Fig. 2: Discovery of potentially unrecognized genetic elements. | Nature Communications

Fig. 2: Discovery of potentially unrecognized genetic elements.

From: Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome

Fig. 2

A The ratio of each microbial genetic element of long-read high-quality contigs. Among the 6852 unclassified contigs, 85 were further analyzed as strong candidates of unrecognized elements. B Abundance and prevalence of candidate contigs of unrecognized genetic elements. The scatter plot shows the average abundance (y-axis), prevalence (x-axis), and number of contigs in each operational contig cluster (plot size) obtained from 85 contigs. C An abundance of Cluster 0001 contigs among all contigs in each sample. The violin plot shows the distribution of the abundance of all contigs in each sample, which includes contigs of Cluster_0001. The red arrow indicates the abundance of Cluster 0001 contigs and their rank in all contig abundance in each sample. Box plots represent the inter-quartile range (IQR), and lines inside the box indicate the median. Whiskers show 1.5 IQR. D The contig length and (E) number of ORFs of 13 contigs of the Cluster 0001. Box plots represent the inter-quartile range (IQR), and lines inside the box indicate the median. Whiskers show 1.5 IQR. F Representative replichore structure of Cluster 0001 contig (Inocle_001). The green line indicates cumulative GC skew, and the gray plots indicate GC skew in each genomic position. The candidate replication origin and terminus are represented by vertical red and blue lines, respectively. G Representative genomic structure of Inocle: from inner to outside, GC skew, GC content, forward strand of ORFs, and reverse strand of ORFs. H Effect of preNuc treatment on the sequence depth of the Cluster 0001 contig. Bar plot shows the mean depth of the Cluster 0001 contig (Inocle_004) obtained from preNuc-treated and untreated saliva samples. I Comparison of the long-read contig and corresponding short-read contigs of the Cluster 0001 contig. The blue bar represents the contig constructed by the long-read assembly, and the red boxes indicate IS regions. The arrows represent fragmented positions in short-read assembly. The upper gray bar plot indicates the depth of the mapped long reads. Colored bars in the depth bar plots indicate single-nucleotide variants: Green = A, red = T, orange = G, and blue = C.

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