Supplemental Figure 6. Comparative organization of the reconstructed cetartiodactyl and pecoran ancestral chromosomes with the cattle genome as a reference. Order and orientation of syntenic fragments are visualized using the Evolution Highway comparative chromosome browser. Blue and pink colors represent orientation of blocks relative to the reference, with blue indicating the same orientation, and pink indicating the opposite orientation. Pink does not always indicate an inversion because the orientation of RACFs is randomly chosen during the reconstruction. The number within each block represents a chromosome number for a reconstructed ancestor, and a lower-case letter indicates a fragment of the chromosome. Light grey blocks indicate mammalian multispecies homologous synteny blocks (msHSBs). Diamonds indicate the position of EBRs, with light and dark green showing EBRs classified as ruminant or pecoran, respectively, using FISH data. Heatmaps show the density of ruminant, cetartiodactyl, and mammalian enhancers, and ruminant gene family expansions in windows of 100 Kbp along cattle chromosomes.
Cattle chr1 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
1
1
1
1 1b 1a
Bases 60000 1
40000 1
1 4.0e+07 20000 1
1a 1b 1 0
1b 1
1
1
1
1 8.0e+07 1
1
1
1a 1 1c
1
1 1 1 classification 1
1 ? 1.2e+08 1 Ruminant
1
1
1a 1b
1a 1b
1b 1b 1b 1a 1 1b 1a 1b
1b 1 1b
1a Cattle chr2 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
6
2
2 2 6 2 Bases
2 20000
2 10000
6 2 6 2 0 2
2 5e+07
2
6
2
2
2
2 2
2
classification 1e+08 6 2 Pecora
Ruminant
2
2
2
3a 2 2 Cattle chr3 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
3
3
3 Bases
3 15000
3 10000 3.0e+07 3 5000 3 0
3
3
3a 3 6.0e+07 3
3
3
3
3
3
3
3 classification 9.0e+07
3 Pecora
3
3
3
3
6 1.2e+08 Cattle chr4 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
8a
4 4 8a 4
8a 4
8a 4
8a 4
8a 4 8a 4 Bases 4 20000
4 15000 10000 3.0e+07 4 8a 4 5000 0
4
8a 4 8a 4
8a 4 4
8b 4 4 8b 4 8b 4
6.0e+07
8b 4
4
4
8a
8a
4
4 classification 9.0e+07 4 Ruminant 4
4
4
4 8b 4
4
4
1.2e+08 Cattle chr5 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
5
5
5 9a
5
5 Bases 80000 60000 5 40000 3.0e+07 20000 5 9a 0
5
9a 5
6 5 6.0e+07
5
5 9a
5
5
5 classification 9.0e+07 Ruminant 9b 5
5
5
9a 5
9a 6
9a 6
9a 6 1.2e+08 9a 6 Cattle chr6 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
4b
6
6
6 4a Bases
6 10000
6 3e+07 5000
6
6 0
6
6
5 6
6e+07
4a
6
6
classification
6 9e+07 Pecora
6
6
6
4c
4c 5 4c 5 4c 5
4c 5
6 4a 5 6
4c Cattle chr7 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
2a
2c
7
2b
2b Bases 2b 15000
7 10000
3e+07 5000 2a 7 0
2a
2d
2b 7
8 7
7 6e+07
7 2a 7
7
7 classification 7 ?
7 Pecora
7 Ruminant 9e+07 7
7 2a
7
7 Cattle chr8 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
25
8
25
25 8
8
8 Bases 8 15000
8 10000
3e+07 5000 8 0
8 11c
8
8
8
8 7 8 6e+07 8
8
25 8
8
8
11c classification
8 Pecora
11e Ruminant 9e+07 11d
8
8
8
11c 8
8
14 Cattle chr9 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
9 10
9 Bases 100000
9 75000 2.5e+07 50000 9 25000 9 0
9
9
9
10 9
5.0e+07 10 9
9
9
9
7.5e+07 9 classification Pecora 9
9
10 9
9
9
1.0e+08
9 Cattle chr10 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
2a
10
2a
2a 10
5
10
5 10 Bases 10 80000 10 60000 2.5e+07 40000 10 20000 5 0
10
10 5 11 10
10
5.0e+07 10
10 5 10
10
10
10
classification 10 7.5e+07 ? 5
10 Pecora
10 Ruminant
10
2a 8
10
10
5 11 10 1.0e+08
10 Cattle chr11 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
14 11
11
14 11
11
11 Bases
11 20000 15000 2.5e+07 11 10000 14 5000 11 0
11
11
14
5.0e+07 11
14 9 11
11
11
14 11
11
11
7.5e+07 classification 11 ?
14 11 Pecora
11 Ruminant
11
11
11c 11
1.0e+08 11
11b 11c 11a 9 11c Cattle chr12 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
12
Bases 13a 20000 12 15000 10000 5000 2.5e+07 12 0
12
12
13 12
5.0e+07
13a
12
12
classification 12 ?
7.5e+07 13b
12
12
13a 12 Cattle chr13 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
19 17b
13
13 24b 17a Bases 13 15000 24a
2e+07 10000 5000 24a 13 0
24a
4e+07 19
24b 13
19 13 17a 13 19
19 13 6e+07 classification
13 ?
Ruminant
19
8e+07 Cattle chr14 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
14
15 14
14
15 Bases 20000 15 14 15000 2e+07 10000
14 5000 0 14
15 14
14 4e+07 14 14
14
14
6e+07 classification Pecora 15 14
14
14
8e+07 14
15 Cattle chr15 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
7a
15
7a
15
Bases
15 30000 2e+07 20000 15 10000
0 7b 15
15
15 4e+07 7a 15
7c
7a 15
6e+07 15 classification 15 Pecora
7a
15
15 8e+07
7b Cattle chr16 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
16
3a 16
16 Bases
15000 10000 2e+07 3b 16 5000 0
16 16
16 3a 4e+07 16
3a 16
16
3b 16
3a 16
3a
16 classification 6e+07 16 Pecora
16 3a
16
16 16
8e+07 3b Cattle chr17 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
17
17 Bases 5000 17 4000 3000 4a 2000 2e+07 1000 17 0
17
17
17
18 4e+07 4b 17
17
17
17
17 classification Ruminant
23a 17 6e+07
17
23b
23b Cattle chr18 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
18b
18 18a
Bases 80000 18 60000 40000 20000 0 2e+07 18c 18
18a
18a 22 18
18
4e+07
18
classification ?
Pecora 18b Ruminant
18
6e+07
18d
18d Cattle chr19 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
19
Bases 19 50000 40000 30000
19 20000 10000 0
2e+07 19
16
19 21
19
4e+07 19
19
classification
19 ?
19
16 19
6e+07 19 Cattle chr20 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
2a
20
20
20 Bases 20000 20 15000 10000 5000 2e+07 20 0
20
20 19
20 4e+07 2a
20
20
classification 20 ?
20
20 6e+07
20
20 Cattle chr21 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
5 20
21
21 5 Bases
21 75000 50000
21 25000 2e+07 0
5
5
5
5 20 5 21
4e+07 21
5 21
classification ?
Pecora
5 Ruminant
5
6e+07 22
21
27 5 Cattle chr22 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
8a
22
24 1a 22
Bases
15000
1a 24 10000
1a 24
1a 5000 0
2e+07 22
22
22 1a
24 4e+07 22
classification ? 22 Ruminant
22
1a
1a
6e+07 1a Cattle chr23 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
20
23
Bases 1e+07 23 30000
20000
10000
0 20 23
2e+07
26
3e+07
23
23
classification 20 ? 4e+07 23
23
5e+07 Cattle chr24 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
17b
24
24 Bases
20000 15000 10000 24 5000 0
2e+07
24
24
17a 24 23
24
24
4e+07 24
24 classification Ruminant
24
17b 24
6e+07 Cattle chr25 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
25
Bases 12500
25 10000 1e+07 7500 5000 2500 0
25 2e+07 21 28
25
3e+07 classification
25 ?
4e+07 Cattle chr26 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
26
Bases 1e+07 50000 12b 12a 40000 30000 26 20000 10000 0
26 2e+07
12b 12a
3e+07
26
12b 12a classification ? 4e+07 26
26
26
5e+07
12b 12a 12b 12a Cattle chr27 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
27 Bases
20000 1e+07 15000 27 10000 5000 0
27
27 2e+07 22
27 27
27 3e+07
classification ?
4e+07
1a Cattle chr28 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions 0e+00
12a 12b
12a 12a
28
Bases 12a 1e+07 28 10000
5000
0
28
2e+07
28 12a
28
3e+07 12b
28
classification Ruminant
28 4e+07 Cattle chr29 DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions
29 Bases 1e+07 7a 80000 60000 29 40000 20000 0
29
2e+07
7a
29 25
3e+07 7b 29
7b 29
classification 7b ?
4e+07 Ruminant
29
7a
29
5e+07 Cattle chrX DESCHR_Cetartio DESCHR_Pecora Mammal 0 Cattle Ruminant Cetartiodactyl Mammal Expansions Xb Xh Xh
Xb
X Xb X Xb X
X Bases Xe X
Xe Xf X 20000 X Xe Xf 10000
Xh X 0 Xd Xe X 5e+07 Xd
Xg Xd X Xd Xg X Xf Xd Xf Xd X
Xb Xb Xi X Xb Xi
Xg Xc Xb Xg Xc X
X
Xc X X
Xa X
1e+08 Xc Xa X
X
Xa X classification ?
X Xa
X
X
Xa Xc Xa Xc Xa Xc Xa Xa Xc
Xa Xc