Additional file 1 of Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study
Creators: name: Liu, Yan
name: Štefanič, Polonca
name: Miao, Youzhi
name: Xue, Yansheng
name: Xun, Weibing
name: Zhang, Nan
name: Shen, Qirong
name: Zhang, Ruifu
name: Xu, Zhihui
name: Mandic-Mulec, Ines
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics

description: Additional file 1: Figure S1 The agarose gel electrophoresis of DNA amplification products of three gyrA gene primer pairs: gyrA1 (A), gyrA2 (B) and gyrA3 (C). 1-7 indicates strains LY18, LY25, LY37, FZB42, SXL408, SXL277 and ACCC01043. Figure S2 The amplification ability of the primer pair gyrA1 and gyrA2 in Bacillus species by computer simulation. The eight Bacillus species were amplified by gyrA1 and nine Bacillus species were amplified by gyrA2. The phylogenetic trees were constructed based on gyrA gene (2403 bp). Figure S3 Polymorphisms in the 16S rRNA and gyrA gene’s regions of B. amyloliquefaciens (116 genomes). (A) The proportion of variation at different base sites along the 16S rRNA V3-V4 region. (B) The proportion of variation at the different base positions of the gyrA gene region. (C) The proportion of variants along 16S rRNA (red column) and gyrA gene (blue column) region in different genomes. Figure S4 Polymorphisms in the 16S rRNA and gyrA gene’s region of B. pumilus (140 genomes). (A) The proportion of variation at different base sites along the 16S rRNA (B) and the gyrA gene. (C) The proportion of variable base sites in 16S rRNA (red column) and gyrA (blue column) sequences in different genomes. Figure S5 Alignment of the 16S rRNA and gyrA sequences of B. megaterium (117 genomes) and B. anthracis (226 genomes). Sequences were aligned using L-INS-I method of MAFFT (v7.487). The analysis involved positions along 16S rRNA from 330-810 and along gyrA from 350-850. On the left side of the graph GCF reference numbers of genomes were displayed, with reference sequence GCF_002577645.1 displayed at the top for B. megaterium and GCF_000007845.1 for B. anthracis. The display of base site variation was drawn using MEGA (v.5.05). The colored line (red or blue) indicates a variation of specific base sites as compared to the reference sequence. Figure S6 Polymorphisms in the 16S rRNA and gyrA gene’s regions of B. megaterium (117 genomes). (A) The proportion of variation at different base sites along the 16S rRNA V3-V4 region. (B) The proportion of variation at the different base positions of the gyrA gene region. (C) The proportion of variants along 16S rRNA (red column) and gyrA gene (blue column) region in different genomes. Figure S7 Polymorphisms in the 16S rRNA and gyrA gene’s region of B. anthracis (226 genomes). (A) The proportion of variation at different base sites along the 16S rRNA gene (B) and the gyrA gene. (C) The proportion of variable base sites in 16S rRNA (red column) and gyrA (blue column) sequences in different genomes. Figure S8 Description of gyrA gene primer pairs for amplicon sequencing. (A) The position of gyrA amplicons was obtained by primer pairs gyrA3, gyrA4 and gyrA5. (B) PCR amplification of eight Bacillus strains by gyrA gene primer pairs. The orange square indicates positive and white square unsuccessful amplification. The phylogenetic tree was contracted based on the complete gyrA genes (2469 bp) (Supplemental Dataset S2) by using the Neighbor-Joining method in MEGA 5.05 software. The reliability of clades was tested by the 1000 bootstrap replications.