Fig 1.
Genome organization of Taro bacilliform CH virus (TaBCHV).
The putative ORFs of TaBCHV are indicated by rectangles, domains identified within ORF 3 are shown (A), contigs obtained from samples T1 (C1– C5) and T2 (C'1–C'9) are presented by black lines (A1), and fragments F1–F8 amplified from the first cycle of PCR (A2) and F'1–F'7 amplified from the second cycle of PCR (A3) are represented by arrows. The genome organization of Taro bacilliform virus (TaBV) (B) is outlined to show its difference with that of TaBCHV.
Table 1.
Comparison of the nucleotide of genomes and amino acid sequences of six ORFs of TaBCHV-2 with the corresponding sequences of TaBCHV-1 and other badnaviruses.
Fig 2.
Comparison of amino acid sequences of domains highly conserved in the polyproteins encoded by ORF3 of badnaviruses and a tungrovirus.
The virus names and the positions of starting amino acid are indicated before each sequence. Identical (*) and conserved (:) amino acids are marked.
Fig 3.
Neighbor-joining phylogenetic trees of badnaviruses generated from the full genomic sequences (A) and putative amino acid sequences of ORF3 (B).
The phylogenetic trees were rooted by using the genome sequence of Rice tungro bacilliform virus (RTBV) (A) and the polypeptide of RTBV (B). Branch lengths are proportional to genetic distances. Numbers at the nodes of the branches represent bootstrap values (1000 replicates).
Fig 4.
Size distribution of vsRNAs derived from TaBCHV-1 and TaBCHV-2 (A) and the relative frequency of 5' terminal nucleotide of 21- and 22-nt vsRNA (B).
Blue and red bars indicate sense and antisense vsRNAs respectively.
Fig 5.
The distribution of 21- and 22-nt vsRNAs on the genomes of TaBCHV-1 and TaBCHV-2.
The bars above the axis represent sense reads; those below represent antisense reads.
Fig 6.
The silencing hot spots of TaBCHV-1(A) and TaBCHV-2(B) genomes and the predicated secondary structure around the vsRNA at 6432 nt (C).
The start and stop positions of the vsRNA6432 are marked by bold arrows.