D (3 Khipu elements)
1
44 D (3 Khipu elements) 14 12 Phaseolus vulgaris B4 locus 410 Kb contig 1 5 8 k b 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 [2] Unknown protein At1g63930 Calcium homeostasis regulator-like protein CHoR1 [1] Basic blue protein Hypothetical protein AY341443 Formate dehydrogenase [9] MtN24 [7] Formate dehydrogenase [9] Farnesyl transferase [4] Basic blue protein Formate dehydrogenase [9] At3g21600 unknown protein. [6] Quinone oxidoreductase-like protein [21] Quinone oxidoreductase like protein [21] Carboxylic ester hydrolase [102] Kinesin light chain-like protein [6] L- Aspartate oxidase [3] Expressed protein similar to At3g27930 [1] Serine type peptidase [13] Carbonic anhydrase 2 [6] Expressed protein similar to At3g27880 [7] CNL-B12 CNL-B13 CNL-B14 CNL-B15 CNL-B16 CNL-B17 CNL-B18 ATPase, E1-E2 type [21] NADH dehydrogenase CNL-B8 CNL-B3 CNL-B5 CNL-B4 CLN-B2 CNL-B1 CNL-B6 CNL-B7 CNL-B9 CNL-B10 CNL-B11 9 Quinone oxidoreductase like protein 1 At3g01490 protein kinase 3 At5g27990 unknown protein 24 AT5g14720 protein kinase family 10 Quinone oxidoreductase like protein 8 MtN24 7 Farnesyl transferase 5 Formate dehydrogenase 4 Calcium homeostasis regulator-like protein CHoR1 2 At5g40270 metal-dependant phosphohydrolase 6 Formate dehydrogenase 11 Quinone oxidoreductase like protein 12 Quinone oxidoreductase like protein 13 Quinone oxidoreductase like protein 14 Kinesin light chain-like protein 15 Carboxylic ester hydrolase 17 At3g 27930 Unknown protein 18 Serine type peptidase 19 Carbonic anhydrase 2 20 Expressed protein similar to At3g27880 21 ATPase 8 22 CNL_Gm19 23 ATPase 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 1 At3g01490 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 16 L-Aspartate oxidase Chr 5 ~42 Mb Chr 13 ~44 Mb Chr 19 ~50 Mb 53 kb 2 Kinesin light chain-like protein 1 Quinone 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 avid_ 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
description
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. - PowerPoint PPT Presentation
Transcript of D (3 Khipu elements)
44
D (3 Khipu elements)
14
12
Phaseolus vulgarisB4 locus
410 Kb contig
15
8 kb
Sub-cluster C
400 Kb
300 Kb
250 Kb
200 Kb
150 Kb
100 Kb
50 Kb
28
21
1516
33
2726
29
25
1234
11
13
17
18
1920
23
3130
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 kinaseAt5g40270 metal-dependent phosphohydrolase [2]Unknown protein At1g63930
Calcium homeostasis regulator-like protein CHoR1 [1]
Basic blue protein Hypothetical protein AY341443
Formate dehydrogenase [9]
MtN24 [7]
Formate dehydrogenase [9]
Farnesyl transferase [4]
Basic blue proteinFormate dehydrogenase [9]
At3g21600 unknown protein. [6]
Quinone oxidoreductase-like protein [21]Quinone oxidoreductase like protein [21]
Carboxylic ester hydrolase [102]Kinesin light chain-like protein [6]
L- Aspartate oxidase [3]
Expressed protein similar to At3g27930 [1]
Serine type peptidase [13]
Carbonic anhydrase 2 [6]
Expressed protein similar to At3g27880 [7]
CNL-B12
CNL-B13
CNL-B14
CNL-B15
CNL-B16
CNL-B17
CNL-B18
ATPase, E1-E2 type [21]
NADH dehydrogenase
CNL-B8
CNL-B3
CNL-B5
CNL-B4
CLN-B2CNL-B1
CNL-B6CNL-B7
CNL-B9CNL-B10
CNL-B11
9 Quinone oxidoreductase like protein
1 At3g01490 protein kinase
3 At5g27990 unknown protein
24 AT5g14720 protein kinase family
10 Quinone oxidoreductase like protein
8 MtN247 Farnesyl transferase
5 Formate dehydrogenase
4 Calcium homeostasis regulator-like protein CHoR1
2 At5g40270 metal-dependant phosphohydrolase
6 Formate dehydrogenase
11 Quinone oxidoreductase like protein12 Quinone oxidoreductase like protein
13 Quinone oxidoreductase like protein
14 Kinesin light chain-like protein15 Carboxylic ester hydrolase
17 At3g 27930 Unknown protein
18 Serine type peptidase
19 Carbonic anhydrase 2
20 Expressed protein similar to At3g27880
21 ATPase 8 22 CNL_Gm19
23 ATPase
Gm chr 19703,347-861,494 bp
2 At5g40270 metal-dependant phospho hydrolase
4 Calcium homeostasis regulator-like protein
Gm chr 1327,096,894-27,149,916 bp
1 At3g01490 protein kinase
3 Hypothetical protein At5g27990
5 Formate dehydrogenase6 Farnesyl transferase
Gm chr 58,372,893-8,464,947 bp
7 MtN24
92
kb
350 KbSub-
cluster B
16 L-Aspartate oxidase
Chr 5~42 Mb
Chr 13~44 Mb
Chr 19~50 Mb
53
kb
2 Kinesin light chain-like protein
1 Quinone 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)RetrotransposonOther gene
Truncated geneKhipu tandem repeatF-box
[ ] : number BLASP (1e-5) hits in the Arabidopsis thaliana genome
Soybean chromosome
Soybean pericentromeric regionSoybean 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.
