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Molecular Evolution of the Genomic RNA of Apple Stem Grooving Capillovirus

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Abstract

The complete genome of the German isolate AC of Apple stem grooving virus (ASGV) was sequenced. It encodes two overlapping open reading frames (ORFs), similarly to previously described ASGV isolates. Two regions of high variability were detected between the ASGV isolates, variable region 1 (V1, from amino acids (aa) 532 to 570), and variable region 2 (V2, from aa 1,583 to 1,868). The phylogenetic analysis of the V1 and V2 regions suggested that the ASGV diversity was structured by host plant species rather than geographical origin. The dN/dS ratio between nonsynonymous and synonymous nucleotide substitution rates varied greatly along the ASGV genome. Most of ORF1 showed predominant negative selection except for the two regions V1 and V2. V1 showed an elevated dN and an average dS when compared to the ORF1 background but no significant positive selection was detected. The V2 region of ORF1 showed an elevated dN and a low dS when compared to the ORF1 background with an average dN/dS ≈ 3.0 indicative of positive selection. However, the V2 area includes overlapping ORFs, making the dN/dS estimate biased. Joint estimates of the selection intensity in the different ORFs by a recent method indicated that this region of ORF1 was in fact evolving close to neutrality. This was convergent with previous results showing that introduction of stop codons in this region of ORF1 did not impair plant infection. These data suggest that the elimination of a stop codon caused the overprinting of a novel coding region over the ancestral ORF.

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Acknowledgments

Annerie Liebenberg was supported by a grant from the Fonds für die Entwicklung ländlicher Räume in Rheinland-Pfalz (F.E.L.R.). We thank Dr. Fiona Constable, Department of Plant Science, Waite Campus, University of Adelaide, Glen Osmond, South Australia, 5064, Australia, Dr. Margit Laimer, Plant Biotechnology Unit, Institute of Applied Microbiology, University of agricultural sciences, Nussdorffer lande 11, 1190 Vienna, Dr. Mike Bernardy, Pacific Agri-Food Research Centre, Agriculture & Agri-Food Canada, Summerland, British Columbia V0H 1Z0, Dr. Pascal Gentit, Centre Technique Inter professionnel des Fruits et Légumes (CTIFL), 22 rue Bergère, 75009 Paris, France, and Michael Petruschke, Landwirtschaftliches Technologiezentrum Augustenberg—Außenstelle Stuttgart, Rötestrasse 16a, 70197 Stuttgart, Germany, for providing the different isolates of ASGV.

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Authors and Affiliations

  1. RLP Agroscience, AlPlanta—Institute for Plant Research, Breitenweg 71, 67435, Neustadt an der Weinstrasse, Germany

    A. Liebenberg, A. Kappis, W. Jarausch & T. Wetzel

  2. INRA, UR407 Pathologie Végétale, Domaine St Maurice, BP94, 84140, Montfavet, France

    B. Moury

  3. Institute of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland

    N. Sabath

  4. The Swiss Institute of Bioinformatics, Basel, Switzerland

    N. Sabath

  5. Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany

    A. Liebenberg & R. Hell

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  1. A. Liebenberg
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Correspondence to T. Wetzel.

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Liebenberg, A., Moury, B., Sabath, N. et al. Molecular Evolution of the Genomic RNA of Apple Stem Grooving Capillovirus. J Mol Evol 75, 92–101 (2012). https://doi.org/10.1007/s00239-012-9518-z

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  • DOI: https://doi.org/10.1007/s00239-012-9518-z

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