Comparative genomic analysis of Bacillus mycoides Gnyt1 strain

This study focused on the comparative genomic analyses of five carrying Bacillus strains which might give us insights on the difference and similarity in the genomic evolutionary kinships and contexts of Bacillus mycoides Gnyt1.Comparative genomic analyses of the carrying Bacillus strains genomes with emphasis on their antimicrobial resistance genes and virulence factors were performed.Most nitrogen-fixing genes and the phosphate-dissolving genes of the comparative genomic strain existed and the gene type was significantly different. And the action to nitrogen-fixing gene and phosphate-dissolving gene are dependent on different genes. Sharing some adherence, similarity, and the Bacillus mycoides strain Gnyt1 developed evolution is consistent with other Bacillus. Related functions absorb different gene-specific acquisitions, pigments, proteases, regulatory, secretory systems and functional factors associated with nitrogen-fixing phosphorus.Sharing most 16S rDNA analysis, Mauve-based genome-wide, Gene family analysis and phylogenetic tree, the Bacillus strain Gnyt1 and Bacillus mycoides strain AH621 differ in composition gene expression and expression cause conditions and factors. proteases,


Introduction
Bacillus mycoides Gnyt1 is a significant plant growth promoting rhizobacteria (PGPR), which could swarm by thousands of biological of the rhizosphere, the nutrient-enriched zone in the immediate vicinity of the soil-root interface and bacterical species (Bais et al., 2006;Mendes et al., 2013). In reported, PGPR strains can promote plant growth of promoting nutrient availability and improving plants to adapt more and more environmental stresses, etc (Kumar et al., 2014;Glickmann et al., 1995). Bacillus and Pseudomonas are often interrelated with the plant growth and soil quality, Bacillus mycoides has an important role in soil remediation and plant growth (Ahmed et al., 2014;Aeron et al., 2011;Orhan et al., 2006). Absorbing soil nutrients and water by root, which affecting morphological development lead to plant grow. Plant root play an important role on nutrient availability (Kapulnik et al., 1985).
The use of comparative genomics can more directly determine the evolutionary relationship of strains. However, the infections caused by Bacillus mycoides comparative genomic have also been incidentally reported (G. Lombardi et al., 2002;S. Ladhani et al., 1998). The Gnyt1 is part of Bacillus mycoides is a normal isolate from the rhizosphere of the dominant plant polygonum viviparum of the alpine grassland where was suffering from Tianzhu in Gansu province, China, in 2014 (Liu T et al., 2017). The performance of the strain has been previously studied and genome-wide sequencing (Li JH, 2017), the complete genomes of five strains had been sequenced and annotated in reported study.
In this study, we also demonstrate the strain sequence and compare its similar Bacillusgenome with the three major representative strains (CM000719, CM000743, and CM000749) that are economically considerable species of plant microorganism. By comparing the four strains genomic analysis, our aim was to compare to obtain the information of the target genome based on the gene sequence and the genomic map, our comparisons revealed not only conserved components of the Gnyt1 core genome but also unique genes for each pathogen. In particular, this study focused on the comparative genome analyses of four Bacillus strains which might give us insights on the similarity and difference in the genomic contexts of Bacillus mycoides Gnyt1 gene. These data will provide a foundation for the molecular mechanisms and functional analyses of the Gnyt1 relevant to their Nitrogen-fixing phosphorus mechanism, etc.

Nucleotide accession numbers
The complete sequence of Bacillus mycoides Gnyt1 strain genome, preserved in the microbiology laboratory of Gansu Agricultural University and plasmid are available in GenBank Datebase under accession number CM000719, CM000743, and CM000749, respectively.

Genome alignment and functional analysis
The genome of Gnyt1 strain and reported four strains were using the progressive Mauve algorithm in

General genomic features
The whole genome sequence of the strain indicates the total length of sequence after genomic sequence splicing is 5,597,907bp and GC content of 35.57% (Table 1). The strain Gnyt1 ORF prediction is 5,876, the average of ORF is 792.17bp, some plasmids were identified in the genome of Bacillus strain Gnyt1 which has 4,654,818bp in ORF total length.  (Fig.2).

based genome-wide sequence alignment
To clarify the level of genomic disagreement, multiple alignments of four Bacillus strains genome sequences were conducted in Mauve software, the results are as follows (Fig 3)  obtained by clustering are collated and counted using a self-made Perl script (Fig 4).
To reveal the evolutionary relationships and find the analysis of different genes family by six strains, As shown in Fig.4

Declarations
Availability of data and materials All data generated and analysed during this study are included in this published article and its supplementary information files.
Ethics approval and consent to participate Not applicable. Phylogenetic tree reconstruction based on 16s rDNA of strain Bacillus mycoides Gnyt1 Figure 3 Global alignment of chromosomes of the strain Bacillus mycoides Gnyt1 Gene family analysis of the strain Bacillus mycoides Gnyt1 Figure 5 Phylogenetic tree of single copy genes