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Evolutionary liberties of the Abutilon mosaic virus cluster

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Abstract

Two new strains of Abutilon mosaic virus (AbMV; Geminiviridae) from Germany (Stuttgart) and France (Paris) have been characterized by circomics, direct pyrosequencing of rolling circle amplification (RCA) products, as well as conventional cloning and Sanger sequencing. RCA combined with an analysis of restriction fragment length polymorphisms confirmed the completeness of the sequence determination and a close relationship of both isolates for DNA A with 99 % nucleotide sequence identity. Phylogenetic tree reconstruction supported their clustering with other AbMV strains in a clade with Middle American begomoviruses, whereas South American begomoviruses that infect Abutilon or Sida micrantha are less closely related. Comparing the coat protein (CP) genes of the AbMV cluster, with those of related Middle and South American begomoviruses revealed a remarkable overrepresentation for non-synonymous nucleotide exchanges for certain amino acid positions in the AbMV cluster. Projection of these positions to a structural model of the African cassava mosaic virus CP yielded a non-random distribution at the periphery and, most importantly, highlighted those amino acids that had been identified in whitefly-transmission experiments before. These results establish the basis for an analysis of the evolutionary liberty of certain amino acid positions of the CP, and their impact on the deciphering of insect transmission determinants is discussed.

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Acknowledgments

The authors are grateful to Prof. C. Wege, Drs. P. Wyant and K. Hipp for critical comments on the manuscript and providing leaf samples, to B. Schäfer and S. Kober for excellent technical assistance, and to D. Gotthardt for taking care of the plants. The advices in botanical taxonomy of Profs. P. D. Cantino, Ohio, and J. G. Rohwer, Hamburg, were very helpful. This work was supported by a trilateral ERA-PG/BMBF Project (BMBF 0313986).

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  1. Björn Krenz

    Present address: Department Biologie, Lehrstuhl für Biochemie, Staudtstr. 5, 91058, Erlangen, Germany

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  1. Institut für Biomaterialien und biomolekulare Systeme, Abteilung für Molekularbiologie und Virologie der Pflanzen, Universität Stuttgart, Pfaffenwaldring 57, 70550, Stuttgart, Germany

    Alexander Fischer, Stephan Strohmeier, Björn Krenz & Holger Jeske

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Correspondence to Holger Jeske.

Electronic supplementary material

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11262_2014_1125_MOESM1_ESM.pptx

Supplementary material 1 Spreadsheet calculations to determine the fit between expected and observed fragments of the gels shown in Fig. 1 b, c, d, respectively. The logarithmic values of the molecular weights are plotted against migration distances transformed to Rf value probits as described previously [28].(PPTX 77 kb)

11262_2014_1125_MOESM2_ESM.xlsx

Supplementary material 2 Suppl. Table 1: Pairwise comparison of nucleotide sequence identities (SI) for AbMV DNA A and DNA B components after aligning using codaln algorithm. The values for AbMV D(S) and F(P) are highlighted.Suppl. Table 2: List of DNA A sequences compared to those of AbMV with accession numbers, long names and countries of collection as far as they can be retrieved from the data base entries.Suppl. Table 3: List of DNA B sequences compared to those of AbMV with accession numbers, long names and countries of collection as far as they can be retrieved from the data base entries.Suppl. Table 4: List of DNA A sequences of South American Abutilon-infecting and Sida micrantha mosaic viruses used for CP ORF comparisons, with accession numbers, long names and countries of collection as far as they can be retrieved from the data base entries.(XLSX 26 kb)

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Fischer, A., Strohmeier, S., Krenz, B. et al. Evolutionary liberties of the Abutilon mosaic virus cluster. Virus Genes 50, 63–70 (2015). https://doi.org/10.1007/s11262-014-1125-1

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