Prevalence of Reversed Genome Organizations for Viruses in the Family Iflaviridae , Order Picornavirales

Figures

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  FIG 1. Genome structure and read coverage of Ischnura senegalensis iflavirus 1 (A) and Ischnura senegalensis iflavirus 2 (B). Positions of the designed primer sets were shown beneath the genome structures of each virus. Abbreviations: rhv, picornaviruslike capsid domain; CRPV, cricket paralysis virus capsid superfamily domain; Hel, viral helicase domain; Pro, 3-chymotrypsin-like protease; RdRp, RNA dependent RNA polymerase domain.

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  FIG 2. Profiles of virus-derived small interfering RNAs (vsiRNAs) of Ischnura senegalensis iflavirus 1 (IsIV1) and Ischnura senegalensis iflavirus 2 (IsIV2). The size distribution of IsIV1 and IsIV2 derived siRNAs (non-redundant reads) (A) and (D). Distribution of IsIV1 and IsIV2 derived siRNA across the viral genome (B) and (E). 5′ terminal nucleotide preference of siRNAs derived from IsIV1 and IsIV2 (C) and (F). Red represents siRNAs derived from the viral sense genomic strand (Plus), and black represents small RNAs derived from the viral antisense genomic strand (Minus). All the virus-derived siRNAs used for this analysis are redundant (total siRNAs).

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  FIG 3. Genome structure analysis of picornaviruses with canonical and non-canonical genome types. (A) Genome organization of iflaviruses with canonical (TypeI) and non-canonical (TypeII) genome types. (B) Genome organization of secoviruses with canonical (TypeI) and non-canonical (TypeII) genome types. (C) Genome organization of dicistroviruses with canonical (TypeII) and non-canonical (TypeI and TypeII-1) genome types. Structural proteins and nonstructural proteins are shown with green and blue box, respectively. The pink, blue, and green boxes (dotted line) represent TypeI, TypeII, and TypeII-1 genome organizations, respectively.

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  FIG 4. Maximum likelihood phylogenetic tree of picornaviruses in the families of Iflaviridae, Secoviridae, and Dicistrovidae constructed based on the deduced RNA dependent RNA polymerase (A) and coat protein (B) domain. Bootstrap values are shown at each node of the tree. Scale bars represent percent divergence. Two iflaviruses identified in this study are indicated with red bold font. The pink, blue, and green boxes (dotted line) represent TypeI, TypeII, and TypeII-1 genome organizations, respectively.