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Genetic variation of eggplant mottled dwarf virus from annual and perennial plant hosts

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Abstract

The genetic diversity of eggplant mottled dwarf virus (EMDV), a member of the family Rhabdoviridae, was studied using isolates collected from different herbaceous and woody plant species and remote geographic areas. Sequences corresponding to the N, X, P, Y, M and G ORFs as well as the untranslated regions (UTRs) between ORFs were determined from all isolates. Low genetic diversity was found in almost all genomic regions studied except for the X ORF and the UTRs, which were more variable, while interestingly, an EMDV isolate from caper possessed a truncated G gene sequence. Furthermore, low d N /d S ratios, indicative of purifying selection, were calculated for all genes. Phylogenetic analysis showed that the EMDV isolates clustered in three distinct subgroups based on their geographical origin, with the exception of one subgroup that consisted of isolates from northern Greece and Cyprus. Overall, the level of genetic diversity of EMDV differed between seed- and asexually propagated plants in our collection, and this could be related to the mode of transmission.

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Acknowledgements

The authors thank Prof. Benham E. L. Lockhart (Department of Plant Pathology, University of Minnesota, St. Paul, USA) and Dr. Lambros C. Papayiannis (Agricultural Research Institute, Nicosia, Cyprus) for kindly providing EMDV-specific antiserum and the EMDV-pt isolate, respectively.

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Authors and Affiliations

  1. Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54 124, Thessaloníki, Greece

    Polyxeni G. Pappi, Varvara I. Maliogka & Nikolaos I. Katis

  2. Department of Biochemistry and Biotechnology, University of Thessaly, 41 221, Larissa, Greece

    Gregory D. Amoutzias

Authors
  1. Polyxeni G. Pappi
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  2. Varvara I. Maliogka
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  3. Gregory D. Amoutzias
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  4. Nikolaos I. Katis
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Corresponding author

Correspondence to Varvara I. Maliogka.

Electronic supplementary material

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705_2015_2705_MOESM1_ESM.pdf

Fig. S1 Multiple nucleotide sequence alignment of a part of the G gene from the eight EMDV isolates, including the 275-nt deletion fragment of the EMDV-caps isolate from C. spinosa (PDF 341 kb)

705_2015_2705_MOESM2_ESM.pdf

Fig. S2 Gel electrophoresis of RT-PCR products amplified using the primers G do 1398 and G up read (5’-GGACGATCCTGAATGCACTTACTG-3’). Lane 1, EMDV-caps isolate with a 275-nt deletion in the G gene; lanes 2, 4, 5, 6, 9, 10, and 12, isolates from infected C. spinosa tested with no deletion; lane 13, isolate from infected C. spinosa in which the two EMDV variants coexist; lanes 3, 7, 8, and 11, healthy capers; lane LD: 100 bp DNA ladder (PDF 21 kb)

705_2015_2705_MOESM3_ESM.pdf

Fig. S3 Simplot analysis of the sequence spanning the 5’ end of the EMDV genome up to the 3’ end of the G ORF. The EMDV-pt isolate is used as a reference. The region corresponding to the 275-nt deletion was removed from all isolates before the analysis. The parameters used were a window size of 100 bp, a step size of 10 bp, and the Kimura 2-parameter model (PDF 42 kb)

705_2015_2705_MOESM4_ESM.pdf

Fig. S4 Phylogenetic analysis of the region where potential recombination was detected (nt 862 to 1080 of the G [glycoprotein] gene). The tree was constructed by the BIONJ method, using the Jukes-Cantor model of evolution and 500 bootstrap replicates (PDF 14 kb)

Supplementary material 5 (DOC 39 kb)

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Pappi, P.G., Maliogka, V.I., Amoutzias, G.D. et al. Genetic variation of eggplant mottled dwarf virus from annual and perennial plant hosts. Arch Virol 161, 631–639 (2016). https://doi.org/10.1007/s00705-015-2705-7

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  • DOI: https://doi.org/10.1007/s00705-015-2705-7

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