Evolutionary history of Cucumber mosaic virus deduced by phylogenetic analyses

Abstract

Cucumber mosaic virus (CMV) is an RNA plant virus with a tripartite genome and an extremely broad host range. Previous evolutionary analyses with the coat protein (CP) and 5' nontranslated region (NTR) of RNA 3 suggested subdivision of the virus into three groups, subgroups IA, IB, and II. In this study 15 strains of CMV whose nucleotide sequences have been determined were used for a complete phylogenetic analysis of the virus. The trees estimated for open reading frames (ORFs) located on the different RNAs were not congruent and did not completely support the subgrouping indicated by the CP ORF, indicating that different RNAs had independent evolutionary histories. This is consistent with a reassortment mechanism playing an important role in the evolution of the virus. The evolutionary trees of the 1a and 3a ORFs were more compact and displayed more branching than did those of the 2a and CP ORFs. This may reflect more rigid host-interactive constraints exerted on the 1a and 3a ORFs. In addition, analysis of the 3' NTR that is conserved among all RNAs indicated that evolutionary constraints on this region are specific to the RNA component rather than the virus isolate. This indicates that functions other than replication are encoded in the 3' NTR. Reassortment may have led to the genetic diversity found among CMV strains and contributed to its enormous evolutionary success.

FIG. 1.

Genome organization of CMV. Nucleotide (nt) numbers and the sizes for encoded proteins are given for the Fny strain. K, kilodalton.

FIG. 2.

Phylogenetic analysis of the CP ORF, with aligned nucleotide sequences. Strains designated in green are from subgroup II, strains designated in blue are from subgroup IB, and strains designated in red are from subgroup IA. Bootstrap percentage values are shown below the branches, and distance, in number of nucleotide (nt) changes, is shown above the branch lines.

FIG. 3.

Phylogenetic analysis of the 3a ORF, with aligned nucleotide sequences. Strains designated in green are from subgroup II, strains designated in blue are from subgroup IB, and strains designated in red are from subgroup IA. Bootstrap percentage values are shown below the branches, and the distance, shown in number of nucleotide (nt) changes, is shown above the branch lines.

FIG. 4.

Phylogenetic analysis of the 2a ORF, with aligned nucleotide sequences. Strains designated in green are from subgroup II, strains designated in blue are from subgroup IB, and strains designated in red are from subgroup IA. Bootstrap percentage values are shown below the branches, and the distance, in number of nucleotide (nt) changes, is above below the branch lines.

FIG. 5.

Phylogenetic analysis of the 2b ORF, with aligned nucleotide sequences (A) and aligned amino acid sequences (B). Strains designated in green are from subgroup II, strains designated in blue are from subgroup IB, and strains designated in red are from subgroup IA. Bootstrap percentage values are shown below the branches, and the distance, in number of nucleotide (nt) or amino acid (aa) changes, is shown above the branch lines.

FIG. 6.

Phylogenetic analysis of the 1a ORF, with aligned nucleotide sequences. Strains designated in green are from subgroup II, strains designated in blue are from subgroup IB, and strains designated in red are from subgroup IA. Bootstrap percentage values are shown below the branches, and the distance, in number of nucleotide (nt) changes, is shown above the branch lines.

FIG. 7.

Phylogenetic analysis of the 3′ NTR, with aligned nucleotide sequences. RNAs designated in blue are from RNA 1, RNAs designated in green are from RNA 2, and RNAs designated in red are from RNA 3. Bootstrap percentage values are shown below the branches, and distance, in number of nucleotide (nt) changes, is shown above the branch lines.