Fig. 2: Motif usage bias analysis and distribution of methylation sites in Lacticaseibacillus paracasei isolates.
From: Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei
Motif usage bias revealed by the Markov chain approach based on the analysis of 26 motifs identified in this study. The data of each strain/isolate are represented by a data dot of different color, and each motif is assigned to a specific motif number. The distance between a data dot and its projection on the diagonal line measures the extent of motif usage biases between coding sequences (CDSs) and intergenic regions. Data dots below and above the diagonal line represent skewing toward CDSs and the intergenic regions, respectively (a). Notched boxplots of the average frequency of 6mA methylation of the 26 motifs in the CDSs and the intergenic regions (b); distribution of methylation sites across CDSs of the top 10 Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KOs) of 20 Lacticaseibacillus paracasei isolates (c). The x- and y-axes represent the KO groups and methylation density, respectively. X-axis is sorted according to the median methylation density of the KO group. KO groups: K02795, mannose PTS system EIIC component; K01223, 6-phospho-beta-glucosidase; K01182, oligo-1,6-glucosidase; K03332, fructan beta-fructosidase; K01624, fructose-bisphosphate aldolase, class II; K02800, mannitol PTS system EIICBA or EIICB component; K00158, pyruvate oxidase; K02770, fructose PTS system EIIBC or EIIC component; K02761, cellobiose PTS system EIIC component; K02775, galactitol-PTS system EIIC component. The length of the box represents the range between the 25th and 75th percentile; the lines inside the boxes represent the median values; the whiskers denote the lowest and highest values within 1.5 times the interquartile range of each group; the dots above/below the upper/lower line are the outliers.
