Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes
Figure 7
Plant genome sequence related to positive-strand RNA virus.
(A) Chromosomal position of the flexivirus replicase-like sequence (FRLS) found in the cucumber ‘Chinese long’ inbred line 9930 and the genome structure of a positive-sense RNA virus, citrus leaf blotch virus (CLBV) [39]. A sequence related to the 5′ terminal half of the CLBV genome (CsFRLS1) is detected in scaffold 507. Genes for small potential ORFs (Cucsa 038520 and 038540) reside near CsFRLS1 as well as a retrotransposon-like sequence (shown by thick black lines). Three short sequences identical to CsFRLS1 are found in the GSS database (NCBI) from a different cucumber line, ‘Borszczagowski’ B10 (http://csgenome.sggw.pl/) (shown by dashed bars above CsFRLS1 in red). Functional domains of the CLBV replicase polyprotein are indicated in ocher: Met, methyltransferase; AlkB, Fe(II)/2OG-dependent dioxygenase superfamily domain; peptidase; Hel, RNA helicase; RdRp, RNA-dependent RNA polymerase. (B) Detection of CsFRLS1 from cucumber line by genomic PCR. See Materials and Methods for DNA isolation and PCR reaction. Template genomic DNA was prepared from the cucumber cultivar ‘Borszczagowski’ line B10 (top panel) and Citrullus lanatus (watermelon) (bottom panel). Primers (FR1-1 to FR1-6, FR1-6*, CS-1F, and CS-1R) used are shown on the top of the panel. The positions of the primers are shown by arrows below CsFRLS1 in A, except primer pairs used for amplification of the ITS region (ITS-F and ITS-R) (Table S3). (C) Phylogenetic analysis of CsFRLS1. CsFRLS1 and corresponding amino acid sequences from plant flexiviruses including members of the genera Citrivirus, Carlavirus, Foveavirus, Vitivirus, Capillovirus, Trichovirus and Potexvirus, were aligned using MAFFT program (Figure S6). The alignment was then utilized to generate a phylogram. Numbers at the branches show aLRT values using an SH-like calculation (only values greater than 0.5 are shown).