Codon Usage Bias of Chloroplast Genome in <i>Liparis bootanensis</i>

LIU Jiangfeng

doi:10.19303/j.issn.1008-0384.2021.06.002

Volume 36 Issue 6

Jun. 2021

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LIU J F. Codon Usage Bias of Chloroplast Genome in Liparis bootanensis [J]. Fujian Journal of Agricultural Sciences，2021，36（6）：629−635 doi: 10.19303/j.issn.1008-0384.2021.06.002

Citation:

LIU J F. Codon Usage Bias of Chloroplast Genome in Liparis bootanensis [J]. Fujian Journal of Agricultural Sciences，2021，36（6）：629−635 doi: 10.19303/j.issn.1008-0384.2021.06.002

LIU J F. Codon Usage Bias of Chloroplast Genome in Liparis bootanensis [J]. Fujian Journal of Agricultural Sciences，2021，36（6）：629−635 doi: 10.19303/j.issn.1008-0384.2021.06.002

Citation:

LIU J F. Codon Usage Bias of Chloroplast Genome in Liparis bootanensis [J]. Fujian Journal of Agricultural Sciences，2021，36（6）：629−635 doi: 10.19303/j.issn.1008-0384.2021.06.002

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Codon Usage Bias of Chloroplast Genome in Liparis bootanensis

doi: 10.19303/j.issn.1008-0384.2021.06.002

LIU Jiangfeng

Management Office of Yushan Scenic Park, Fuzhou, Fujian　350001, China

Received Date: 2021-02-20
Rev Recd Date: 2021-04-22

Available Online: 2021-05-17

Publish Date: 2021-06-28

Abstract

Abstract

Objective The coden usage bias and its infulence factor in the chloroplast genome of Liparis bootanensis were analyzed in this study. Method CodonW and CUSP software were used to analyze the codon usage bias based on 47 codon DNA sequences of the chloroplast genome of L. bootanensis. Result The GC content in the 3^rd position of the codons was 27.99%, which was lower than those in the 1^st and the 2^nd. The effective number of codons ranged from 40.85 to 56.80, averaging 47.27. The ENC showed no significant correlation to GC1 and GC2 but a significant positive correlation to GC3. The correlation between GC12 and GC3 was not significant with a coefficient of 0.05. The frequency of ENC ratio of 47% genes was distributed between −0.05 and 0.05, while that of 53% genes outside -0.05 and 0.05 range. A PR2-plot analysis indicated the base usage frequencies to be A＞T and G＞C. There were 17 codons selected after screening. Conclusion The 3^rd position of codons was rich in A or T. The codon usage bias was weak, complex, and affected by mutation and selection besides other factors.
- Liparis bootanensis,
- chloroplast genome,
- codon usage bias

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References(25)

References

[1]	CHEN S C, WOOD J J, ORMEROD P. Liparis L. C. Richard. In: WU Z Y, RAVEN P H, HONG D. (Eds.) Flora of China, vol. 25[M]. Science Press, Beijing & Missouri Botanical Garden Press, St. Louis, 2009: 211–228.
[2]	乔永刚, 贺嘉欣, 王勇飞, 等. 药用植物苦参的叶绿体基因组及其特征分析 [J]. 药学学报, 2019, 54(11):2106−2112. QIAO Y G, HE J X, WANG Y F, et al. Analysis of chloroplast genome and its characteristics of medicinal plant Sophora flavescens [J]. Acta Pharmaceutica Sinica, 2019, 54(11): 2106−2112.(in Chinese)
[3]	DANIELL H, KHAN M S, ALLISON L. Milestones in chloroplast genetic engineering: an environmentally friendly era in biotechnology [J]. Trends in Plant Science, 2002, 7(2): 84−91. doi: 10.1016/S1360-1385(01)02193-8
[4]	LIANG W, GUO X, NAGLE D G, et al. Genus Liparis: A review of its traditional uses in China, phytochemistry and pharmacology [J]. Journal of Ethnopharmacology, 2019, 234: 154−171. doi: 10.1016/j.jep.2019.01.021
[5]	国家中医药管理局编委会. 中华本草[M]. 上海: 上海科学技术出版社, 1999.
[6]	方志先, 廖朝林. 湖北恩施药用植物志（下册）[M]. 武汉: 湖北科学技术出版社, 2006.
[7]	吴润. 镰翅羊耳蒜中化学成分的研究[D]. 成都: 西南交通大学, 2017. WU R. Study on chemical constituents of Liparis bootanensis[D]. Chengdu: Southwest Jiaotong University, 2017. (in Chinese).
[8]	林爱英. 福建3种野生兰科植物繁殖生物学的初步研究[D]. 福州: 福建师范大学, 2015. LIN A Y. A preliminary study on reproductive biology of three wild orchids in Fujian province[D]. Fuzhou: Fujian Normal University, 2015. (in Chinese).
[9]	LIU J F. The complete chloroplast genome sequence of Liparis bootanensis (Orchidaceae) [J]. Mitochondrial DNA Part B, 2020, 5(3): 2058−2059. doi: 10.1080/23802359.2020.1763866
[10]	BULMER M. The selection-mutation-drift theory of synonymous codon usage [J]. Genetics, 1991, 129: 897−907. doi: 10.1093/genetics/129.3.897
[11]	ROMERO H, ZAVALA A, MUSTO H. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces [J]. Nucleic Acids Research, 2000, 28(10): 2084−2090. doi: 10.1093/nar/28.10.2084
[12]	HIRAOKA Y, KAWAMATA K, HARAGUCHI T, et al. Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe [J]. Genes to Cells, 2009, 14(4): 499−509. doi: 10.1111/j.1365-2443.2009.01284.x
[13]	SHARP P M, EMERY L R, ZENG K. Forces that influence the evolution of Codon bias [J]. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences, 2010, 365(1544): 1203−1212. doi: 10.1098/rstb.2009.0305
[14]	杨国锋, 苏昆龙, 赵怡然, 等. 蒺藜苜蓿叶绿体密码子偏好性分析 [J]. 草业学报, 2015, 24(12):171−179. doi: 10.11686/cyxb2015016 YANG G F, SU K L, ZHAO Y R, et al. Analysis of Codon usage in the chloroplast genome of Medicago truncatula [J]. Acta Prataculturae Sinica, 2015, 24(12): 171−179.(in Chinese) doi: 10.11686/cyxb2015016
[15]	王婧, 王天翼, 王罗云, 等. 沙枣叶绿体全基因组序列及其使用密码子偏性分析 [J]. 西北植物学报, 2019, 39(9):1559−1572. WANG J, WANG T Y, WANG L Y, et al. Assembling and analysis of the whole chloroplast genome sequence of Elaeagnus angustifolia and its Codon usage bias [J]. Acta Botanica Boreali-Occidentalia Sinica, 2019, 39(9): 1559−1572.(in Chinese)
[16]	WRIGHT F. The ‘effective number of codons’ used in a gene [J]. Gene, 1990, 87(1): 23−29. doi: 10.1016/0378-1119(90)90491-9
[17]	JIANG Y, DENG F, WANG H L, et al. An extensive analysis on the global Codon usage pattern of baculoviruses [J]. Archives of Virology, 2008, 153(12): 2273−2282. doi: 10.1007/s00705-008-0260-1
[18]	SUEOKA N. Directional mutation pressure and neutral molecular evolution [J]. Proceedings of the National Academy of Sciences of the United States of America, 1988, 85(8): 2653−2657. doi: 10.1073/pnas.85.8.2653
[19]	SUEOKA N. Near homogeneity of PR2-bias fingerprints in the human genome and their implications in phylogenetic analyses [J]. Journal of Molecular Evolution, 2001, 53(4/5): 469−476.
[20]	胡莎莎, 罗洪, 吴琦, 等. 苦荞叶绿体基因组密码子偏爱性分析 [J]. 分子植物育种, 2016, 14(2):309−317. HU S S, LUO H, WU Q, et al. Analysis of Codon bias of chloroplast genome of Tartary buckwheat [J]. Molecular Plant Breeding, 2016, 14(2): 309−317.(in Chinese)
[21]	续晨, 贲爱玲, 蔡晓宁. 蝴蝶兰叶绿体基因组密码子使用的相关分析 [J]. 分子植物育种, 2010, 8(5):945−950. doi: 10.3969/mpb.008.000945 XU C, BEN A L, CAI X N. Analysis of synonymous Codon usage in chloroplast genome of Phalaenopsis aphrodite subsp. Formosana [J]. Molecular Plant Breeding, 2010, 8(5): 945−950.(in Chinese) doi: 10.3969/mpb.008.000945
[22]	李冬梅, 吕复兵, 朱根发, 等. 文心兰叶绿体基因组密码子使用的相关分析 [J]. 广东农业科学, 2012, 39(10):61−65. doi: 10.3969/j.issn.1004-874X.2012.10.019 LI D M, LV F B, ZHU G F, et al. Analysis on Codon usage of chloroplast genome of Oncidium Gower Ramsey [J]. Guangdong Agricultural Sciences, 2012, 39(10): 61−65.(in Chinese) doi: 10.3969/j.issn.1004-874X.2012.10.019
[23]	刘慧, 王梦醒, 岳文杰, 等. 糜子叶绿体基因组密码子使用偏性的分析 [J]. 植物科学学报, 2017, 35(3):362−371. doi: 10.11913/PSJ.2095-0837.2017.30362 LIU H, WANG M X, YUE W J, et al. Analysis of Codon usage in the chloroplast genome of Broomcorn millet (Panicum miliaceum L.) [J]. Plant Sclence Journal, 2017, 35(3): 362−371.(in Chinese) doi: 10.11913/PSJ.2095-0837.2017.30362
[24]	INGVARSSON P K. Gene expression and protein length influence Codon usage and rates of sequence evolution in Populus tremula [J]. Molecular Biology and Evolution, 2007, 24(3): 836−844.
[25]	陆奇丰, 骆文华, 黄至欢. 两种梧桐叶绿体基因组密码子使用偏性分析 [J]. 广西植物, 2020, 40(2):173−183. doi: 10.11931/guihaia.gxzw201811035 LU Q F, LUO W H, HUANG Z H. Codon usage bias of chloroplast genome from two species of Firmiana Marsili [J]. Guihaia, 2020, 40(2): 173−183.(in Chinese) doi: 10.11931/guihaia.gxzw201811035