Systematic identification and characterization of repeat sequences in African swine fever virus genomes

Figures

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  Figure 1. The number, position, and distribution of repeat sequences in the genome. A The number of repeat sequences identified in 86 genomes (per kb). B The phylogenetic tree on the left side was built with MEGA based on the C-terminal sequences (415 bp) of the p72 gene (see Materials and methods), and the genotypes of ASFV isolates are labelled with Greek numerals. The three types of repeat sequences in ASFV genomes are indicated by different colours. The black and red arrows refer to examples of genotype-specific repeat sequences in genotypes II and I, respectively.

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  Figure 2. The distribution of three types of repeat sequences in the ASFV genome. A The number of different types of repeat sequences per 10 kb in 86 ASFV genomes. B The ratio of genomic regions covered by three types of repeat sequences in 86 ASFV genomes. C The number of repeat units for the three repeat sequence types in 86 ASFV genomes. D The number of repeat units of different lengths. The microsatellites, minisatellites, and SINEs are coloured red, green, and blue, respectively.

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  Figure 3. The function of repeat sequences in noncoding regions. A The distribution of the noncoding ratio for three types of repeat sequences in the ASFV genome. B Comparison of the ratio of enhancers in the repeat and nonrepeat sequences in ASFV genomes. C Comparison of the ratio of promoters in repeat and nonrepeat sequences in ASFV genomes. “**”, p value < 0.01.

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  Figure 4. The characteristics of repeat sequences in coding regions. A The ratio of amino acids in repeat protein sequences versus nonrepeat protein sequences in ASFV strains. B The ratio of secondary structures in repeat protein sequences versus nonrepeat protein sequences. C The ratio of amino acids exposed in repeat protein sequences versus nonrepeat protein sequences. An exposed amino acid was defined as a residue with a relative solvent accessible surface area (rASA) greater than 0.25. D–F The ratio of disordered, penetrating peptides and antimicrobial peptides in repeat protein sequences versus nonrepeat protein sequences. For subfigures B to D, only nonredundant protein sequences were used. “*”, p value < 0.05; “**”, p value < 0.01.

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  Figure 5. Pan-repeat sequence analysis of ASFVs. A Flower plot showing the core repeat and dispensable repeat sequence clusters of the 86 ASFV strains. The diagram depicts the core repeat sequence cluster number (orange) and the dispensable repeat sequence cluster number (blue) for the 86 ASFV strains. The number of unique repeat sequences in each strain is shown beside the accession number of the ASFV genomes. For clarity, only the strains with unique repeat sequences are shown. B The relationship between genome number and dispensable repeat and core repeat sequence profiles. The black and blue curves refer to the least-squares fitting for the average number of dispensable repeat clusters and core repeat clusters versus the number of genomes, respectively. The mathematical functions and the R-squared values of both models are delineated on the graph.

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  Figure 6. Distribution of the CpG islands and repeat sequences in each genome. A The number of CpG islands per 10 kb in each ASFV genome. B The number of repeat sequences in a sliding window of 10 kb (with a step size of 1 kb) versus the number of CpG islands. C Comparison of the number of CpG islands in a sliding window of 10 kb (with a step size of 1 kb) with and without CpG islands in ASFV genomes. “**”, p value < 0.01.