Identification of Shewanella at species level based on16S rRNA and gyrB genes

  Objective   To establish an assay for the identification of Shewanella based on 16S 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 16S rRNA and gyrB genes of 54 Shewanella strains. Adjacency distance matrix method of software MEGA 6.06 was used to construct the phylogenetic tree 16S 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 16S rRNA and gyrB genes were calculated. The difference of identification power for the two genes was compared.

  Results   The 16S 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 16S 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. 16S rRNA had a small range in intraspecific and interspecific similarities.

  Conclusion   Compared with 16S rRNA gene, the phylogenetic tree of gyrB gene can identify Shewanella at species level more accurately.