Abstract
Banana streak virus (BSV) is the causal agent of the most prevalent diseases in banana and causes serious economic losses to banana production worldwide. To examine variability in BSV, 65 isolates were obtained from 99 samples collected from Guangdong, Hainan, Guangxi and Yunnan provinces in South China. The 65 BSV isolates shared 62.8–97.8% nt identity over the RT/RNase H regions when compared to eight BSV species with published complete genomes. Sequence and phylogenetic analyses based on the RT/RNase H region indicated that there was great genetic diversity among BSV isolates in South China, and some isolates belonged to species of badnavirus that had never before been reported in China, including banana streak OL virus (BSOLV) (DN6–2), banana streak IM virus (BSIMV) (DN1–7 and DN5–1), and banana streak VN virus (BSVNV) (YLJ-8). The full genomes of two isolates (DN5–1and DN5–4) were cloned and sequenced. The genetic characteristics of both isolates were very close to those of typical badnaviruses. Based on percentage nucleotide sequence identity and phylogenetic relationships, DN5–1 was categorized as BSIMV. Interestingly, while DN5–4 was similar to both sugarcane bacilliform viruses (SCBVs) and BSVs based on sequence identities of the RT/RNase H region, analysis of its complete sequence and genome organization revealed that it can be further classified as sugarcane bacilliform Guadeloupe A virus-2 (SCBGAV-2). To our knowledge, this is the first report of natural infection of banana by SCBGAV-2 in China. In addition, our results suggest that considering the complete genomic sequence rather than the RT/RNase H region alone is important when classifying badnavirus isolates.
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The study was supported part by Special Fund of China for Agro-scientific Research in the Public Interest (Grant No. 201203076–07) and National Key R&D Program of China (Grant No.2019YFD1001800).
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LHP designed the study and revised the manuscript. RXQ analyzed the data and wrote the draft of the manuscript. WZL analyzed the data. ZL, WW and SJ performed the experiments. All authors read and approved the final manuscript.
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Fig. S1
Unrooted tree indicating the species identified in Fig. 1 grouped into two groups according to the criterion of nucleotide sequence identities of greater than 72% based on the BSV RT/RNase H region. Details of the viruses are provided in Table S1. CYMV (citrus yellow mosaic badnavirus), CSSV (cacao swollen shoot virus), DBV (dioscorea bacilliform virus), ComYMV (commelina yellow mottle virus), SCBV (sugarcane bacilliform virus), and TaBV (taro bacilliform virus) are used as the outgroups. (PNG 3639 kb)
Fig. S2
The phylogeny tree was established with the nucleotide sequences (A) and amino acid (B) sequences of ORF 2 of DN5–1 and DN5–4 isolates from China. The trees were constructed using the neighbor-joining method. The numbers at the nodes indicate bootstrap support (1000 replicates). Details of the viruses are given in Table S1. KTSV (kalanchoe top-spotting virus), ComYMV (commelina yellow mottle virus), TaBV (taro bacilliform virus), BCVBV (bougainvillea chlorotic vein banding virus), DBSNV (dracaena bacilliform SN virus), CYMV (citrus yellow mosaic virus), CSSV (cacao swollen shoot virus), and RTBV (rice tungro bacilliform virus) are used as the outgroups. (PNG 223 kb)
Fig. S3
Phylogenetic analysis of the nucleotide sequences (A) and amino acid (B) sequences of ORF 3 of DN5–1 and DN5–4 isolates from China. The trees were constructed using the neighbor-joining method. The numbers at the nodes indicate bootstrap support (1000 replicates). Details of the viruses are given in Table S1. KTSV (kalanchoe top-spotting virus), ComYMV (commelina yellow mottle virus), TaBV (taro bacilliform virus), BCVBV (bougainvillea chlorotic vein banding virus), DBSNV (dracaena bacilliform SN virus), CYMV (citrus yellow mosaic virus), CSSV (cacao swollen shoot virus), and RTBV (rice tungro bacilliform virus) are used as the outgroups. (PNG 259 kb)
Table S1
Badnaviruses obtained from GenBank. (DOC 66 kb)
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Rao, XQ., Wu, ZL., Wang, W. et al. Genetic diversity analysis reveals new badnaviruses infecting banana in South China. J Plant Pathol 102, 1065–1075 (2020). https://doi.org/10.1007/s42161-020-00646-8
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DOI: https://doi.org/10.1007/s42161-020-00646-8