D (3 Khipu elements)

1. Phaseolus vulgaris B4 locus 410 Kb contig 10 7 6 4 9 3 2 8 5 L-Aspartate oxidase Carboxylic ester hydrolase Carbonic anhydrase Expressed protein similar to At3g27880 ATPase, E1-E2 type At5g40270 metal-dependant phospho hydrolase Serine type peptidase Expressed protein similar to At3g27930 CNL_Gm5 Kinesin light chain-like protein [6] Carboxylic ester hydrolase [102] L- Aspartate oxidase [3] Expressed protein similar to At3g27930 [1] Serine type peptidase [13] Carbonic anhydrase 2 [6] Expressed protein similar to At3g27880 [7] CC-NBS-LRR (CNL) Retrotransposon Other gene F-box Khipu tandem repeat Truncated gene [ ] : number BLASP (1e-5) hits in the Arabidopsis thaliana genome Soybean chromosome Soybean centromere Soybean pericentromeric region David_SupplementalFigure S3 1 At3g01490 protein kinase 2 At5g40270 metal-dependent phosphohydrolase [2] 3 Unknown protein At1g63930 Gm chr 13 27,096,894-27,149,916 bp Calcium homeostasis regulator-like protein CHoR1 [1] 4 Gm chr 19 703,347-861,494 bp Chr 13 ~44 Mb 50 Kb 11 CNL-B1 12 CLN-B2 13 CNL-B3 14 CNL-B4 15 CNL-B5 16 CNL-B6 Sub-cluster C 100 Kb CNL-B7 17 Chr 19 ~50 Mb 1 At3g01490 protein kinase 18 CNL-B8 1 At3g01490 protein kinase A (8 Khipu elements) 3 Hypothetical protein At5g27990 2 At5g40270 metal-dependant phosphohydrolase B (3 Khipu elements) 4 3 At5g27990 unknown protein Calcium homeostasis regulator-like protein 19 CNL-B9 53 kb 4 Calcium homeostasis regulator-like protein CHoR1 20 CNL-B10 5 Formate dehydrogenase 5 Formate dehydrogenase 150 Kb CNL-B11 21 6 Formate dehydrogenase 6 Farnesyl transferase 7 Farnesyl transferase 7 MtN24 8 MtN24 23 NADH dehydrogenase 9 Quinone oxidoreductase like protein C (29 Khipu elements) D (3 Khipu elements) 10 Quinone oxidoreductase like protein 11 Quinone oxidoreductase like protein 12 Quinone oxidoreductase like protein 25 Hypothetical protein AY341443 26 Basic blue protein 13 Quinone oxidoreductase like protein 27 Basic blue protein 200 Kb Formate dehydrogenase [9] 28 Formate dehydrogenase [9] 29 14 Kinesin light chain-like protein 158 kb Formate dehydrogenase [9] 30 15 Carboxylic ester hydrolase Farnesyl transferase [4] 31 16 L-Aspartate oxidase 17 At3g 27930 Unknown protein MtN24 [7] 32 Gm chr 5 8,372,893-8,464,947 bp 33 At3g21600 unknown protein. [6] 18 Serine type peptidase Quinone oxidoreductase like protein [21] 34 35 Quinone oxidoreductase-like protein [21] 19 Carbonic anhydrase 2 250 Kb 36 20 Expressed protein similar to At3g27880 Chr 5 ~42 Mb 37 21 ATPase 8 38 22 CNL_Gm19 39 23 ATPase 40 24 AT5g14720 protein kinase family 41 1 Quinone oxydoreductase-like protein E (3 Khipu elements) 300 Kb 42 2 Kinesin light chain-like protein 43 CNL-B12 F (5 Khipu elements) 44 CNL-B13 45 CNL-B14 350 Kb Sub-cluster B 92 kb 46 CNL-B15 47 CNL-B16 CNL-B17 48 G (6 Khipu elements) H (22 tandem repeats) 400 Kb CNL-B18 49 50 ATPase, E1-E2 type [21] Supplemental Figure S3.Sequence comparison between the Phaseolus vulgaris BAT93 B4-410 kb contig (central position) and syntenic regions identified onthe Glycine max genome (assembly version 1.01) (http://soybase.org/gbrowse/cgi-bin/gbrowse/gmax1.01/). Two homoeologous regions syntenic with the Pv B4 locus have been identified: the Gm H1 (homeologous 1) Pv B4 syntenic region (left of the scheme) and the Gm H2 (homeologous 2) Pv B4 syntenic region (right of the scheme). The Gm H1 Pv B4 syntenic region is located on the chromosome 19 (coordinates 703,347-861,494 bp) and the Gm H2 Pv B4 syntenic region is divided on chromosome 13 (coordinates 27,096,894-27,149,916 bp) and chromosome 5 (coordinates 8,372,893-8,464,947 bp). The location of Gm H1 and H2 Pv B4 syntenic regions according soybean chromosomes (1.01 assembly) is indicated by black dotted lines. Genes 10 and 11 of Gm chr5, are separated by 2 Mb according to the 1.01 version of soybean genome, but by only 1.7 kb in the 7 X Whole Genome Shotgun (WGS) (http://www.phytozome.net/soybean.php). Due to some uncertainties suspected in the 1.01 assembly in this region of Gm chr 5 (Steven Cannon, unpublished data), we have represented an intergenic region of 1.7 kb between genes 10 and 11 (7X WGS information). Yellow lines indicate significant homology matches between predicted genes. Blue lines indicate significant homology matches between CNL genes. The scheme is represented to scale.