Analysis of codon usage patterns in citrus based on coding sequence data

doi:10.1186/s12864-020-6641-x

	Analysis of codon usage patterns in citrus based on coding sequence data
	Shen,Zenan 1,2; Gan,Zhimeng 3; Zhang,Fa 1,2; Yi,Xinyao 4; Zhang,Jinzhi 3; Wan,Xiaohua 1,2
	2020-12-16
发表期刊	BMC Genomics
卷号	21 期号:Suppl 5
摘要	AbstractBackgroundCodon usage is an important determinant of gene expression levels that can help us understand codon biology, evolution and mRNA translation of species. The majority of previous codon usage studies have focused on single species analysis, although few studies have focused on the species within the same genus. In this study, we proposed a multispecies codon usage analysis workflow to reveal the genetic features and correlation in citrus.ResultsOur codon usage analysis workflow was based on the GC content, GC plot, and relative synonymous codon usage value of each codon in 8 citrus species. This approach allows for the comparison of codon usage bias of different citrus species. Next, we performed cluster analysis and obtained an overview of the relationship in citrus. However, traditional methods cannot conduct quantitative analysis of the correlation. To further estimate the correlation among the citrus species, we used the frequency profile to construct feature vectors of each species. The Pearson correlation coefficient was used to quantitatively analyze the distance among the citrus species. This result was consistent with the cluster analysis.ConclusionsOur findings showed that the citrus species are conserved at the genetic level and demonstrated the existing genetic evolutionary relationship in citrus. This work provides new insights into codon biology and the evolution of citrus and other plant species.
关键词	Citrus Codon usage GC biology Evolution Correlation
DOI	10.1186/s12864-020-6641-x
语种	英语
WOS记录号	BMC:10.1186/s12864-020-6641-x
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/16148
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Wan,Xiaohua
作者单位	1.High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences 2.University of Chinese Academy of Sciences 3.Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University 4.Department of Computer Science and Engineering, University of South Carolina
推荐引用方式 GB/T 7714	Shen,Zenan,Gan,Zhimeng,Zhang,Fa,et al. Analysis of codon usage patterns in citrus based on coding sequence data[J]. BMC Genomics,2020,21(Suppl 5).
APA	Shen,Zenan,Gan,Zhimeng,Zhang,Fa,Yi,Xinyao,Zhang,Jinzhi,&Wan,Xiaohua.(2020).Analysis of codon usage patterns in citrus based on coding sequence data.BMC Genomics,21(Suppl 5).
MLA	Shen,Zenan,et al."Analysis of codon usage patterns in citrus based on coding sequence data".BMC Genomics 21.Suppl 5(2020).