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Genomic Heterogeneity in a Natural Archaeal Population Suggests a Model of tRNA Gene Disruption

Figure 4

Dinucleotide bias analysis of the insertion sequence.

(A) The average absolute dinucleotide relative abundance difference (δ*-value) for the composite genome and the insertion sequence (1,868 bp) was compared with the δ*-values for the composite genome and each of the computationally generated 2-kb genomic segments (n = 1,681). An error bar represents the standard deviation. Statistical significance was determined by calculating the proportion of δ*-values for the 2-kb segments that were greater than or equal to that of the insertion sequence. (B) Relative abundances of various types of archaeal DNA sequences, ranked according to the similarity of their dinucleotide content to the insertion sequence. In total, 180 DNA sequences were sorted in ascending order of their δ*-values and divided into 10 bins. The sequences in each bin were categorized into five groups: plasmids encoding pNOB8-type integrases (pink, n = 10); plasmids in the order Sulfolobales (red, n = 11); chromosomes in the order Sulfolobales (dark red, n = 11); other plasmids (dark grey, n = 74), and other chromosomes (black, n = 74). See Table S2 for the complete list of all 180 DNAs.

Figure 4