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Codon usage patterns across seven Rosales species

文献类型：期刊论文

作者Zhang, Yao2,3; Shen, Zenan1; Meng, Xiangrui2,3; Zhang, Liman2,3; Liu, Zhiguo4; Liu, Mengjun4; Zhang, Fa1; Zhao, Jin2,3
刊名BMC PLANT BIOLOGY
出版日期2022-02-05
卷号22期号:1页码:10
ISSN号1471-2229
关键词Rosales Codon usage bias Natural selection Evolutionary relationships
DOI10.1186/s12870-022-03450-x
英文摘要Background Codon usage bias (CUB) analysis is an effective method for studying specificity, evolutionary relationships, and mRNA translation and discovering new genes among various species. In general, CUB analysis is mainly performed within one species or between closely related species and no such study has been applied among species with distant genetic relationships. Here, seven Rosales species with high economic value were selected to conduct CUB analysis. Results The results showed that the average GC1, GC2 and GC3 contents were 51.08, 40.52 and 43.12%, respectively, indicating that the A/T content is more abundant and the Rosales species prefer A/T as the last codon. Neutrality plot and ENc plot analysis revealed that natural selection was the main factor leading to CUB during the evolution of Rosales species. All 7 Rosales species contained three high-frequency codons, AGA, GTT and TTG, encoding Arg, Val and Leu, respectively. The 7 Rosales species differed in high-frequency codon pairs and the distribution of GC3, though the usage patterns of closely related species were more consistent. The results of the biclustering heat map among 7 Rosales species and 20 other species were basically consistent with the results of genome data, suggesting that CUB analysis is an effective method for revealing evolutionary relationships among species at the family or order level. In addition, chlorophytes prefer using G/C as ending codon, while monocotyledonous and dicotyledonous plants prefer using A/T as ending codon. Conclusions The CUB pattern among Rosales species was mainly affected by natural selection. This work is the first to highlight the CUB patterns and characteristics of Rosales species and provides a new perspective for studying genetic relationships across a wide range of species.
资助项目National Key RD Program[2018YFD1000607] ; Foundation for 100 Innovative Talents of Hebei Province[SLRC2019031] ; National Natural Science Foundation of China[31772285]
WOS研究方向Plant Sciences
语种英语
出版者BMC
WOS记录号WOS:000751618000002
源URL[http://119.78.100.204/handle/2XEOYT63/19016]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Zhang, Fa; Zhao, Jin
作者单位1.Chinese Acad Sci, High Performance Comp Res Ctr, Inst Comp Technol, Beijing 100190, Peoples R China
2.Hebei Agr Univ, Coll Life Sci, Baoding, Peoples R China
3.Hebei Agr Univ, Hebei Key Lab Plant Physiol & Mol Pathol, Baoding, Peoples R China
4.Hebei Agr Univ, Res Ctr Chinese Jujube, Baoding, Peoples R China
推荐引用方式
GB/T 7714		 Zhang, Yao,Shen, Zenan,Meng, Xiangrui,et al. Codon usage patterns across seven Rosales species[J]. BMC PLANT BIOLOGY,2022,22(1):10.
APA Zhang, Yao.,Shen, Zenan.,Meng, Xiangrui.,Zhang, Liman.,Liu, Zhiguo.,...&Zhao, Jin.(2022).Codon usage patterns across seven Rosales species.BMC PLANT BIOLOGY,22(1),10.
MLA Zhang, Yao,et al."Codon usage patterns across seven Rosales species".BMC PLANT BIOLOGY 22.1(2022):10.

入库方式： OAI收割

来源：计算技术研究所

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