Advance Search
Jin Gang, Wang Li-Ping, Long Ling-Yun, Wu Feng, Tang Yu-Juan, Qin Jian-Feng, Wei Dan-Ni, Huang Qiu-Wei, Su Wen-Pan. Analysis of codon usage bias in the mitochondrial protein-coding genes of Oryza rufipogon[J]. Plant Science Journal, 2019, 37(2): 188-197. DOI: 10.11913/PSJ.2095-0837.2019.20188
Citation: Jin Gang, Wang Li-Ping, Long Ling-Yun, Wu Feng, Tang Yu-Juan, Qin Jian-Feng, Wei Dan-Ni, Huang Qiu-Wei, Su Wen-Pan. Analysis of codon usage bias in the mitochondrial protein-coding genes of Oryza rufipogon[J]. Plant Science Journal, 2019, 37(2): 188-197. DOI: 10.11913/PSJ.2095-0837.2019.20188
shu

Analysis of codon usage bias in the mitochondrial protein-coding genes of Oryza rufipogon

  • Guangxi Subtropical Crops Research Institute, Nanning 530001, China

Funds: 

This work was supported by grants from the Natural Science Foundation of Guangxi (2016GXNSFAA380093, 2018GXNS-FBA281109).

More Information
  • Received Date: August 25, 2018
  • Revised Date: October 31, 2018
  • Available Online: October 31, 2022
  • Published Date: April 27, 2019
    Graphical Abstract
    • 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.
    • FullText(HTML)
    • References (32)
  • [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.
    • Related Articles

  • Related Articles

    [1]Li Li-Jun, Miao Ling-Feng, Li Da-Dong, Yang Fan. Effects of drought and nitrogen application on the growth and chlorophyll fluorescence characteristics of Dalbergia odorifera T. Chen - Hevea brasiliensis Muell. Arg seedlings[J]. Plant Science Journal, 2023, 41(3): 358-369. DOI: 10.11913/PSJ.2095-0837.22196
    [2]Guo Lu-Yao, Miao Ling-Feng, Li Da-Dong, Xiang Li-Shan, Yang Fan. Effects of nitrogen addition and warming on growth, development, and physiological characteristics of Dalbergia odorifera T. Chen seedlings[J]. Plant Science Journal, 2022, 40(2): 259-268. DOI: 10.11913/PSJ.2095-0837.2022.20259
    [3]Cai Yuan-Bao, Yang Xiang-Yan. Codon usage bias and its influencing factors in the chloroplast genome of Macadamia integrifolia Maiden & Betche[J]. Plant Science Journal, 2022, 40(2): 229-239. DOI: 10.11913/PSJ.2095-0837.2022.20229
    [4]Wang Yu-Chen, Wang Wen-Juan, Zhong Yue-Ming, Lei Shan-Qing, Li Jing-Wen. Study on the foraging behavior of clonal roots and its influencing factors in Populus euphratica Oliv.[J]. Plant Science Journal, 2020, 38(3): 410-417. DOI: 10.11913/PSJ.2095-0837.2020.30410
    [5]Pu Yu-Jin, Zhang Li-Jia, Miao Ling-Feng, Yang Fan. Effects of different calcium concentrations on the growth and physiological characteristics of Dalbergia odorifera under low temperatures[J]. Plant Science Journal, 2019, 37(2): 251-259. DOI: 10.11913/PSJ.2095-0837.2019.20251
    [6]Wang Yue-Lin, Xu Da-Ping, Yang Zeng-Jiang, Liu Xiao-Jin, Hong Zhou, Zhang Ning-Nan. Effects of transplantation and potassium fertilizer on the photosynthetic characteristics and chlorophyll content of Dalbergia odorifera[J]. Plant Science Journal, 2018, 36(6): 879-887. DOI: 10.11913/PSJ.2095-0837.2018.60879
    [7]ZHU Xia-Xia, ZHANG Hua, ZHU Yan, LIU Jian-Gang, ZHU Ye-Ping, LÜ Rui, WANG Ying, MA Ming-Jun. Forest Community Species Diversity and the Influencing Factors in the Rock Stream Periglacial Landforms of Mt. Laotudingzi[J]. Plant Science Journal, 2016, 34(1): 67-77. DOI: 10.11913/PSJ.2095-0837.2016.10067
    [8]YANG Qi-He, YE Wan-Hui, LIAO Fu-Lin, LIU Zhi-Wei, YIN Xiao-Juan. Experimental Factors Affecting Studying Characteristics of Seed Storage[J]. Plant Science Journal, 2006, 24(5): 469-475.
    [9]HUANG Xuan, XU Zi-Qin, HAO Jian-Guo, LI Jing. Factors Affecting Wheat(Triticum aestivum L.)Transformation Mediated by Biolistic Bombardment[J]. Plant Science Journal, 2004, 22(2): 111-115.
    [10]Zhang Youde, Zhang Junzhi, Mei Fangzhu, Zhou Daming, Hu Delin, Wang Yuanfu. THE TILLERING RULE ON EULALIOPSlS BINATA AND ITS CONTROLLING FACTORS[J]. Plant Science Journal, 1993, 11(2): 185-192.

  • Cited by

    Periodical cited type(6)

    1. Hui Wang，Jiping Zhang，Benyong Wei，Qing Qiao，Wentao Zhang，Yangcui Ning，Chunlan Liu. The effects of climate change on Pinus tabulaeformis radial growth in the Xiaowutai Mountains, northern China. Journal of Forestry Research. 2025(01): 115-125 .
    2. 常素玲. 山西省关帝山林区油松径向生长对气候的响应. 山西林业科技. 2024(01): 24-27 .
    3. 韦晓旭，彭剑峰，彭猛，李轩，崔佳月，李金宽，魏亚飞. 中国南北过渡带油松径向生长对气候因子的响应研究——以鸡公山国家级自然保护区为例. 地理科学. 2024(09): 1643-1652 .
    4. 李镇江，于晨一，刘升云，闫瑞环，黄心邓，刘晓静，陈志成，王婷. 伏牛山南坡3种针叶树径向生长对气候变化的响应. 应用生态学报. 2023(05): 1178-1186 .
    5. 李夏榕，陈怡歆，陈静飞，朱济友，孙广鹏，韦柳端，张新娜，徐程扬. 气候变化对北京近远郊地区油松径向生长影响的比较研究. 北京林业大学学报. 2022(01): 19-28 .
    6. 乔梁，陈雪，高梦竹，王子洋. 气候旅游资源-植被观赏气象指数研究. 黑龙江气象. 2022(03): 18-21 .

    Other cited types(4)

Catalog

    Get Citation
    PDF
    XML
    Article views PDF downloads Cited by(10)
    Turn off MathJax
    Article Contents
    Abstract
    References
    Related Articles
    Copyright © 2022 Plant Science Journal 鄂ICP备05004779号-3
    Address：No. 201, Jiufeng 1st Road, Donghu High tech Zone, WuhanPostal Code：430074

    Supported by: Beijing Renhe Information Technology Co., Ltd.  Baidu Analytics

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return