莠去津降解菌泛基因组测序及比较基因组分析

Pan-genome Sequencing and Comparative Genomic Analysis of Atrazine-degrading Bacteria

Arthrobacter aurescens TC1和Pseudomonas sp.ADP是目前莠去津降解菌的模式菌株,筛选出Microbacterium sp.HBT4,旨在挖掘这3株不同种属细菌基因组间生物学信息的异同,并预测重要基因。通过Illumina Hiseq 4000测序平台采用DNA小文库制备和测序技术,进行了泛基因组测序,使用相关软件进行基因组组分分析、基因功能注释、基因间变异检测和比较基因组学分析,将分离得到的微杆菌HBT4与模式菌株进行核苷酸组成、共线性及菌株间变异差异分析。得到该菌株基因组大小约为3.53 Mb,预测到菌株HBT4编码基因3 397个、重复序列含量为1.33%、非编码RNA 63个,通用数据库基因功能注释共3 324个,专用数据库基因功能注释共1 149个,通过菌株间差异变异分析发现SNP、Small InDel和水平转移基因,未发现结构变异基因,获得该菌株特有基因中GO注释到的基因在细胞组分、分子功能和生物学进程中的数量和比例,从KEGG代谢通路富集图中发现特有基因编码的二氢硫基赖氨酸残基琥珀酰转移酶位于三羧酸循环中α-酮戊二酸和琥珀酰辅酶A的代谢通路之间。获得3个菌株核心基因组与非必需基因组比例分布、系统进化树和共线性关系,发现三者之间共有基因家族986个、菌株HBT4特有基因家族1 171个。得到的菌株HBT4与两株模式菌株相比,其基因家族之间既有相同之处,又有较大差异。

Arthrobacter aurescens TC1 and Pseudomonas sp.ADP are currently the model strains of atrazine-degrading bacteria.Microbacterium sp.HBT4 was screened in this experiment for discovering the similarities and differences of biological information among the 3 bacterial genomes and predicting important genes.In this study,pan-genome sequencing was carried out by using small DNA library preparation and sequencing technology on Illumina Hiseq 4000 sequencing platform.Genome composition analysis,gene function annotation,gene mutation detection and comparative genomics analysis were carried out by using related software.The nucleotide composition,collinearity and variation differences between the isolated Microbacterium HBT4 and model strains were analyzed.The genome size of the strain was about 3.53 Mb.It was predicted that there were 3 397 coding genes,1.33%repetitive sequences and 63 non-coding RNA in the strain HBT4.There were 3 324 annotations of gene function in general database and 1 149 annotations of gene function in special database.SNP,Small InDel and horizontal transfer genes were found through analyzing variance among strains and no structural variation genes were found.The number and proportion of GO-annotated genes in the specific genes of the strain in cell components,molecular functions and biological processes were obtained.From KEGG metabolic pathway enrichment map,it was found that the dihydrothiosyllysine residue succinyltransferase encoded by the specific gene was located between the metabolic pathway ofα-ketoglutaric acid and succinyl coenzyme A in the tricarboxylic acid cycle.The proportional distribution,phylogenetic tree and collinearity of the core genome and non-essential genome of the three strains were obtained.It was found that there were 986 common gene families among the three strains,and 1171 specific gene families strain HBT4.Compared with the two model strains,the strain HBT4 obtained in this study had both similarities and differences in gene family.