Complete genome sequence of a novel badnavirus infecting Fatsia japonica in China.

The complete genome sequence of a novel badnavirus, tentatively named "fatsia badnavirus 1" (FaBV1, OM540428), was identified in Fatsia japonica. The infected plant displayed virus-like symptoms on leaves, including yellowing and chlorosis. The genome of FaBV1 is 7313 bp in length and similar in size and organization to other members of the genus Badnavirus (family Caulimoviridae), containing four open reading frames (ORFs), three of which are found in all known badnaviruses, and the other of which is only present in some badnaviruses. The virus has the genome characteristics of badnaviruses, including a tRNAMet binding site (5'-TCTGAATTTATAGCGCTA-3') and two cysteine-rich domains (C-X-C-2X-C-4X-H-4X-C and C-2X-C-11X-C-2X-C-4X-C-2X-C). Pairwise sequence comparisons of the RT+RNase H region indicated that FaBV1 shares 61.4-71.2% nucleotide (nt) sequence identity with other known badnaviruses, which is below the threshold (80% nt sequence identity in the RT+RNase H region) used for species demarcation in the genus Badnavirus. Phylogenetic analysis revealed that FaBV1, ivy ringspot-associated virus (IRSaV, MN850490.1), and cacao mild mosaic virus (CMMV, KX276640.1) together form a separate clade within the genus Badnavirus, suggesting that FaBV1 is a new member of the genus Badnavirus in the family Caulimoviridae. To our knowledge, this is the first report of a badnavirus infecting F. japonica.

Complete genome sequence analysis of Valeriana jatamansi tymovirus 1: a novel member of the genus Tymovirus infecting Valeriana jatamansi Jones.

A new positive-sense, single-stranded RNA virus, tentatively named "Valeriana jatamansi tymovirus 1" (VaJV1, OQ730267), was isolated from Valeriana jatamansi Jones displaying symptoms of vein-clearing in Yunnan Province, China. The complete genome of VaJV1 consists of 6,215 nucleotides and contains three open reading frames (ORFs). The genome structure of VaJV1 is typical of members of the genus Tymovirus. BLASTn analysis and multiple sequence alignments showed that the complete genome and coat protein of VaJV1 shared the most sequence similarity (65.5% nucleotides and 50.5% amino acid sequence identity) with an isolate of the tymovirus okra mosaic virus (NC_009532). Phylogenetic analysis confirmed that VaJV1 clustered most closely with other tymoviruses. We propose that Valeriana jatamansi tymovirus 1 represents a new species within the genus Tymovirus.

Complete genome sequence of a novel fusarivirus from the phytopathogenic fungus Fusarium sp.

Fusarium diseases include wilts, blights, rots, and cankers of many horticultural, field, ornamental, and forest crops in both agricultural and natural ecosystems, and they significantly hinder food plant production. Here, we describe a novel mycovirus, tentatively designated as "Fusarium fusarivirus 1" (FuFV1), which was discovered in an isolate of the phytopathogenic fungus Fusarium sp. FuFV1 has a positive-sense single-stranded RNA (+ssRNA) genome of 6,391 nucleotides (nt) containing three open reading frames (ORFs). ORF1 encodes a large polypeptide of 1,501 amino acids (aa) with conserved RNA-dependent RNA polymerase (RdRp) and helicase (Hel) domains. ORF2, overlapping ORF1 by 122 nucleotides, encodes a polypeptide with a conserved Smc domain. The third and smaller ORF (ORF3) encodes a polypeptide with an unknown function. BLASTp analysis of the ORF1-encoded polypeptide revealed that FuFV1 shares the highest aa sequence similarity (68.5% identity, E-value 0.0) with Fusarium poae fusarivirus 1 (FpFV1, genus Alphafusarivirus). Phylogenetic analysis of the RdRp and helicase (Hel) sequences indicated that FuFV1 clustered closely with FpFV1 in a separate branch within the clade containing members of the genus Alphafusarivirus. Based on these results, we propose that FuFV1 should be considered a novel mycovirus belonging to the genus Alphafusarivirus of the family Fusariviridae.

Complete genome sequence analysis of a novel citlodavirus isolated from the leaves of Myrica rubra in Yunnan.

Through high-throughput sequencing, a novel citlodavirus, tentatively named "Myrica rubra citlodavirus 1" (MRV1, accession no. OP374189), was isolated from the leaves of Myrica rubra in Yunnan exhibiting narrow deformity of leaf tips, shrinkage, and chlorosis along the veins. The complete genome sequence was determined and analyzed using cloning and Sanger sequencing. MRV1 is a single-stranded circular non-enveloped DNA virus with a genome size of 3775 nucleotides and contains six open reading frames (ORFs). The virion-sense genome strand encodes a coat protein (CP, nt 750-1,493, 247 aa), two hypothetical movement proteins (V3, nt 382-666, 94 aa; and V2, nt 461-895, 144 aa), and one movement protein (MP, nt 1,527-2,438, 303 aa). The complementary strand of the genome encodes two replication proteins (RepA, nt 3,712-2,834, 292 aa; Rep, nt 2,867-2,553, 104 aa). The MRV1 genome contains the stem-loop motif 5'-TAATATTAC-3', which is a highly conserved nonanucleotide motif found in the origin of virion-strand replication in geminiviruses. Genome sequence alignment analysis showed that citrus chlorotic dwarf associated virus (CCDaV, accession no. JQ920490) shared the highest nucleotide sequence similarity (66.10% identity) with MRV1. Phylogenetic analysis showed that CCDaV is the closest known relative of MRV1, and that these viruses clustered in a single branch within a clade consisting of citlodaviruses. These results indicate that MRV1 should be regarded as a new species of the genus Citlodavirus in the family Geminiviridae.