11个柑橘轮斑病菌线粒体基因组最优密码子，分别为UGA、UGU、GAU、UUU、GGA、CAU、CCU、AGU、ACU、CUU、UAU，其均以A/U结尾。【结论】柑橘轮斑病菌线粒体基因组密码子偏好以A/U结尾，但偏好程度较弱，自然选择对密码子偏好性形成起主要作用。筛选出11个最优密码子，且均已以A/U结尾。研究结果为病原真菌不同种属间线粒体基因组的研究提供了数据支持。 |
| 英文摘要: |
| 【Objective】To comprehend the mitochondrial genome codon utilization and its formation in P. citricarpar bacteria,and to offer a novel perspective for understanding its genetic evolution and pathogenic mechanism.【Methods】Phylosuite V1.2.3, CodonW1.4.2, RSCU, EMBOSS and other online software were employed to analyze the codon preference of 14 CDS sequences in the mitochondrial genome of the selected P. citricarpar bacteria and to screen the optimal codon.【Results】The overall content of the mitochondrial genome codon GC was low, with an average value of 29.42%.The GC content demonstrated a trend of GC2(34.13%)>GC1(33.65%)>GC3(19.85%),and the GC content at the third position was significantly lower than that at the first and second positions.The range of CAI was 0.108-0.173,and the average was 0.142<1,indicating that CAI exhibited a certain degree of preference for the use of codons, but this preference was not intense.There was a significant negative correlation between GC1 and GC3s and ENC (P<0.01),and a significant positive correlation between GC2 and GC,GC3 and GC3s,ENC,GC3s and ENC,CBI and FOP (P<0.01). Through RSCU analysis, 26 high-frequency codons such as UUA,AUA,and AAU were identified(RSCU value>1),and all of them ended with base A and U.Both neutral mapping analysis and ENC-plot analysis indicated that the codon preference of the mitochondrial genome was influenced by both gene mutation and natural selection,but natural selection was the dominant factor.Eleven optimal codons of the mitochondrial genome were identified,namely UGA,UGU,GAU,UUU,GGA,CAU,CCU,AGU,ACU,CUU,and UAU,and all of the 11 codons ended with A/U.【Conclusion】The codon of the mitochondrial genome of P. citricarpar favored ending with A/U,but the degree of preference was weak.Natural selection played a major role in the formation of codon preference,and 11 optimal codons were selected, all of which ended with A/U.The results provide data support for the study of the mitochondrial genome among different species of pathogenic fungi. |
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