Genetic Diversity and Characterization of Circular Replication (Rep)-Encoding Single-Stranded (CRESS) DNA Viruses

Figures

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  FIG 1. CLANS analysis-based classification of CRESS-DNA virus Rep protein. (A) Representative CRESS-DNA virus Rep protein sequences were clustered using CLANS Toolkit by their pairwise sequence similarity network. A total of 1,160 amino acid sequences of Rep protein (Supplemental Data 1) of CRESS-DNA viruses were used in this analysis. Classification of clusters was carried out by a network-based method using offset values and global average with maximum rounds 10,000 in CLANS Toolkit analysis. The P value of ≤1e−02 was used to show the lines connecting the sequences. (B) Phylogenetic relationship of Rep protein of CRESS-DNA viruses. The maximum-likelihood method inferred the evolutionary history using the Subtree-Pruning-Regrafting algorithm in PhyML 3.3_1. A total of 1,509 amino acid sequences of Rep protein (Supplemental Data 5) of CRESS-DNA viruses were used in this analysis.

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  FIG 2. Sequence similarities (CLANS) analysis-based CRESS-DNA virus capsid protein clustering. (A) A total of 1,823 amino acid sequences of Cap protein of CRESS-DNA viruses (Supplemental Data 6) were used and classified by their pairwise sequence similarity network using CLANS. The clusters were classified using the network-based method using offset values and global average with a maximum of 10,000 in CLANS Toolkit analysis. The P value of ≤1e−05 was used to show the lines connecting the sequences. (B) Pairwise sequence similarity based on CRESS-DNA virus capsid protein and +RNA viruses relationship. Representative CRESS-DNA virus capsid protein sequences and their relationship with RNA viruses using CLANS Toolkit. A total of 1,967 amino acid sequences of Cap protein of CRESS-DNA viruses and +RNA viruses were used in this analysis (Supplemental Data 8). The clusters were classified using the network-based method using offset values and global average with a maximum of 10,000 in CLANS Toolkit analysis. The P value of ≤1e−02 was used to show the lines connecting the sequences.

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  FIG 3. Phylogenetic relationship of CRESS-DNA virus Cap protein superclusters. (A) Phylogenetic tree depicting the genetic relationship between the CRESS-DNA virus Cap protein supercluster formed by the clusters C1, C14, and C17. The details of sequences in each cluster (Supplemental Data 7) and alignment are provided in Supplemental Data 10. (B) The phylogenetic tree depicting the genetic relationship between the CRESS-DNA virus Cap protein supercluster created by the clusters C2, C7, C8, C11, C12, C15, and C18. The details of sequences in each cluster (Supplemental Data 7) and alignment are provided in Supplemental Data 11. The maximum-likelihood method inferred the evolutionary history using the Subtree-Pruning-Regrafting algorithm and bootstrap values in PhyML 3.3_1.

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  FIG 4. Host codon usage selection pressure on Rep gene of CRESS-DNA virus evolution. (A) Representing the A, T, G, and C fraction; (B) representing the ENc values; (C) representing the codon usage fraction and RSCU values; (D) representing ENc plotted against GC3s; (E) neutrality plot analysis of the GC12 and that of the GC3; and (F) parity rule 2 (PR2)-bias plot. (Total of 1,115 nucleotide sequences of Rep gene of CRESS-DNA viruses were used in this analysis.

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  FIG 5. Host codon usage selection pressure on Cap gene of CRESS-DNA virus evolution. (A) A, T, G, and C fraction; (B) ENc values; (C) codon usage fraction and RSCU values; (D) ENc plotted against GC3s; (E) neutrality plot analysis of the GC12 and that of the GC3; and (F) parity rule 2 (PR2)-bias plot. (Total of 1,134 nucleotide sequences of Cap gene of CRESS-DNA viruses used in this analysis.)