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Characterisation of siRNAs derived from new isolates of bamboo mosaic virus and their associated satellites in infected ma bamboo (Dendrocalamus latiflorus)

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Abstract

We characterised the virus-derived small interfering RNAs (vsiRNA) of bamboo mosaic virus (Ba-vsiRNAs) and its associated satellite RNA (satRNA)-derived siRNAs (satsiRNAs) in a bamboo plant (Dendrocalamus latiflorus) by deep sequencing. Ba-vsiRNAs and satsiRNAs of 21–22 nt in length, with both (+) and (-) polarity, predominated. The 5′-terminal base of Ba-vsiRNA was biased towards A, whereas a bias towards C/U was observed in sense satsiRNAs, and towards A in antisense satsiRNAs. A large set of bamboo genes were identified as potential targets of Ba-vsiRNAs and satsiRNAs, revealing RNA silencing-based virus-host interactions in plants. Moreover, we isolated and characterised new isolates of bamboo mosaic virus (BaMV; 6,350 nt) and BaMV-associated satRNA (satBaMV; 834 nt), designated BaMV-MAZSL1 and satBaMV-MAZSL1, respectively.

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Authors and Affiliations

  1. Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Wenwu Lin, Wenkai Yan, Wenting Yang, Chaowei Yu, Huihuang Chen, Wen Zhang, Zujian Wu, Liang Yang & Lianhui Xie

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  1. Wenwu Lin
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  2. Wenkai Yan
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Correspondence to Liang Yang or Lianhui Xie.

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Funding

This work was supported by grants from Natural Science Foundation of Fujian Province of China (Grant No. 2014J06011), Education Department of Fujian Province Office Program (Grant No. JA13092), FAFU Science Fund for Distinguished Young Scholars (Grant No. xjq201402) and the China Scholarship Council (CSC No. 201608350081).

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All authors declare that they have no conflict of interest.

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This article does not contain any studies with human participants.

Electronic supplementary material

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705_2016_3092_MOESM1_ESM.pdf

Fig. S1. Maximum-likelihood (ML) tree constructed from the complete genomes of nine BaMV isolates (A) and 70 satBaMV isolates (B). ML topology was evaluated with 1,000 bootstrap replicates. For each node, the ML bootstrap percentages (BPs >70) are given on the branches. A foxtail mosaic virus isolate (NC_001483) served as an outgroup (PDF 928 kb)

Fig. S2. The origins of the 21–24 nt Ba-vsiRNAs (A) and satsiRNAs (B) along the genomic RNAs (PDF 947 kb)

705_2016_3092_MOESM3_ESM.pdf

Fig. S3 Analysis of the nucleotide percentages in the genomes of BaMV-MAZSL1 and satBaMV-MAZSL1, indicating strong preferences of 5′-terminal nucleotides of Ba-vsiRNAs and satsiRNAs (sense and antisense). (A) % of A. (B) % of C. (C) % of G. (D) % of U (PDF 443 kb)

705_2016_3092_MOESM4_ESM.docx

Table S1. Percentage identities of the genomic regions of BaMV-MAZSL1 and satBaMV-MAZSL1 (amino acids in parentheses) to other BaMV isolates (A) and selected satBaMV (B) isolates deposited in GenBank (DOCX 17 kb)

Table S2. The predicted target genes of vsiRNAs and satsRNAs (XLSX 849 kb)

Table S3. Hotspots of vsiRNAs and satsiRNAs (XLSX 13 kb)

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Lin, W., Yan, W., Yang, W. et al. Characterisation of siRNAs derived from new isolates of bamboo mosaic virus and their associated satellites in infected ma bamboo (Dendrocalamus latiflorus). Arch Virol 162, 505–510 (2017). https://doi.org/10.1007/s00705-016-3092-4

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