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Tobamovirus evolution: gene overlaps, recombination, and taxonomic implications
R T Lartey1, T C Voss, U Melcher
1Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater 74078-3035, USA.
Molecular Biology and Evolution
|December 1, 1996
Summary
This study reveals three tobamovirus subgroups, supporting ancient codivergence with plants, but also shows evidence of rare host jumps and recombination events. Tobamovirus evolution is complex, involving both host-virus co-evolution and cross-family transmission.
Area of Science:
- Virology
- Molecular Evolution
- Phylogenetics
Background:
- Tobamoviruses, often found in solanaceous plants, may represent ancient virus lineages that have co-evolved with their hosts.
- Previous studies suggested tobamovirus diversity, but a comprehensive analysis of genomic sequences was needed to clarify their evolutionary relationships.
Purpose of the Study:
- To assess the tobamovirus codivergence hypothesis using newly available nucleotide sequences from nonsolanaceous tobamoviruses.
- To investigate the evolutionary relationships and potential subgroupings within the Tobamovirus genus.
- To explore the origins and evolutionary dynamics of tobamovirus genome organization, including protein-coding region overlaps.
Main Methods:
- Comparative analysis of complete and partial genomic sequences from 23 tobamoviruses.
- Prediction and comparison of protein sequences to identify evolutionary clusters.
- Phylogenetic analyses using nucleotide and amino acid sequences, including codon-position-dependent base composition analysis.
- Examination of open reading frame (ORF) overlaps and sequence similarities.
Main Results:
- Genomic sequence analysis identified three distinct tobamovirus subgroups, supporting the codivergence hypothesis and suggesting a third subgroup.
- Odontoglossum ringspot tobamovirus exhibits characteristics of a recombinant, with different genomic regions associating with distinct subgroups.
- Phylogenetic analyses suggest that codivergence was occasionally interrupted by host jumps between plant families.
- Subgroup 3 tobamoviruses may have originated from a recombination event involving movement and coat protein genes, with evidence suggesting an ancestral non-overlapping organization.
Conclusions:
- The study provides strong evidence for three tobamovirus subgroups and supports the hypothesis of ancient codivergence with their plant hosts.
- Recombination and host jumps represent significant factors in tobamovirus evolution, leading to genomic diversity and complex evolutionary histories.
- The ancestral state of tobamovirus genome organization likely involved minimal or no overlap between movement and coat protein ORFs.