摘要
基因组平均核苷酸相似度(average nucleotide identity,ANI)已成为鉴定细菌种内关系的黄金方法,开发可用于快速分析大量基因组之间ANI值的生物信息学工具具有重要意义。本研究以广泛应用的ANI分析软件JSpecies为基础,采用Perl集成编写了能够根据设置的线程数、自动生成多个JSpecies配置文件以完成基因组序列载入与成对选择,快速完成大量基因组ANI计算与分析的工具Batch-ANIm(下载地址:http://www.microbialgenomic.com/Batch-ANIm.html)。采用该工具对已测序的109株无色杆菌属(Achromobacter)菌株进行ANIm(基于MUMmer算法)计算,共获得5886个ANIm值。整体上,基于"100-ANIm"进化距离获得的聚类分析结果与核心基因组进化树比较一致,表明ANIm聚类分析可用于快速展示无色杆菌属菌株之间亲缘关系。很多无色杆菌属种内菌株之间的ANIm值小于95%,但种间ANIm值却大于95%,这表明从基因组水平上部分无色杆菌属菌株的分类学命名存在错误,特别是无色杆菌属的代表种A.xylosoxidans,命名为A.xylosoxidans的50个菌株,只有40个菌株真正属于A.xylosoxidans。同时,基于全基因组序列的ANI值比较可以将部分种名不确定的菌株分类学命名精确到种水平。
Average nucleotide identity(ANI)between genomes has been a golden approach for bacterial classification.Developing a highly efficient tool to fast determine ANI values between a huge number of genomes is becoming urgent in genomic era.In this study,we report a comprehensive ANI analysis tool,Bacth-ANIm(available from the website http://www.microbialgenomic.com/Batch-ANIm.html),which depends on JSpecies software and enables to accelerate calculation of ANIm(using MUMmer)by automatically generation of JSpecies configuration files to start multiple JSpecies in parallel.To test its powerful feature,Bacth-ANIm was applied to calculate 5886 ANIm values between pairs of genomes for 109 Achromobacter genomes.Overall,the result of cluster analysis based on distance matrix"100-ANIm"was relatively consistent with the topology of the core-gene based phylogenetic tree,suggesting that cluster analysis for ANIm was a robust approach to analysis genetic relationship for Achromobacter.Some pairs of intra-species genomes had ANIm values less than 95%,however some intra-species genomes had ANIm values more than 95%.The results showed that there were some mistakes in nomenclature for several strains,especially for A.xylosoxidans(representative species in Achromobacter),only 40 out of 50 strains belonging to this species actually.In addition,based on the result of ANIm analysis in this study,some strains without clear species names could be classified actually at the species level.
作者
李向阳
杨紫琳
汤宏
潘佳莉
Li Xiangyang;Yang Zilin;Tang Hong;Pan Jiali(School of Life and Health Science,Kaili University,Kaili,556011;Department of Environmental Science and Engineering,Fudan University,Shanghai,200433)
出处
《基因组学与应用生物学》
CAS
CSCD
北大核心
2021年第2期695-704,共10页
Genomics and Applied Biology
基金
国家自然科学基金项目(21507012和21966015)
中国博士后科学基金项目(2015M570329)
贵州省科学技术基金项目(黔科合基础[2019]1287号)
贵州省科技厅联合基金项目(黔科合LH字[2017]7176)
凯里学院博士专项基金项目(BS201412)共同资助。
