Figure S1
Sequence organization between the two receptor kinase genes in T. urartu , T. monococcum , and
T. aestivum . The receptor kinase genes are indicated in boxes and their transcriptional directions indicated by arrows. The numbers in bp represent the start position for each receptor kinase genes in the sequenced region. Retroelements are boxed and their insertion positions indicated by either triangles or solid lines. The letter "p" following the names of retroelements stands for a partial element, indicating that the retroelement was truncated or not intact element, likely due to sequence deletion events. The intact Erika-2 from T. urartu and truncated Erika-2P from T. aestivum are colinear and both highlighted with yellow color. The receptor kinase 2 gene was disrupted by insertions of TEs as indicated.

Figure S2
Nested TE insertion structure in the region between the protein kinase and Gda-1 genes. Genes are presented by shaded boxes and their start positions in the sequenced regions indicated. In the
A a genome, the sequenced region ended before the Gda-1 gene, resulting in partial sequences of
WHAM-4 , Angela-3 , and Angela-2 elements as shown in the figure. The dashed line indicates the end point of the sequence. The nested TE insertion structure in T. aestivum was depicted based on the comparison with the A u
genome. The letter "p" following the names of retroelements stands for a partial element, indicating that the retroelement was truncated.

Figure S3
Nested TE insertion structure in the intergenic region between x- and y- type HMW glutenin genes. The x-type and y-type HMW-glutenin genes are represented by shaded boxes.
Retrotransposons are boxed and their insertion positions indicated with either a triangle or a solid vertical line. The letters "s" and "p" following the names of the retrotransposons indicate solo and partial, respectively. In this intergenic region, T. urartu and T. aestivum have shared nested
TE insertions except in the region where a deletion occurred only in the A u genome. Based on comparison with the T. aestivum A genome, putative TEs involved in the deletion in the A u genome are circled by a dashed line.

Table S1. Genotyping tetraploid wheat accessions with RJM20 and RJM4 markers
Accessions Species
RJM20
Haplotype
RJM4
Haplotype
PI254174
PI254177
PI254180
PI254181
PI254183
PI254185
PI352364
PI182743
PI254176
PI347230
PI60730
PI60732
PI60737
5109/887 YUGOSLAVIA
PI193881
PI384332
PI355507
CITR14866
PI57659
8600394 IRAN
8602218 IRAN
8611956 IRAN
8613400 IRAN
8610302 IRAN
8610576 IRAN
8600067 IRAN
5109/966 HUNGARY
5109/1867-1 USSR
IRAN 11956
SITE1-KAROUN SPIKE 13
SITE1-KAROUN SPIKE 14
QOWK (LOWER SITE) -43
SITE8 2KM BEFORE AIN ARAB -29
T. dicoccoides
T. dicoccoides
60 ITALIA CENTRACE T. dicoccum
*Triticum turgidum ssp. dicoccum Schrank.
**Triticum turgidum ssp. durum (Desf.) Husn.
***Triticum turgidum L. ssp. dicoccoides (Korn.) Thell.
T. dicoccum*
T. dicoccum
T. dicoccum
T. dicoccum
T. dicoccum
T. dicoccum
T. dicoccum
T. dicoccum
T. dicoccum
T. dicoccum
T. durum **
T. durum
T. durum
T. durum
T. dicoccum
T. dicoccum
T. dicoccum
T. dicoccum
T. durum
T. durum
T. durum
T. durum
T. durum
T. durum
T. durum
T. durum
T. durum
T. durum
T. durum
T. dicoccoides***
T. dicoccoides
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H1
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H2
H1
H1
H1
H2
H2
H2
H1
H1
H1
H1
H1
H1
H1
H1
H1
H1
H1
H2
H2
H2
H2
H2
H2
H2
H2
H2