44 D (3 Khipu elements) 14 12 Phaseolus vulgaris B4 locus 410 Kb contig 158 kb Sub- cluster C 400 Kb 300 Kb 250 Kb 200 Kb 150 Kb 100 Kb 50 Kb 28 21 15 16 33 27 26 29 25 1 2 3 4 11 13 17 18 19 20 23 31 30 35 36 32 34 40 38 41 39 37 42 43 45 46 47 48 49 50 A (8 Khipu elements) B (3 Khipu elements) C (29 Khipu elements) E (3 Khipu elements) F (5 Khipu elements) G (6 Khipu elements) H (22 tandem repeats) At3g01490 protein kinase At5g40270 metal-dependent phosphohydrolase  Unknown protein At1g63930 Calcium homeostasis regulator-like protein CHoR1  Basic blue protein Hypothetical protein AY341443 Formate dehydrogenase  MtN24  Formate dehydrogenase  Farnesyl transferase  Basic blue protein Formate dehydrogenase  At3g21600 unknown protein.  Quinone oxidoreductase-like protein  Quinone oxidoreductase like protein  Carboxylic ester hydrolase  Kinesin light chain-like protein  L- Aspartate oxidase  Expressed protein similar to At3g27930  Serine type peptidase  Carbonic anhydrase 2  Expressed protein similar to At3g27880  CNL-B12 CNL-B13 CNL-B14 CNL-B15 CNL-B16 CNL-B17 CNL-B18 ATPase, E1-E2 type  NADH dehydrogenase CNL-B8 CNL-B3 CNL-B5 CNL-B4 CLN-B2 CNL-B1 CNL-B6 CNL-B7 CNL-B9 CNL-B10 CNL-B11 9Quinone oxidoreductase like protein 1At3g01490 protein kinase 3At5g27990 unknown protein 24AT5g14720 protein kinase family 10Quinone oxidoreductase like protein 8MtN24 7Farnesyl transferase 5Formate dehydrogenase 4Calcium homeostasis regulator-like protein CHoR1 2At5g40270 metal-dependant phosphohydrolase 6Formate dehydrogenase 11Quinone oxidoreductase like protein 12Quinone oxidoreductase like protein 13Quinone oxidoreductase like protein 14Kinesin light chain-like protein 15Carboxylic ester hydrolase 17At3g 27930 Unknown protein 18Serine type peptidase 19Carbonic anhydrase 2 20Expressed protein similar to At3g27880 21ATPase 8 22CNL_Gm19 23ATPase Gm chr 19 703,347-861,494 bp 2 At5g40270 metal-dependant phospho hydrolase 4 Calcium homeostasis regulator-like protein Gm chr 13 27,096,894-27,149,916 bp 1At3g01490 protein kinase 3 Hypothetical protein At5g27990 5 Formate dehydrogenase 6 Farnesyl transferase Gm chr 5 8,372,893-8,464,947 bp 7 MtN24 92 kb 350 Kb Sub- cluster B 16L-Aspartate oxidase Chr 5 ~42 Mb Chr 13 ~44 Mb Chr 19 ~50 Mb 53 kb 2 Kinesin light chain-like protein 1Quinone oxydoreductase-like protein 3 Carboxylic ester hydrolase 4 L-Aspartate oxidase 6 Serine type peptidase 7 Carbonic anhydrase 8 Expressed protein similar to At3g27880 9 CNL_Gm5 5 Expressed protein similar to At3g27930 10 ATPase, E1-E2 type CC-NBS-LRR (CNL) Retrotransposon Other gene Truncated gene Khipu tandem repeat F-box [ ] : number BLASP (1 e -5) hits in the Arabidopsis thaliana genome Soybean chromosome Soybean pericentromeric region Soybean centromere David_ Supplemental Figure S3 Supplemental Figure S3. Sequence comparison between the Phaseolus vulgaris BAT93 B4-410 kb contig (central position) and syntenic regions identified on the 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.http://www.phytozome.net/soybean.php
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