Genomes of Alphanucleorhabdovirus Physostegiae Isolates from Two Different Cultivar Groups of Solanum melongena

Abstract

Plant rhabdoviruses cause considerable economic losses and are a threat to the agriculture of Solanaceae plants. Two novel virus isolates belonging to the family Rhabdoviridae are identified by high-throughput sequencing (HTS) in Russian eggplant cultivars grown in the Volga river delta region for the first time. The phylogenetic inference of L protein (polymerase) shows that these virus isolates belong to Alphanucleorhabdovirus physostegia (Physostegia chlorotic mottle virus-PhCMoV), and their minus-sense RNA genomes have the typical gene order 3'-nucleocapsid (N)-X protein (X)-phosphoprotein (P)-Y protein (Y)-matrix protein (M)-glycoprotein (G)-polymerase (L)-5' observed in some plant-infecting alphanucleorhabdoviruses. One of the PhCMoV isolates from the eggplant cultivar Almaz is genetically very similar to the Russian PhCMoV isolate from tomato and grouped in a subclade together with four isolates from Belgium, Germany, the Netherlands, and France. However, another eggplant-infecting isolate from the Russian cultivar Boggart is the most divergent compared with the other 45 virus genomes of European PhCMoV isolates. Thus, our comparative analysis reveals that two virus isolates from Russia may either share a close evolutionary relationship with European isolates or significantly diverge from all known virus isolates. The potential to use the protein sequence comparative analysis of accessory polypeptides, along with the early developed strategy of the nucleotide sequence comparison of the RNA genomes, is shown.

Keywords: PhCMoV European isolates; Physostegia chlorotic mottle virus (PhCMoV); Russian PhCMoV isolates; high-throughput sequencing; nucleorhabdoviruses.

Figure 1

Pairwise identity matrix of the amino acid (A–F) and nucleotide (G) sequences in nucleorhabdovirus proteins and genomes: (A) RNA polymerase (L protein); (B) G protein; (C) M protein; (D) Y protein; (E) P protein; (F) nucleocapsid protein; (G) RNA genome sequences.

Figure 1

Pairwise identity matrix of the amino acid (A–F) and nucleotide (G) sequences in nucleorhabdovirus proteins and genomes: (A) RNA polymerase (L protein); (B) G protein; (C) M protein; (D) Y protein; (E) P protein; (F) nucleocapsid protein; (G) RNA genome sequences.

Figure 1

Pairwise identity matrix of the amino acid (A–F) and nucleotide (G) sequences in nucleorhabdovirus proteins and genomes: (A) RNA polymerase (L protein); (B) G protein; (C) M protein; (D) Y protein; (E) P protein; (F) nucleocapsid protein; (G) RNA genome sequences.

Figure 1

Pairwise identity matrix of the amino acid (A–F) and nucleotide (G) sequences in nucleorhabdovirus proteins and genomes: (A) RNA polymerase (L protein); (B) G protein; (C) M protein; (D) Y protein; (E) P protein; (F) nucleocapsid protein; (G) RNA genome sequences.

Figure 2

Genome organization in nucleorhabdovirus species. Accessory genes are colored blue (X protein). Hatches: P protein. Two novel isolates (RU31-Bog and RU32-Alm) are marked with orange stars.

Figure 3

The phylogenies of the 45 PhCMoV strains based on X protein sequences. Accession numbers, host species, and countries of isolation are shown. Russian isolates are shown in blue. The cluster of Slovenian strains is shown in yellow. Strains related to RU32-Alm are shown in pink. The scale bar indicates the number of substitutions per site. The green and light blue colors indicate sequence clusters including isolates from Western Europe.