Figure 1.
Chromosome Atlas of the chromosome of Lactobacillus delbrueckii subsp. Bulgaricus 2038.
Each concentric circle, number from outermost circle to innermost circle, represents genomic data for Lactobacillus delbrueckii subsp. Bulgaricus strain LBU2038 and comparison with ACCT11842 and ACCT BAA-365. First and second circles show predicted coding sequences (ORFs) on the plus and minus strands, respectively, colored by functional role categories according to COG: [J]: “Translation, ribosomal structure and biogenesis” = salmon; [A]: “RNA processing and modification” = light blue; [K]: “Transcription” = light green; [L]: “Replication, recombination and repair” = red; [B]: “Chromatin structure and dynamics” = brown; [D]: “Cell cycle control, cell division, chromosome partitioning” = yellow; [Y]: “Nuclear structure” = green; [V]: “Defense mechanisms” = purple; [T]: “Signal transduction mechanisms” = pink; [M]: “Cell wall/membrane/envelope biogenesis” = orange; [N]: “Cell motility” = blue; [Z]: “Cytoskeleton” = grey; [W]: “Extracellular structures” = sea green; [U]: “Intracellular trafficking, secretion, and vesicular transport” = black; [O]: “Posttranslational modification, protein turnover, chaperones” = aqua; [C]: “Energy production and conversion” = fuchsia; [G]: “Carbohydrate transport and metabolism” = lime; [E]: “Amino acid transport and metabolism” = maroon; [F]: “Nucleotide transport and metabolism” = navy; [H]: “Coenzyme transport and metabolism” = olive; [I]: “Lipid transport and metabolism” = silver; [P]: “Inorganic ion transport and metabolism” = lime green; [Q]: “Secondary metabolites biosynthesis, transport and catabolism” = cadet blue; [R]: “General function prediction only” = coral; [S]: “Function unknown” = dodger blue. Third and forth circles represent the conservation of the ORFs sequences compared to ACCT11842 on the plus and minus strands, respectively, colored by conservation levels: gain gene = pink; INDEL gene = yellow; non-synonymous SNP gene = green; synonymous SNP gene = blue; equal gene = dark red. Fifth and Sixth circle display the sequence comparison of each ORF to ACCT BAA-365 on the plus and minus strands, with same colors with third and forth circles for conservation levels. Seventh circle show the IS sequences. Eighth circle present the GC content of the chromosome. Ninth circle displays the GC skew of the chromosome (red circle line represent the value of zero of GC skew).
Table 1.
Basic information of seventeen microorganisms' genome.
Figure 2.
GC scan and the duplication regions of Lb. bulgaricus 2038 genome.
(A) The GC content of Lb. bulgaricus 2038 genome (30% to 60%). It was scanned with a window size of 5000 bp and step of 1000 bp. (B) Alignment result of genomes between Lb. bulgaricus 2038, ATCC 111842 and ATCC BAA-365 by Mummer. Pink: same direction; Blue: reverse direction. The characteristic duplication regions (A and B) flanking the predicted replication terminus are specially labeled. (C) Genes existed in the insertion and duplication regions (950k bp to 968k bp) of Lb. bulgaricus 2038. Their corresponding COG families are labeled by colors with letter specifications. [C]: Energy production and conversion; [E]: Amino acid transport and metabolism; [H]: Coenzyme transport and metabolism; [J]: Translation, ribosomal structure and biogenesis; [K]: Transcription; [L]: Replication, recombination and repair; [M]: Cell wall/membrane/envelope biogenesis; [O]: Posttranslational modification, protein turnover, chaperones; [R]: General function prediction only; [S]: Function unknown; [T]: Signal transduction mechanisms; [V]: Defense mechanisms.
Figure 3.
Homologous genes in the strains of Lb. bulgaricus.
Orthologous genes existed in each pair of strains and in all three strains of Lb. bulgaricus are counted and shown in corresponding sectors. Three types of orthologous genes were counted and illustrated in the parentheses from left to right: genes with identical DNA sequence, genes with synonymous variations, and genes with amino acid variations. Each orthologous gene pair was identified based on the best Blast hit (BBH) approach. The numbers in the white square frames represent the percentage value of hypothetical genes in each category. The numbers in the non-overlap segments of Venn Diagram represent the number of non-orthologous genes specific to each of the three strains, consisting of two types, unique vs. duplicated. The numbers in the yellow square frames represent the percentage value of pseudogenes in each strain. The numbers in the outside frames of the diagram represent the numbers of the annotated (known function) genes and hypothetical genes in the part of non-orthologous genes specific to each strain.
Table 2.
Enzymes in the pathway of Lysine biosynthesis.
Figure 4.
Phylogenetic trees for genome wide comparative analysis.
Phylogenetic trees of seventeen bacteria based on the basis of the alignments of gene relationship networks derived from genome context information, with all branches supported at >70% bootstrap values. All notes from gene networks are homologous genes in these microorganisms, and the branches in the gene networks are constructed using three kinds of relationships: predicted by phylogenetic profiles method, gene neighbors method and gene fusions method.