Analysis of codon usage bias in the mitochondrial protein-coding genes of Oryza rufipogon
-
摘要: 以普通野生稻（Oryza rufipogon Griff.）线粒体基因组为对象，分析其蛋白质编码基因的密码子使用特征及与亚洲栽培稻（O.sativa L.）的差异，探讨其密码子偏性形成的影响因素和进化过程。结果显示：普通野生稻线粒体基因组编码序列第1、第2和第3位碱基的GC含量依次为49.18%、42.67%和40.86%；有效密码子数（Nc）分布于45.32~61.00之间，其密码子偏性较弱；Nc值仅与GC3呈显著相关，密码子第3位的碱基组成对密码子偏性影响较大；第1向量轴上显示9.91%的差异，其与GC3s、Nc、密码子偏好指数（CBI）和最优密码子使用频率（Fop）的相关性均达到显著水平；而GC3和GC12的相关性未达到显著水平。因此，普通野生稻线粒体基因组密码子的使用偏性主要受自然选择压力影响而形成。本研究确定了21个普通野生稻线粒体基因组的最优密码子，大多以A或T结尾，与叶绿体密码子具有趋同进化，但是与核基因组具有不同的偏好性。同义密码子相对使用度（RSCU）、PR2偏倚分析和中性绘图分析显示，普通野生稻线粒体基因功能和其密码子使用密切相关，且线粒体密码子使用在普通野生稻、粳稻（O.sativa L.subsp.japonica Kato）和籼稻（O.sativa L.subsp.indica Kato）内具有同质性。Abstract: The mitochondrial genome of Oryza rufipogon Griff. was used to analyze the codon usage characteristics of protein-coding genes and the differences with Asian cultivated rice (O.sativa L.), and to explore the influencing factors of codon usage bias and codon evolution. Results showed that the effective number of codons (Nc) ranged from 45.32 to 61.00, indicating that codon bias was weak. GC content at the three codon positions was 49.18%, 42.67%, and 40.86%. The Nc value was significantly correlated with GC3 but not with GC1 or GC2, suggesting that base composition at the third codon position had a greater effect on codon bias. In the corresponding analysis, the first axis showed 9.91% variation and was significantly correlated with GC3s, Nc, CBI, and Fop. Furthermore, GC12 showed non-significant correlation with GC3. Codon bias in the mitogenome of O. rufipogon was mainly affected by natural selection. In addition, we identified 21 optimal codons, with most of the preferred synonymous codons ending in A or T. The mitochondrial codons showed convergent evolution with Oryza chloroplast codons, but different preferences with the nuclear genome. Based on neutrality plot analysis, PR2-plot analysis, and RSCU analysis, we found no significant differences among the three Oryza species. Our results also confirmed homogeneity in mitochondrial codon usage among the three Oryza species.
-
Keywords:
- Oryza rufipogon Griff. /
- Mitogenome /
- Codon usage bias /
- Optimal codon
-
-
[1] Hanson G, Coller J. Codon optimality, bias and usage in translation and mRNA decay[J]. Nat Rev Mol Cell Biol, 2018, 19(1):20-30.
[2] Qiu S, Zeng K, Slotte T, Wright S, Charlesworth D. Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species[J]. Genome Biol Evol, 2011, 3:868-880.
[3] Supek F. The code of silence:widespread associations between synonymous codon biases and gene function[J]. J Mol Evol, 2016, 82(1):65-73.
[4] Duret L. Evolution of synonymous codon usage in meta-zoans[J]. Curr Opin Genet Dev, 2002, 12(6):640-649.
[5] Sharp MP, Li W. Codon usage in regulatory genes in Escherichia coli does not reflect selection for rare codons[J]. Nucleic Acids Res, 1986, 14(19):7737-7749.
[6] Bulmer M. The selection-mutation-drift theory of synonymous codon usage[J]. Genetics, 1991, 129(3):897-907.
[7] Li WH, Gojobori T, Nei M. Pseudogenes as a paradigm of neutral evolution[J]. Nature, 1981, 292(5820):237-239.
[8] Song H, Gao H, Liu J, Tian P, Nan Z. Comprehensive analysis of correlations among codon usage bias, gene expression, and substitution rate in Arachis duranensis and Arachis ipaënsis orthologs[J]. Sci Rep, 2017, 7(1):14853.
[9] Clément Y, Sarah G, Holtz Y, Homa F, Pointet S, et al. Evolutionary forces affecting synonymous variations in plant genomes[J]. PLoS genetics, 2017, 13(5):e1006799.
[10] Olejniczak M, Uhlenbeck OC. tRNA residues that have coevolved with their anticodon to ensure uniform and accurate codon recognition[J]. Biochimie, 2006, 88(8):943-950.
[11] Gu W, Zhou T, Ma J, Sun X. The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens[J]. Biosystems, 2004, 73(2):89-97.
[12] Fickett JW. Recognition of protein coding regions in DNA sequences[J]. Nucleic Acids Res, 1982, 10:5303-5318.
[13] Gualberto JM, Newton KJ. Plant mitochondrial genomes:dynamics and mechanisms of mutation[J]. Annu Rev Plant Biol, 2017, 68:225-252.
[14] Liberatore KL, Dukowic-Schulze S, Miller ME, Chen C, Kianian SF. The role of mitochondria in plant development and stress tolerance[J]. Free Radic Biol Med, 2016, 100:238-256.
[15] Curole JP, Kocher TD. Mitogenomics:digging deeper with complete mitochondrial genomes[J]. Trends Ecol Evol, 1999, 14(10):394-398.
[16] Liang X, Tian X, Liu W, Wei T, Wang W, et al. Comparative analysis of the mitochondrial genomes of Colletotrichum gloeosporioides sensu lato:insights into the evolution of a fungal species complex interacting with diverse plants[J]. BMC Genomics, 2017, 18(1):171.
[17] Fujii S, Kazama T, Yamada M, Toriyama K. Discovery of global genomic reorganization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes[J]. BMC Geno-mics, 2010, 11:209.
[18] 陈乐天, 刘耀光. 水稻野败型细胞质雄性不育的发现利用与分子机理[J]. 科学通报, 2016, 61(35):3804-3812. Chen LT, Liu YG. Discovery, utilization and molecular mechanisms of CMS-WA in rice[J]. Chinese Science Bulletin, 2016, 61(35):3804-3812.
[19] 刘庆坡, 谭军, 薛庆中. 籼稻品种93-11同义密码子的使用偏性[J]. 遗传学报, 2003, 30(4):335-340. Liu QB, Tan J, Xue QZ. Synonymous codon usage bias in the rice cultivar 93-11(Oryza sativa L. ssp. indica)[J]. Acta Genetica Sinica, 2003, 30(4):335-340.
[20] 刘庆坡, 薛庆中. 粳稻叶绿体基因组的密码子用法[J]. 作物学报, 2004, 30(12):1220-1224. Liu QP, Xue QZ. Codon usage in the chloroplast genome of rice (Oryza sativa L. ssp. japonica)[J]. Acta agronomica sinica, 2004, 30(12):1220-1224.
[21] Tian X, Zheng J, Hu S, Yu J. The rice mitochondrial genomes and their variations[J]. Plant Physiol, 2006, 140(2):401-410.
[22] Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, et al. The complete sequence of the rice (Oryza sativa L.) mitochondrial genome:frequent DNA sequence acquisition and loss during the evolution of flowering plants[J]. Mol Genet Genomics, 2002, 268(4):434-445.
[23] Puigbo P, Bravo IG, Garcia-Vallve S. CAIcal:a combined set of tools to assess codon usage adaptation[J]. Biol Direct, 2008, 3:38.
[24] Sueoka N. Two aspects of DNA base composition:G + C content and translation-coupled deviation from intra-strand rule of A=T and G=C[J]. J Mol Evol, 1999, 49(1):49-62.
[25] Sueoka N. Directional mutation pressure and neutral molecular evolution[J]. Proc Natl Acad Sci USA, 1988, 85(8):2653-2657.
[26] Maria D, Ermolaeva. Synonymous codon usage in bac-teria[J]. Curr Issues Mol Biol, 2001, 3(4):91-97.
[27] Wang L, Xing H, Yuan Y, Wang X, Saeed M, et al. Genome-wide analysis of codon usage bias in four sequenced cotton species[J]. PLoS One, 2018, 13(3):e0194372.
[28] Mazumdar P, Binti Othman R, Mebus K, Ramakrishnan N, Ann Harikrishna J. Codon usage and codon pair patterns in non-grass monocot genomes[J]. Ann Bot, 2017, 120(6):893-909.
[29] Nair RR, Nandhini MB, Sethuraman T, Doss G. Mutational pressure dictates synonymous codon usage in freshwater unicellular α-cyanobacterial descendant Paulinella chromatophora and β-cyanobacterium Synechococcus elongatus PCC6301[J]. Springer Plus, 2013, 2:492.
[30] Kannaujiya VK, Rastogi RP, Sinha RP. GC constituents and relative codon expressed amino acid composition in cyanobacterial hycobiliproteins[J]. Gene, 2014, 546(2):162-171.
[31] Zhou M, Li X. Analysis of synonymous codon usage patterns in different plant mitochondrial genomes[J]. Mol Biol Rep, 2009, 36(8):2039-2046.
[32] Zhang WJ, Zhou J, Li ZF, Wang L, Gu X, Zhong Y. Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L.[J]. J Integr Plant Biol, 2007, 49(2):246-254.
-
期刊类型引用(9)
1. 尹明华，李文婷，欧阳茜，王美暄，徐子林，张钦荣，张牧彤，黄添慧，何凡凡，乐芸，张嘉欣，柴桑雪. 苏丹草叶绿体基因组特征及系统发育分析. 草业科学. 2025(01): 101-118 . 
百度学术
2. 邱春桃，梁芳梅，吕颖，王鹏良，朱鹏，张虹，许尤厚. 细基江蓠线粒体基因组密码子偏好性分析. 分子植物育种. 2024(08): 2555-2563 . 百度学术
3. 包国媛，李文辛，杨鑫光，王雅琼. 海甜菜线粒体和叶绿体基因组密码子使用偏好性分析. 江苏农业学报. 2023(09): 1804-1817 . 百度学术
4. 张扬，孙曙光，李晴，魏珍. 莴苣线粒体基因组密码子使用偏好性分析. 河南农业科学. 2022(10): 114-124 . 百度学术
5. 李凤，辛静，辛雅萱，肖遥，屈亚亚，王军辉，麻文俊，辛培尧. 楸树叶绿体基因组密码子偏性分析. 南方农业学报. 2021(10): 2735-2743 . 百度学术
6. 黄蔚虹，陈永杰，孙彦阔，孙卫东. H9N2禽流感病毒全基因组密码子使用偏好性及影响因素分析. 华南农业大学学报. 2020(03): 15-22 . 百度学术
7. 李翔，范作义，王井源，王淇，李喜鹏，王德秋，孔令远，曹森林，孟庆刚，赵曦阳. 红松查尔酮合成酶基因CHS密码子偏好性分析. 植物研究. 2020(03): 447-457 . 百度学术
8. 唐向民，杨守臻，陈怀珠，孙祖东，赖振光，曾维英，韦清源. 栽培大豆和野生大豆线粒体基因组密码子使用偏性的比较分析. 广西植物. 2020(07): 926-934 . 百度学术
9. 谭景发，贺文闯，董西龙，党腾飞，谢怿，席锟，孙勇胜，胡亚林，靳德明. 不同水稻种质中渗透胁迫抗性基因DREB2A的遗传多样性分析. 中国农学通报. 2020(35): 1-13 . 百度学术
其他类型引用(5)
计量
- 文章访问数: 887
- HTML全文浏览量: 3
- PDF下载量: 674
- 被引次数: 14
下载:
