Transposon insertion sequence from the GmMER3 gene was amplified by conducting long-range PCR and compared to both Tgm9 and Tgmt*, the two highly similar transposons characterized from soybean. A) The orientation of the Tgm9 insertion in the MER3 gene and primers used for nested PCR and sequencing are shown. B) First PCR product was amplified using primers 1 and 2. The amplified PCR product was 2,823 bp. C) The nested PCR product was amplified using primers 3 and 4. The amplified PCR product was 2,758 bp. Primer 3 was used for sequencing the PCR product represented by the dashed line X. Primer 4 was used to sequence the PCR product and produced sequence represented by the dashed line Y. D) Sequence from primer 3 matched the MER3 gene and the start of the 5’ end of the Tgm9 transposon sequence shown with the red font. E) Sequence from primer 4 aligned to the Tgm9 and Tgmt*. The PCR product matches the Tgm9 sequence perfectly. Polymorphic nucleotides between the insertion sequence and Tgmt* sequence are shown in red font.