Codon usage patterns across seven Rosales species

doi:10.1186/s12870-022-03450-x

	Codon usage patterns across seven Rosales species
	Zhang, Yao 1,2; Shen, Zenan 3; Meng, Xiangrui 1,2; Zhang, Liman 1,2; Liu, Zhiguo 4; Liu, Mengjun 4; Zhang, Fa 3; Zhao, Jin 1,2
	2022-02-05
发表期刊	BMC PLANT BIOLOGY
ISSN	1471-2229
卷号	22 期号:1 页码:10
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.
关键词	Rosales Codon usage bias Natural selection Evolutionary relationships
DOI	10.1186/s12870-022-03450-x
收录类别	SCI
语种	英语
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
WOS类目	Plant Sciences
WOS记录号	WOS:000751618000002
出版者	BMC
引用统计	被引频次：21[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/19017
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.Hebei Agr Univ, Coll Life Sci, Baoding, Peoples R China 2.Hebei Agr Univ, Hebei Key Lab Plant Physiol & Mol Pathol, Baoding, Peoples R China 3.Chinese Acad Sci, High Performance Comp Res Ctr, Inst Comp Technol, Beijing 100190, 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.