Gene 5 TE Gene 3 Gene Body N2743

Gene 5’ TE Gene 3’ Gene Body N=2743 N=478 ** TE N=486 TE *** 5’ & 3’ N=298 TE 0 2 4 6 Log 2(FPKM+1) Log 2(FPKAM+1) Supplemental Figure S 1 Supplemental Figure S 2 8

Identification of parental and translocated copy based on collinearity Gene translocation WGD Translocated Parental P. vulgaris G. max Tandem Duplication Identification of parental and translocated copy based on collinearity Gene translocation P. vulgaris G. max Parental P. vulgaris G. max Identification of parental and translocated copy based on collinearity Single Gene Duplication P. vulgaris Translocated G. max Translocated Parental P. vulgaris G. max Large scale duplication Gene relocation after duplication Small scale duplication Gene relocation by duplication Supplemental Figure S 3

A CG CHH RNA-seq parental Glyma 01 g 02480 translocated CG CHH RNA-seq Parental C *** Translocated tal ted ren loca Pa ns Tra 0 1 2 3 4 5 Log(FPKM+1) Translocated D lo ns Tra l nta re Pa Parental Translocated Parental ted ca *** B Glyma 11 g 25890 TE 0 10 20 Exons Numbers Supplemental Figure S 4 30

copy ated sloc copy Tran ntal Pare I /Ks >1 II Ka =1 /Ks Ka <1 /Ks Ka 40% 60% 74% 62% 60% 40% 26% 38% Supplemental Figure S 5 III I IV I I II II IV II I III IV III IV IV IV

CG CHH D G. soja RNA-seq 40 TE in G. soja Ambiguous G. max 50 G. max Glyma 04 g 35060 G. soja TE soy. B_108056. 1 CG CHH G. soja RNA-seq G. max B CG CHH 232 G. soja RNA-seq A Shared TE G. Soja specific m. C genes Total number of specific m. C genes per category G. max TE G. soja TE G. max Glyma 01 g 24990 soy. B_77331. 4 E G. max CG CHH G. soja RNA-seq 0 C Supplemental Figure S 6 1 2 3 Log 2(FPKM+1) 4 5

A G. max-specific m. C genes (N=185) B Supplemental Figure S 7 G. soja-specific m. C genes (N=323)