A novel strain of Beet western yellows virus infecting sugar beet with two distinct genotypes differing in the 5′-terminal half of genome

Abstract

The complete genomic sequences of two distinct Beet western yellows virus (BWYV) genotypes infecting sugar beet in Beijing, named as BWYV-BJ(A) and BWYV-BJ(B) (GenBank accession number HM804471, HM804472, respectively), were determined by RT-PCR sub-cloning approach. BWYV-BJ(A) and BWYV-BJ(B) were 5674 and 5626nt in length, respectively. BWYV-BJ(B) was 48nt shorter than BWYV-BJ(A) in the regions 1589-1615 and 1629-1649nt. Sequence alignment analysis showed that the full length of BWYV-BJ(A) and BWYV-BJ(B) shared 93% nucleotide sequence identity, with relatively high variability within ORFs 0, 1, 2 (at the nucleotide level was 86.3-88.8%) and high conservation within ORFs 3, 4, 5 (at the nucleotide level was 99.3-99.5%). The complete nucleotide sequences of BWYV-BJ(A) and BWYV-BJ(B) were most related to BWYV-US (80.6 and 79.0%, respectively). ORFs 1, 2 of BWYV-BJ(A) and BWYV-BJ(B) shared the highest homology with BWYV-US (nucleotide identity 91.2-93.3, 86.7-89.5%, respectively) and their ORFs 3, 4 were more closely related to BWYV-IM. However, their ORF5 were more closely related to that of Cucurbit aphid-borne yellows virus China strain (CABYV-CHN), with 68.1 and 68.5% nucleotide identity, respectively. Based on the sequence and phylogenetic analysis, we proposed that BWYV-BJ was at least a novel strain of BWYV, and BWYV-BJ(A), BWYV-BJ(B) were two distinct genotypes of BWYV-BJ. In addition, phylogenetic analysis and recombination analysis suggested that BWYV-BJ(A) and BWYV-BJ(B) might be recombinant viruses.

Host range and molecular analysis of Beet leaf yellowing virus, Beet western yellows virus‐JP and Brassica yellows virus in Japan

“…However, those viruses showed much lower levels of sequence identity (56–68%) with the BrYV group, which had much higher identity (90%) within isolates. As an exception, P5 sequences of BrYV‐CS and BWYV‐BJA (and BWYV‐BJB) have low levels of identity (41–42%) with BrYV and BWYV (Zhou et al ., ; Lim et al ., ), which were excluded from the P5 tree.…”

“…For BWYV‐JP, nucleotide sequences of two spinach isolates (S14 and S19) were 98.7% identical, but varied slightly from the radish isolate R3a (96.8% identity) (Table S3). They were found to share higher nucleotide sequence identity (96.7%) to a Korean BWYV isolate (LS‐DY) that was detected from motherwort ( Leonurus sibiricus ) (Kwon et al ., ), and to Chinese BWYV isolates BJA and BJB from sugar beet (Zhou et al ., ), with the exception of the region of ORF5. Lengths of the nucleotide sequences were 5700 nt for S14 and S19, 5744 nt for R3a, 5670 nt for LS‐DY, 5674 nt for BJA and 5626 nt for BJB (Table S3).…”

“…It should be noted in particular that, within the P5 domain, whereas the N‐terminal region is highly conserved, the C‐terminal region, which has a role for facilitating long‐distance virus movement in phloem tissue, is more variable (Peter et al ., ). Indeed, it is of interest that P5‐recombinant viruses such as BWYV‐BJA and ‐BJB from sugar beet (Zhou et al ., ), BrYV‐CS from Chinese cabbage (Lim et al ., ) and BrYV‐NtabQJ from tobacco (Wang et al ., ) that were generated by recombination events within the P5 domain, have been reported in Asia. Further work will be needed to clarify to what extent the sequences of the P5 C‐terminal region have a role in host range determination (host adaptation) of poleroviruses in nature.…”

Development of Beet necrotic yellow vein virus‐based vectors for multiple‐gene expression and guide RNA delivery in plant genome editing

“…Thus, development of BNYVV‐based vectors will facilitate genomics research in sugar beets and related plants that are susceptible to BNYVV. To date, the reported plant viruses infecting sugar beet plants include BNYVV, BSBMV, Beet western yellows virus (Zhou et al ., ), Beet yellows virus (Vinogradova et al ., ), Beet mosaic virus (Glasa et al ., ) and Beet curly top virus (Bach and Jeske, ). Nonetheless, previous reports of BNYVV gene expression vectors have only used in B. macrocarpa , C. quinoa and N. benthamiana, but not B. vulgaris (Delbianco et al ., ; Schmidlin et al ., ).…”

A Multiyear Survey and Identification of Pepper- and Tomato-Infecting Viruses in Yunnan Province, China

“…The membrane was incubated for 30 min in 10 ml PBST buffer (0.01 M PBS containing 0.05% Tween-20, pH 7.4) supplemented with 5% skim milk powder and then probed with a diluted monoclonal antibody for 1 h at 37 • C. (Li et al, 2008a). Degenerated and specific primers for polymerase chain reaction (PCR) or reverse transcription (RT)-PCR were as reported (Ha et al, 2006(Ha et al, , 2008Hirota et al, 2010;Zhou et al, 2011;Zhang et al, 2017b;Li et al, 2018aLi et al, ,b,c, 2020Liu et al, 2019) or made in this study ( Supplementary Table 1). First-strand cDNA was synthesized using the Reverse Transcriptase M-MLV (RNase H − ) Kit (TaKaRa Biotech, Dalian, China).…”