Abstract
A novel citrus viroid was discovered in a non-symptomatic Lisbon lemon (Citrus x limon L. Burm.f.) tree in New South Wales, Australia. Bioindexing, molecular detection and characterization involving sequencing combined with in silico analysis for the identification of the viroid-RNA hallmark properties of transmissibility and autonomous replication as well as specific sequence and structural motifs suggest that this viroid is a member of a new species in the genus Apscaviroid, family Pospiviroidae, which we have tentatively named “citrus viroid VII” (CVd-VII).
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Acknowledgements
The authors would like to gratefully thank Noora Siddiqi for assistance with creating the viroid structure figure (University of California, Riverside), and Allise Fail (NSW Department of Primary Industries) for nursery maintenance. The financial support of Auscitrus and the USDA National Institute of Food and Agriculture, Hatch project 233744, is acknowledged.
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705_2017_3591_MOESM1_ESM.doc
Fig. S1 Multiple sequence alignment of five CVd-VII variants with ASSVd reference sequence NC_001340 and AGVd (FJ746829) using ClustalW [15]. The alignment numbering is based on the sequence of the putative CVd-VII reference isolate LD4 (KX013551). The terminal conserved region (TCR) is outlined by a red box (CVd-VII nucleotides 10-25), the upper central conserved region (CVd-VII nucleotides 96-111) is outlined by a green box, and the lower central conserved region (CVd-VII nucleotides 259-275) is outlined by a blue box. Substitutions and deletions are relative to the CVd-VII reference isolate LD4. (DOC 72 kb)
705_2017_3591_MOESM2_ESM.docx
Fig. S2 a. Consensus phylogenetic tree (based on 10,000 bootstrap replicates) obtained for all members of the family Pospiviroidae [3] (RefSeq genome sequences from GenBank) and citrus viroid VII - LD4 variant (CVd-VII). b. The alignment to produce the above phylogenetic tree was performed using ClustalW using gap open gap extend costs of 15 and 1, respectively. Phylogenetic reconstruction was performed by the UPGMA method, and genetic distances were estimated according to the Jukes and Cantor model. Phylogenetic analyses were conducted with Geneious 9.1. (DOCX 1647 kb)
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Chambers, G.A., Donovan, N.J., Bodaghi, S. et al. A novel citrus viroid found in Australia, tentatively named citrus viroid VII. Arch Virol 163, 215–218 (2018). https://doi.org/10.1007/s00705-017-3591-y
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DOI: https://doi.org/10.1007/s00705-017-3591-y