Figure 1.
Schematic TARE1 and the LTR sequence comparison.
(A) Structural annotation for the TARE1 element. The U3, R and U5 regions of LTR (Long terminal repeat) are shown in gray boxes; ‘TSD’ indicates the 5-bp target site duplication; ‘PBS’ means the primer binding site; ‘PPT’ indicates the polypurine tract; int, rt and rh are the abbreviations for integrase, reverse transcriptase and RNAase-H, respectively. (B) The sequence alignment of two LTRs from a randomly selected intact TARE1 element. The identical nucleotides are shown with gray shadow. The insertions/deletions are marked by dots. The physical positions of this element are located at Chromosome 1 from 27235875 to 27240535.
Table 1.
Structure of LTR Retrotransposons identified in tomato.
Figure 2.
The distribution of TARE1 elements along 12 tomato chromosomes.
Each chromosome is represented by a vertical blue box. The insertions and the total repetitive DNA are marked by circles and purple regions, respectively. The potential centromeric regions are indicated by a black blur in the middle [16].
Figure 3.
Timing and activities of TARE1 amplification in tomato.
Figure 4.
Phylogenetic tree based on the nucleotide sequences from a conserved copia-like RT domain.
The RT sequences from tomato, rice, soybean and Arabidopsis were aligned using the MUSCLE program, and then the tree was reconstructed using the MEGA 5 program (see Materials and Methods). For a better visualization, only the elements from tomato TARE1, TGRE1, and TARE2 families, and exemplars from other species are shown.
Figure 5.
Phylogenetical relationship and sequence similarity between TGRE1, TARE2, and TARE1.
The phylogenetically closest family TGRE2 was set as an outgroup. The physical positions of each representative element are located at chromosome 1 from 27235875 to 27240535 for TARE1, chromosome 7 from 61990209 to 61994987 for TARE2, chromosome 5 from 23621836 to 23626419 for TGRE1, and chromosome 11 from 7616310 to 7621220 for TGRE2, respectively.
Figure 6.
A model for the evolution and amplification of TARE1.
The horizontal arrows flanking the elements indicate the target site duplications (TSDs). The black line within the U3 of LTR indicates the mutation from ‘G’ to ‘A’.