Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes
Figure 1
ILR2 (PCLS1) homologs from members of the family Brassicaceae.
(A) Schematic representation of RnPV2 CP-related ILR2 genes from Arabidopsis-related species. Green boxes refer to the coding regions of ILR2 homologs, while orange and blue thick arrows indicate those of cellular genes. Ar. thaliana Col-0, No-0, C24 and Shokei have long versions of ILR2, while those of the other Ar. thaliana ecotypes and Ar. lyrata have large deletions at the 5′-terminal portion. ILR2 homologs of Arabidopsis and closely related genera reside on the orthologous position. These plant homologs were most closely related to the CP gene of a fungal partitivirus, RnPV2. Symbols referring to mutations are shown at the bottom: waved line, major deletion; dashed line, undetermined sequence; open triangle, nucleotide insertion; filled triangle, small deletion (<30 nt); asterisk, internal stop codon; F, frame-shift; filled diamond, transcription start site; open diamond, poly(A) addition site. These symbols were utilized in this and subsequent figures. (B) Genomic PCR analysis of ILR2. The top and middle panels show amplification patterns with two primer sets (PC-1 and PC-2; PC-1 and At-1R). Primer positions and sequences are shown in Figure 1A and Table S3. A primer set, At-IRS-FW (ITS-F) and At-IRS-RV (ITS-R) [66], was used for amplification of the complete ribosomal internal transcribed spacer (ITS) regions 1 and 2 including the 5.8S rDNA. (C) Southern blotting of plant species in different families. Ten microgram of Eco RI-digested genomic DNA (per lane), except for that from Ar. thaliana Col-0 (2.5 µg/lane), was probed with a DIG-labeled ILR2 (top panel) or ITS DNA fragment (bottom panel) derived from Ar. thaliana Col-0. (D) Genomic PCR analysis of the ILR2-flanking region. PCR fragments were amplified by a primer set (At-1F and At-1R) on ILR2-carrying genomic DNAs from Ar. thaliana, Ar. lyrata, Cap. bursa-pastoris, and O. korshinskyi, and ILR2-non-carrying DNAs from Cru. lasiocarpa, Sis. irio, and B. rapa.