Piper DNA virus 1 and 2 are endogenous pararetroviruses integrated into chromosomes of black pepper (Piper nigrum L)

Abstract

A previous study named 7178 and 892 bp contigs obtained through high-throughput sequencing (HTS) of black pepper as Piper DNA virus 1 (PDV-1) and PDV-2 respectively. In the present study, HTS results were confirmed through polymerase chain reaction and Sanger sequencing. The sequenced region of both PDV-1 and PDV-2 contained partial genomes with motifs characteristic of pararetroviruses. BLAST analysis of PDV-1 and PDV-2 against the whole genome sequence of the black pepper showed integration of the PDV-1 at 22 loci in chromosome number 14, and PDV-2 at two loci in chromosome number 12 of black pepper. The integration was confirmed through amplification and sequencing of the junction regions. The present study suggests that both PDV-1 and PDV-2 occur as endogenous viruses in black pepper. Further studies are needed to determine whether these endogenous viruses occur in episomal forms, their complete genome sequence and whether they are activable under abiotic stress conditions.

Supplementary information: The online version contains supplementary material available at 10.1007/s13337-021-00752-w.

Keywords: Caulimoviridae; Integrated virus; PCR; Sequencing; Tungrovirus.

Figure 1

Agarose gel electrophoresis of PCR products obtained with different primer pairs used for the amplification of Piper DNA virus 1 and Piper DNA virus 2 in black pepper. Lane M: Molecular size marker; Lanes 1-9: PCR products obtained with primer pairs, 297–495; 496–497; 422–423; 424–425; 498–499; 171–172, 500–501; 430–431 and 173–174 respectively. Details of the primer sequence and their location are provided in Supplementary Table 1 and Supplementary Fig. 1

Figure 2

Phylogenetic tree generated using Mega 6 with maximum likelihood method based on the multiple sequence alignment of conserved amino acid sequence in the reverse transcriptase protein (corresponding to L₂₆₉ to R₆₇₂ of cauliflower mosaic virus, NP_0567728; Geering et al. 2010) of Piper DNA virus 1 (PDV-1) with other recognized species of the family, Caulimoviridae. Details of the virus isolates, their acronym, and GenBank accession number are provided in Supplementary Table 2. Bootstrap values are shown at the nodes

Figure 3

Schematic map showing the integration of Piper DNA virus 1 (PDV-1) in chromosome number 14 of black pepper. Integration in sense and antisense orientations are shown above and below the horizontal line respectively. The numbers on the horizontal line indicate the nucleotide position in chromosome 14 in megabase. The lengths of the integrated sequences at different loci are not represented in the scale (readers may refer to Supplementary Table 4 for details of the integration at each locus including length of the PDV-1 sequence integrated)