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The sequencing of the complete genome of a Tomato black ring virus (TBRV) and of the RNA2 of three Grapevine chrome mosaic virus (GCMV) isolates from grapevine reveals the possible recombinant origin of GCMV

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Abstract

The complete genome of a Tomato black ring virus isolate (TBRV-Mirs) (RNA1, 7,366 nt and RNA2, 4,640 nt) and the RNA2 sequences (4,437; 4,445; and 4,442 nts) of three Grapevine chrome mosaic virus isolates (GCMV-H6, -H15, and -H27) were determined. All RNAs contained a single open reading frame encoding polyproteins of 254 kDa (p1) and 149 kDa (p2) for TBRV-Mirs RNA1 and RNA2, respectively, and 146 kDa for GCMV RNA2. p1 of TBRV-Mirs showed the highest identity with TBRV-MJ (94 %), Beet ringspot virus (BRSV, 82 %), and Grapevine Anatolian ringspot virus (GARSV, 66 %), while p2 showed the highest identity with TBRV isolates MJ (89 %) and ED (85 %), followed by BRSV (65 %), GCMV (58 %), and GARSV (57 %). The amino acid identity of RNA2 sequences of four GCMV isolates (three from this study and one from GenBank) ranged from 91 to 98 %, the homing protein being the most variable. The RDP3 program predicted putative intra-species recombination events for GCMV-H6 and recognized GCMV as a putative inter-species recombinant between GARSV and TBRV. In both cases, the recombination events were at the movement protein level.

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Authors and Affiliations

  1. Istituto Agronomico Mediterraneo di Bari, Via Ceglie 9, 70010, Valenzano, Bari, Italy

    M. Digiaro, E. Yahyaoui & T. Elbeaino

  2. Università degli Studi di Bari “Aldo Moro”, Via Amendola 165/A, 70126, Bari, Italy

    G. P. Martelli

Authors
  1. M. Digiaro
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  2. E. Yahyaoui
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  3. G. P. Martelli
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  4. T. Elbeaino
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Corresponding author

Correspondence to T. Elbeaino.

Electronic supplementary material

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11262_2014_1094_MOESM1_ESM.docx

Supplementary Table 1 Amino acid identity matrix of RNA1- and RNA2-encoded polyproteins (p1 and p2) of subgroup B nepoviruses. Supplementary Table 2 Amino acids identity of each single GCMV RNA2 domain (2AHP, 2BMP and 2CCP) with the homologous domain of other nepoviruses of subgroup B. Supplementary material 1 (DOCX 22 kb)

11262_2014_1094_MOESM2_ESM.docx

Supplementary Fig. 1 Recombination analyses of grapevines nepoviruses of subgroup B using RDP3. (A) Prediction of intra-specific recombination in GCMV-H6 having GCMV (NC_003621) and GCMV-H27 as parents. (B) Prediction of inter-specific recombination in GCMV-H6 having GARSV and TBRV-Mirs as parents. The highlighted windows represent the crossover region indicated for recombination sites. RDP3-implemented methods for recombination sites analyses: R (RDP), G (GENECONV), B (BOOTSCAN), M (MAXCHI), C (CHIMAERA), 3Seq (3s) and S (SISCAN). Supplementary material 2 (DOCX 30 kb)

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Digiaro, M., Yahyaoui, E., Martelli, G.P. et al. The sequencing of the complete genome of a Tomato black ring virus (TBRV) and of the RNA2 of three Grapevine chrome mosaic virus (GCMV) isolates from grapevine reveals the possible recombinant origin of GCMV. Virus Genes 50, 165–171 (2015). https://doi.org/10.1007/s11262-014-1094-4

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