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不同国家和地区SARS-CoV-2序列的密码子使用偏好性及聚类分析

发表时间:2021-09-30  浏览量:80  下载量:7
全部作者: 刘建忠,郑智捷
作者单位: 云南大学云南省软件工程重点实验室
摘 要: 目的:研究8个国家和地区SARS-CoV-2序列的密码子使用偏好性和演化关系。方法:分别求出8个国家和地区SARS-CoV-2序列中的最大相似序列组的基准SARS-CoV-2序列,用CodonW软件分析基准SARS-CoV-2序列的密码子使用偏好,用MEGA-X软件分析各国家和地区基准SARS-CoV-2序列之间演化关系。结果:基准SARS-CoV-2序列的G+C含量均低于A+U含量,其中加拿大最低,中国次之;8个国家和地区的共有使用偏好性密码子有19个,不包括中国的有7个,不包括加拿大的有1个,不包括中国和加拿大的有1个,这总计28个密码子中有25个以A、U结尾;中国有特有偏好性密码子7个,其中6个以C、G结尾,加拿大有1个,以U结尾;3个发育树将基准SARS-CoV-2序列分成两大类,美国、印度、智利和比利时为一类,澳大利亚、加拿大、英格兰和中国为另一类,在大类中进一步划分时存在不确定性。结论:SARS-CoV-2为了适应不同宿主在不断地发生突变,与宿主发生了协同进化,呈现出多源传染、多路演化态势。
关 键 词: 生物工程;SARS-CoV-2;基准SARS-CoV-2序列;密码子使用偏好性;聚类分析
Title: Codon usage bias and cluster analysis of SARS-CoV-2 sequences in different countries and territories
Author: LIU Jianzhong, ZHENG Jeffrey
Organization: Key Laboratory for Software Engineering of Yunnan Province, Yunnan University
Abstract: Objective: The codon usage bias and evolution of the SARS-CoV-2 sequences in eight different countries and territories were studied. Methods: The datum SARS-CoV-2 sequences of the largest similar sequence group among SARS-CoV-2 sequences in eight different countries and territories were calculated, the codon usage bias of the datum SARS-CoV-2 sequences was analyzed using CodonW package, the evolutionary relationships between the datum SARS-CoV-2 sequences were analyzed using MEGA-X. Results: G+C contents of the SARS-CoV-2 sequences were all lower than A+U contents, and the lowest measure was observed in Canada, followed by China. There were 19 commonly owned preference codons in eight different countries and territories, and 7 in seven different countries and territories (excluding China), 1 in seven different countries and territories (excluding Canada), 1 in six different countries and territories (excluding China and Canada). 25 of these 28 codons ended with A and U. There were 7 proprietary preference codons in China, 6 of which ended with C or G, and 1 in Canada that ended with U. The datum SARS-CoV-2 sequences were divided into two major categories by three phylogenetic trees, with the datum SARS-CoV-2 sequences in the USA, India, Chile and Belgium as one category and the datum SARS-CoV-2 sequences in Australia, Canada, England and China as the other category. In further classification, there was uncertainty. Conclusion: In order to adapt to different hosts, SARS-CoV-2 was constantly mutating and co-evolving with the host, showing a trend of multi-source infection and multi-channel evolution.
Key words: biotechnology; SARS-CoV-2; datum SARS-CoV-2 sequence; codon usage bias; cluster analysis
发表期数: 2021年9月第3期
引用格式: 刘建忠,郑智捷. 不同国家和地区SARS-CoV-2序列的密码子使用偏好性及聚类分析[J]. 中国科技论文在线精品论文,2021,14(3):314-323.
 
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