基于16S rRNA和gyrB基因的施万菌种水平鉴定分析

  目的   构建基于16S rRNA和gyrB基因对施万菌(Shewanella)进行种水平鉴定的方法，比较2个基因的鉴定能力差异。   方法   利用DnaSP 6.0软件对施万菌16S rRNA 和gyrB 基因的信息位点数及其百分比、核苷酸多态性值、平均G＋C含量、非同义突变率与同义突变率的比值（Ka/Ks）、Tajima检验进行基因多态性分析。 用MEGA 6.06软件的邻接距离矩阵法对90株测试菌株和54株模式菌株构建16S rRNA 和gyrB 基因的进化树。 用MEGA 6.06软件的Kimura’s 2-parameter模型，确定90株测试菌株的菌种后，计算16S rRNA 和gyrB 基因的遗传距离和序列相似性。 比较两者对施万菌种水平鉴定能力差异。   结果   16S rRNA和gyrB基因序列相似性平均值分别为95.0%、80.8%。 在16S rRNA基因进化树中，S. marinintestina和S. sairae、S. livingstonensis和S. vesiculosa的进化分支几乎完全相同，gyrB基因则能在种水平将所有菌株区分开。 16S rRNA基因的种内和种间相似性范围小。   结论   与16S rRNA基因相比，gyrB基因能够更准确的用于施万菌的种水平鉴定。

Identification of Shewanella at species level based on 16S rRNA and gyrB genes

Objective To establish an assay for the identification of Shewanella based on 16 S rRNA and gyrB genes and compare the identification power of two genes.Methods Software DnaSP 6.0 was used to analyze the number and percentage of information bits,the nucleotide polymorphism,average G+C content,the ratio of non-synonymous mutation rate to synonymous mutation rate(Ka/Ks)and the Tajima test was used for 16 S rRNA and gyrB genes of 54 Shewanella strains.Adjacency distance matrix method of software MEGA 6.06 was used to construct the phylogenetic tree 16 S rRNA and gyrB genes of 90 tested strains and 54 type strains.The kimura’s 2-parameter model of MEGA 6.06 software was used to identify the species of 90 tested strains,then the genetic distance and sequence similarity of 16 S rRNA and gyrB genes were calculated.The difference of identification power for the two genes was compared.Results The 16 S rRNA sequences of Shewanella strains had a similarity range of 89.8%–100.0%(average 95.0%)and gyrB sequence similarity range was 73.2%–99.9%(average 80.8%).In the phylogenetic tree of 16 S rRNA gene,S.marinintestina and S.sairae,S.livingstonensis and S.vesiculosa,showed almost identical evolutionary branches,but the gyrB gene could distinguish all strains at species level.16 S rRNA had a small range in intraspecific and interspecific similarities.Conclusion Compared with 16 S rRNA gene,the phylogenetic tree of gyrB gene can identify Shewanella at species level more accurately.