Tobamovirus evolution: gene overlaps, recombination, and taxonomic implications

Abstract

Tobamoviruses, mostly isolated from solanaceous plants, may represent ancient virus lineages that have codiverged with their hosts. Recently completed nucleotide sequences of six nonsolanaceous tobamoviruses allowed assessment of the codivergence hypothesis and support a third subgroup within tobamoviruses. The genomic sequences of 12 tobamoviruses and the partial sequences of 11 others have been analyzed. Comparisons of the predicted protein sequences revealed three clusters of tobamoviruses, corresponding to those infecting solanaceous species (subgroup 1), those infecting cucurbits and legumes (subgroup 2), and those infecting crucifers. The orchid-infecting odontoglossum ringspot tobamovirus was associated with subgroup 1 genomes by its coat and movement protein sequences, but with the crucifer-pathogenic tobamoviruses by the remainder of its genome, suggesting that it is the progeny of a recombinant. For four of five genomic regions, subgroup 1 and 3 genomes were equidistant from a subgroup 2 genome chosen for comparison, suggesting uniform rates of evolution. A phylogenetic tree of plant families based on the tobamoviruses they harbor was congruent with that based on rubisco sequences but had a different root, suggesting that codivergence was tempered by rare events of viruses of one family colonizing another family. The proposed subgroup 3 viruses probably have an origin of virion assembly in the movement protein gene, a large (25-codon) overlap of movement and coat protein open reading frames, and a comparably shorter genome. Codon-position-dependent base compositions and codon prevalences suggested that the coat protein frame of the overlap region was ancestral. Bootstrapped parsimony analysis of the nucleotides in the overlap region and of the sequences translated from the -1 frame (the subgroup 3 movement protein frame) of this region produced trees inconsistent with those deduced from other regions. The results are consistent with a model in which a no or short overlap organization was ancestral. Despite encoding of subgroup 2 and 3 movement protein C-termini by nonhomologous nucleotides, weak similarities between their amino acid sequences suggested convergent sequence evolution.

Phylogenetic analysis of Tomato mosaic virus from Hemerocallis sp. and Impatiens hawkeri

“…1A). Three main tobamovirus groups have been proposed based on genomic location of their origin of virion assembly, structure of the junction between movement protein and CP open reading frames, phylogenetic position, and botanical family of the hosts (17,2). The hosts of subgroup I are mainly solanaceous, those of subgroup II are cucurbits and legumes, and those of subgroup III are cruciferous.…”

History of the Emergence and Spatiotemporal Spread of Tobacco Mosaic Virus in China

“…This genus currently holds 37 viral species (ICTV; http://www.ictvonline.org/ virustaxonomy.asp). Infection of tobacco and other crops by TMV, greatly diminishes crop yields, financial returns, and threatens farmer livelihoods throughout China [4].…”

“…Tobacco mosaic virus (TMV) infects more than 350 plant species within nine plant families of nutritional, economic, horticultural and ornamental importance [4][5][6]. Here, weeds and members of the Solanaceae (e.g.…”

“…Surveys conducted in China and Turkey have shown that, the risk of MD outbreaks occurring elevates with an increase in TMV reservoirs [1,8]. Mosaic disease (MD) symptoms include, leaf necrosis, curling, malformations, mosaic patterns, stunted growth, and loss of apical dominance which leads to poor flower and fruit development [4,5]. The spread of TMV may be reduced through increased use of pathogen free plantlets or cuttings, biological pesticides, scouting, rouging, disinfecting tools, benches and surfaces from the greenhouse to the field [5,14].…”

Caracterización molecular y desarrollo de métodos de diagnóstico del género Fabavirus Evaluación de BTH como método de control

“…Closterovirus (Rubio et al, 2001a;Vives et al, 2005), Luteovirus (Guyader & Ducray, 2002;Hauser et al, 2002), Nepovirus (Legall et al, 1995;Vigne et al, 2004;Vigne et al, 2005), Ophiovirus (Martín et al, 2006), Potyvirus (Bousalem et al, 2000;Moreno et al, 2004;Desbiez & Lecoq, 2004;Tan et al, 2004;Glasa et al, 2005;Zhong et al, 2005;Lorenzen et al, 2006a;Lorenzen et al, 2006b), Tobamovirus (Lartey et al, 1996) y Tobravirus (Robinson, 1994;Swanson & MacFarlane, 1999). También se han detectado fenómenos de recombinación entre especies virales (White & Morris, 1995;Monci et al, 2002;Lefeuvre et al, 2007;García-Arenal & Fraile, 2008).…”