Table 1.
List of C. glutamicum strains used in this study with their metadata.
Fig 1.
(A) ANI based whole genome comparison of C. glutamicum strains. The linkage method was average linkage, which calculates the average distance between all pairs of points in two clusters. The distance metric was Euclidean distance, which measures the straight-line distance between two points in a multidimensional space. The distance threshold was 0.5, which means that clusters with a distance less than or equal to 0.5 were merged together. This resulted in five clades, as shown by the horizontal dashed line in the plot. (B) ANI comparisons conducted among strains isolated from soil environments and strains isolated from both soil and non-soil environments within C. glutamicum.
Fig 2.
(A) Genome size and CDS. (B) Genomic features (tRNA, rRNA and GC content (%)). (C) Gene number.
Fig 3.
Pan-genome analysis of C. glutamicum.
(A) The number of core genes, soft core genes, shell genes and cloud genes in the pan genome. (B) Gene frequency versus genomes number. (C) The pan genome profile trends obtained using BPGA v1.3. (D) Genomic G+C content (%) and accessory gene counts in various C. glutamicum strains.
Fig 4.
(A) COG distribution of core, accessory and unique genes. (B) KEGG distribution of core, accessory and unique genes. (C) Phylogenetic analysis of C. glutamicum strains based on core genes.
Fig 5.
BGCs among C. glutamicum strains.
(A) Distribution of different classes of BGCs among C. glutamicum strains. (B) BGCs frequency per genome. (C) Different classes of BGCs occurrence in the genomes. (D) BGCs of C. glutamicum AR1.
Table 2.
Predicted terpene BGCs in different clades of C. glutamicum strains.
Table 3.
Predicted bacteriocin BGC in C. glutamicum strains.
Fig 6.
BGCs distribution in C. glutamicum strains.
(A) Correlation of BGCs and genome size. (B) Correlation of BGCs and gene number.
Fig 7.
Major classes of BGCs in the genomes of C. glutamicum strains with phylogenetic distribution.
These BGC classes are categorized into five clades, each delineated based on their specific biosynthetic gene content.
Fig 8.
Hybrid BGCs structure C. glutamicum strains.
Hybrid BGCs in four strains harbour same structure of NAPAA-betalactone. The different locations of NAPAA-betalactone are, 256574–294301 base pairs in strain B253, 334064–369207 base pairs in strain R, 319,462–354,607 base pairs in strain SCgG1, and 319,463–354,608 base pairs in SCgG2.
Table 4.
Different hits of BGCs from different genome mining tools using C. glutamicum genomes.
Fig 9.
BRIG Diagram illustrating homologous chromosome segments of C. glutamicum strains using strain SCgG2 as the reference genome.
Fig 10.
The pairwise whole-genome Mauve alignment analysis revealed substantial structural variations within the circular chromosomes of C. glutamicum strains.
Table 5.
SNPs detected in C. glutamicum strains.
Fig 11.
Visualizing the phylogeny of C. glutamicum strains based on core SNP genes.
Fig 12.
HGT events in C. glutamicum AJ1511 and AR1 Strains.
(A) Scatter plot illustrating horizontally transferred genes in AJ1511 (Colour dots represents horizontally transferred genes and colourless dots represents native genes). (B) Distribution of donor organisms and the corresponding number of genes transferred in AJ1511. (C) Scatter plot showcasing horizontally transferred genes in AR1 (Colour dots represents horizontally transferred genes and colourless dots represents native genes). (D) Distribution of donor organisms and the corresponding number of genes transferred in AR1. (In the scatter plots, coloured dots represent genes transferred through HGT).
Table 6.
Pathogenicity prediction results for various C. glutamicum strains.
Table 7.
Plasmid characteristics in different C. glutamicum strains.