| 灵芝属真菌线粒体基因组特征及进化 |
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| 引用本文： | 刘潮,盛妍妍,姜斌,卢旗阳,韩利红.灵芝属真菌线粒体基因组特征及进化[J].南方农业学报,2022,53(10):2876-2884. |
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| 作者姓名： | 刘潮 盛妍妍 姜斌 卢旗阳 韩利红 |
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| 作者单位： | 曲靖师范学院生物资源与食品工程学院/云南省高校特色果酒技术创新与应用工程研究中心, 云南曲靖 655011 |
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| 基金项目： | 国家自然科学基金项目（32100010，31860005）；云南省地方本科高校基础研究联合专项（202001BA070001-002） |
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| 摘 要： | 【目的】分析灵芝属（Ganoderma）真菌的线粒体基因组特征及进化，为灵芝属物种分类、分子进化和系统发育分析提供理论依据。【方法】基于灵芝属真菌15个线粒体基因组序列，利用MEGA X、MISA、mVISTA、MAFFT、DnaSP、PAML X和IQ-TREE等生物信息学软件对基因组特征、序列多态性、简单重复序列（SSR）、基因进化和系统发育进行分析。【结果】灵芝属真菌线粒体基因组全长为50603~124588 bp，GC含量为25.4%~27.3%，含有15个保守的蛋白编码基因（PCG）、2个rRNA基因和25~29个tRNA基因。SSR主要由AT构成，单核苷酸重复类型比例最高，其次为三核苷酸重复和四核苷酸重复。种间线粒体基因组序列差异较大，非编码区的变异水平高于编码区，nad6、nad3和cob基因编码序列的变异度较高，内含子长度与线粒体基因组大小呈显著正相关。15个保守的线粒体蛋白编码基因主要受纯化选择影响，其中cob、cox1和nad2基因含有正选择位点。基因编码偏好A/T含量高的密码子，27个高频密码子中，13个以A结尾，14个以T结尾。系统发育分析结果显示，灵芝属真菌主要分为2个聚类组，其中紫芝、狭长孢灵芝和G.wiiroense聚为一组；喜热灵芝、白肉灵芝和铁杉灵芝聚成一支，与树舌灵芝、梅氏灵芝、四川灵芝和亮盖灵芝构成姊妹类群，共同构成另一组。【结论】灵芝属真菌的线粒体基因组在进化过程中发生明显的遗传变异，基因组长度主要与内含子插入和删除有关，蛋白编码基因密码子使用偏性强。
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| 关 键 词： | 灵芝属 线粒体基因组 基因进化 系统发育 |
| 收稿时间： | 2022-07-12 |
Mitochondrial genome characteristics and evolution of Ganoderma fungi |
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| LIU Chao,SHENG Yan-yan,JIANG Bin,LU Qi-yang,HAN Li-hong.Mitochondrial genome characteristics and evolution of Ganoderma fungi[J].Journal of Southern Agriculture,2022,53(10):2876-2884. |
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| Authors: | LIU Chao SHENG Yan-yan JIANG Bin LU Qi-yang HAN Li-hong |
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| Affiliation: | College of Biological Resource and Food Engineering/Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, Yunnan 655011, China |
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| Abstract: | 【Objective】 To analyze mitochondrial genome characteristics and evolution of Ganoderma fungi, so as to provide theoretical references for species classification, molecular evolution and phylogenetic analysis of Ganoderma species.【Method】 Based on 15 mitochondrial genome sequences of Ganoderma fungi, mitochondrial genome characteristics, sequence polymorphism, simple repeat sequence(SSR), gene evolution and phylogeny were analyzed by bioinformatics software such as MEGA X, MISA, mVISTA, MAFFT, DnaSP, PAML X and IQ-TREE.【Result】The mitochondrial genomes of Ganoderma fungi were from 50603 bp to 124588 bp, with GC content of 25.4% to 27.3%, 15 conserved protein coding genes(PCG), 2 rRNA genes and 25-29 tRNA genes. SSR was mainly composed of AT base, and the proportion of mononucleotide repeat was the highest, followed by trinucleotide and tetranucleotide repeats. The mitogenome sequences of Ganoderma fungi varied greatly. The nucleotide diversity of non-coding region was higher than that of coding region, and the variation of coding sequence of nad6, nad3 and cob genes was higher. Intron length and mitogenome size were significantly positively correlated. The 15 conservative mitochondrial protein coding genes were mainly affected by purification selection, and cob, cox1 and nad2 genes contained positive selection sites. Gene coding preferred codons with A/T base, and of the 27 high-frequency codons, 13 ended with A and 14 ended with T. The phylogenetic analysis showed that Ganoderma fungi were mainly divided into two groups. Among them, G. sinense, G. boninense and G. wiiroense formed one group. And in the other group, G. calidophilum, G. leucocontextum and G. tsugae gathered together, forming sister groups with G. applanatum, G. meredithae, G. sichuanense and G. lucidum, and they formed a growp together【Conclusion】 Mitochondrial genomes have obvious genetic variation in evolution. The mitogenome length is mainly related to intron insertion or deletion, and a strong codon bias exists in protein coding genes. |
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