Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes
Figure 5
Negative-strand RNA virus-related sequences (RNLSs) from plant nuclear genomes.
(A) Genome organization of a varicosavirus, lettuce big-vein associated virus (LBVaV) [67] and a cytorhabdovirus, lettuce necrotic yellows virus (LNYV) [68]. While LBVaV and LNYV have a bipartite and a monopartite genome architecture, respectively, both viruses share similarities in terminal sequence features such as leader sequences (le) and trailer sequence (tr), genome expression strategy and sequences in encoded proteins (e.g., CP vs. N and L vs. L). (B) Schematic representation of RNLSs and their flanking regions. RNLS found in the genome sequence database of B. rapa (BrRNLS1) is shown to match that of CP from LBVaV. Another RNLS from N. tabacum (NtRNLS2) showed the greatest similarity to the LNYV-N protein. (C, E) Genomic PCR analysis of RNLS1 and RNLS2. Template genomic DNAs from plant species shown on the top of the gel were used to amplify RNLS1 (C, top panel), RNLS2 (E, top panel) or ribosomal RNA ITS regions (C and E, bottom panels). Primer pairs, RN1a-1 and RN1a-2, RN2-1 and RN2-2, and ITS-F and ITS-R were used to amplify RNLS1, RNLS2, and the ITS regions, respectively. Amplified DNA fragments were electrophoresed in 1.0% agarose gel in TAE. (D, F) Southern blot analyses of plant species in different families. The same DNA preparations as for Figure 1 were used for detection of RNLS1 (D) and RNLS2 (F) in which DIG-labeled DNA fragments spanning BrRNLS1, NtRNLS2, and N. tabacum ITS served as probes, respectively. See Figure 3C for hybridization with a B. rapa ITS DNA probe.