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 Aa 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 Au 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 Au genome. Based on comparison with the T. aestivum Agenome, putative TEs involved in the deletion in the Au 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 / T. dicoccum* / H1 / H2
PI254177 / T. dicoccum / H1 / H2
PI254180 / T. dicoccum / H1 / H2
PI254181 / T. dicoccum / H1 / H2
PI254183 / T. dicoccum / H1 / H2
PI254185 / T. dicoccum / H1 / H2
PI352364 / T. dicoccum / H1 / H2
PI182743 / T. dicoccum / H1 / H2
PI254176 / T. dicoccum / H1 / H2
PI347230 / T. dicoccum / H1 / H2
PI60730 / T. durum ** / H1 / H2
PI60732 / T. durum / H1 / H2
PI60737 / T. durum / H1 / H2
5109/887 YUGOSLAVIA / T. durum / H1 / H2
PI193881 / T. dicoccum / H2 / H2
PI384332 / T. dicoccum / H2 / H2
PI355507 / T. dicoccum / H2 / H2
CITR14866 / T. dicoccum / H2 / H2
PI57659 / T. durum / H2 / H2
8600394 IRAN / T. durum / H2 / H2
8602218 IRAN / T. durum / H2 / H2
8611956 IRAN / T. durum / H2 / H2
8613400 IRAN / T. durum / H2 / H2
8610302 IRAN / T. durum / H2 / H2
8610576 IRAN / T. durum / H2 / H2
8600067 IRAN / T. durum / H2 / H2
5109/966 HUNGARY / T. durum / H2 / H1
5109/1867-1 USSR / T. durum / H2 / H2
IRAN 11956 / T. durum / H2 / H2
SITE1-KAROUN SPIKE 13 / T. dicoccoides*** / H2 / H2
SITE1-KAROUN SPIKE 14 / T. dicoccoides / H2 / H2
QOWK (LOWER SITE) -43 / T. dicoccoides / H2 / H2
SITE8 2KM BEFORE AIN ARAB -29 / T. dicoccoides / H2 / H2
60 ITALIA CENTRACE / T. dicoccum / H2 / H2

*Triticum turgidum ssp. dicoccumSchrank.

**Triticum turgidum ssp. durum (Desf.) Husn.

***Triticum turgidum L. ssp. dicoccoides (Korn.) Thell.