The pepper virome: natural co-infection of diverse viruses and their quasispecies

Abstract

Background: The co-infection of diverse viruses in a host plant is common; however, little is known about viral populations and their quasispecies in the host.

Results: Here, we report the first pepper viromes that were co-infected by different types of viral genomes. The pepper viromes are dominated by geminivirus DNA-A followed by a novel carlavirus referred to as Pepper virus A. The two pepper cultivars share similar viral populations and replications. However, the quasispecies for double-stranded RNA virus and two satellite DNAs were heterogeneous and homogenous in susceptible and resistant cultivars, respectively, indicating the quasispecies of an individual virus depends on the host.

Conclusions: Taken together, we provide the first evidence that the host plant resistant to viruses has an unrevealed antiviral system, affecting viral quasispecies, not replication.

Keywords: Cultivar; Pepper; Plant virus; Quasispecies; Virome.

Fig. 1

Experimental scheme for the study of two pepper viromes. Transcriptomes from two different cultivars – Pusa Jwala (PJ) and Taiwan2 (TW) – were analyzed for the study of pepper viromes. Detailed data analyses are described in Methods

Fig. 2

Identification of viruses infecting two pepper cultivars using pepper transcriptome data. a Numbers of contigs in four different datasets that were de novo-assembled from two different libraries named PJ and TW by two different assemblers: Velvet and Trinity. b Numbers of virus-associated contigs in four different datasets. c Venn diagram displays the numbers of identified viruses in four different datasets. d Pie chart displays numbers of contigs assigned to respective virus identified from four different datasets. e Classification of identified viruses based on taxonomy using MEGAN program. Dark red and green colored bars indicate the amount of contigs associated with the assigned virus

Fig. 3

Assembly of a consensus viral genome sequence for four identified viruses. Assembly of consensus viral genome sequences for BPEV (a), ChiLCV DNA-A (b), PepLCVB (c), and CyVMVA (d). Contigs associated with corresponding virus were aligned using BWA and visualized by Tablet program. Black bar represents 1000 nucleotides. Green and orange colored lines and bars indicate contigs assembled by Velvet and Trinity, respectively. The numbers in the bar charts indicate lengths for the longest and shortest contigs, respectively. The genome organizations for four identified viruses were manually drawn based on the reference viral genome annotation. In case of BPEV, conserved domains were indicated. For circular DNA viruses, linear genome types were drawn with corresponding genes

Fig. 4

Identification of a novel virus referred to as PepVA. a Genome organization of newly identified PepVA, contigs associated with PepVA were aligned on the PepVA genome, and lengths of contigs associated with PepVA. Green and orange colored lines and bars indicate contigs assembled by Velvet and Trinity. b Phylogenetic relationships of ORF1 and ORF4 with respective other homologous viral proteins for PepVA

Fig. 5

Phylogenetic relationships of four identified viruses. Phylogenetic trees for BPEV (a), ChiLCV DNA-A (b), PepLCVB (c), and CYVMVA (d) were constructed by MEGA6 program. Consensus genome sequences obtained from PJ and TW cultivars as well as respective known genome sequences for individual virus were used for phylogenetic tree construction

Fig. 6

Analysis of single nucleotide variations for five identified viruses. Single nucleotide variations for BPEV (a), PepVA (b), ChiLCV DNA-A (c), PepLCVB (d), and CYVMVA (e) were identified by SAMtools and visualized by Tablet program. Genome organization for each virus was drawn based on respective reference sequence. Raw sequence data were mapped on the respective consensus viral genome sequences from PJ and TW, respectively. Red and blue bars indicate positions of identified single nucleotide variations on the viral genome

Fig. 7

Mutation rates of five viral genomes and viral populations. a Mutation rates for five viral genomes in PJ and TW cultivars. Numbers of sequence reads associated with respective identified viruses in PJ (b) and TW (c). Virus copy number for each identified virus in PJ (d) and TW (e)