Buffalo Yak Taurine - BioMed Central
100/100
SN8
98/93
SN21 SN18
100/100
MN20 MN7
100/100
JN2 QQ63306 JN14 JN16 77/6 JX21 QQ63307 68/33 90/4 QQ63319 JX19 99/89 JX1 ZS48 71/28 BH931 89/9 BH803 99/98 94/2 65/25 MG8 91/3 HD AX22 58/22 MG1 HN2 93/84 97/73 HN1 81/3 87/35 WN
Buffalo Yak
83/43 86/28 78/19 81/5
98/84
NY9172 0.9
0.8
0.7
LC14 LC12
100/100
82/27 91/41
Taurine
0.6
NY236 NY140 0.5
0.4
0.3
0.2
Figure S1 Clustering results of CNVRs. Chinese bulls are grouped into taurine, yak, and buffalo. The hierarchical clustering of samples by CNVRs was done in R package pvclust with a cluster method of “average” and distance measure of “correlation”, and “approximately unbiased p”/“bootstrap probability value” are shown on the branches.
0.04
A
PC2 (7.8%)
0.02
0.00
Taurine Yak
-0.02
Buffalo
-0.04 -0.06
-0.04
-0.02
0.00
+ + + + +
+SN8 SN21+ +SN18
+MG1+MG8
0.2
0.4
+
HD AX22 JN14 QQ63306 QQ63319 QQ63307 JN16 JX21
NMDS2
++JN2BH931 +
0.0
ZS48
-0.2
B
NY140
-0.4
+MN20 + MN7_M
++
HN1
NY9172 -0.6
+
-1.5
-1.0
0.04
0.02
PC1 (10.9%)
0.6
-0.08
-0.5
0.0
NMDS1
HN2
+ + JX19
+ + + BH803 JX1
+
LC12 + + + NY236 LC14 WN
+
0.5
Figure S2 PCA and NMDS of CNVRs on Chinese bulls. A. PCA of CNVRs on all Chinese bulls. B. NMDS of CNVRs on all Chinese bulls. Taurine, blue; Yak, green; Buffalo, red.
1.0
cell pcell e x tr a e e maxctrracelluacellulanrvelopret mem omol lar re regio n bran ecula gion e-en r com part close plex d lum orga organeel n nelle le p synasynapasrt pse p e art v i auxil r virion ion iary t a rans ntioxidpart port protaent bindi in chem cata ng electoattractlytic enzy ron c ant mole me r arrie c egula r u l a r s t t r r u a trans ctura nsdu tor cripti l mol cer t r on re ecule a n anat s l a t ion r gulato omic egula r al str t r a t u n biolocture fo sporteorr biolo gical a rmatio cellu gical dhes n regu ion cellu lar com la n lar co pon mpo ent bcell kiltliio nent ioge ng orga nesis cellu nizat l a r d p e estab velo roceion p ss lishm men ent o tal pr death f loca ocess immu lizati ne sy stem growon locaplrocesths izatio multi mul meta locom n cellu ti\-or bolic lar o ganis prooction rgan m p ess isma roce pigml processss repro rep entati on resp ductiveroductio onse p oc n ess rhyth to strim m viral ic pr ulus repro oces ducti s on
Percent of genes 10
1
Cellular Component 6
0.1
0.01
Molecular Function Biological Process
Figure S3 Gene ontology (GO) annotations for genes covered by CNVRs. 647 genes are annotated with GO IDs out of 716 genes covered by CNVRs. Gene annotations with Refgene IDs were done based on genome assemblies of Btau_4.0, Btau_4.6, and Btau_4.6.1, and GO IDs were retrieved in R package biomaRt.
0
Number of genes
100 647
Relatived mRNA expression level of PLA2G2D
A
10 9 8 7 6 5 4 3 2 1 0
heart
liver
spleen
lung
10
B
intestine
stomach
muscle
adipose
23563.6
9 Relatived mRNA expression level of MYH3
kidney Tissues
fetal bovine
8
newborn bovine
7 6 5 4 3 2 1 0
heart
liver
lung
kidney Tissues
spleen
muscle
Figure S4 Expression pattern analysis of PLA2G2D gene and MYH3 gene. A. Expression pattern analysis of PLA2G2D gene in several tissues of adult bovine. B. Expression pattern analysis of MYH3 gene in several tissues of fetal and newborn bovine. The expression in muscle of fetal bovine was discontinued because it was far out of the others’ ranges. Relative mRNA expression levels of PLA2G2D gene and MYH3 gene in different tissues were analyzed by qPCR. mRNA expression were normalized against that of GAPDH gene. Error bars represent standard error of the mean (SE). Each column value represents the Means±SE of three replicates.
SN8
98/93
SN21 SN18
100/100
MN20 MN7
100/100
JN2 QQ63306 JN14 JN16 77/6 JX21 QQ63307 68/33 90/4 QQ63319 JX19 99/89 JX1 ZS48 71/28 BH931 89/9 BH803 99/98 94/2 65/25 MG8 91/3 HD AX22 58/22 MG1 HN2 93/84 97/73 HN1 81/3 87/35 WN
Buffalo Yak
83/43 86/28 78/19 81/5
98/84
NY9172 0.9
0.8
0.7
LC14 LC12
100/100
82/27 91/41
Taurine
0.6
NY236 NY140 0.5
0.4
0.3
0.2
Figure S1 Clustering results of CNVRs. Chinese bulls are grouped into taurine, yak, and buffalo. The hierarchical clustering of samples by CNVRs was done in R package pvclust with a cluster method of “average” and distance measure of “correlation”, and “approximately unbiased p”/“bootstrap probability value” are shown on the branches.
0.04
A
PC2 (7.8%)
0.02
0.00
Taurine Yak
-0.02
Buffalo
-0.04 -0.06
-0.04
-0.02
0.00
+ + + + +
+SN8 SN21+ +SN18
+MG1+MG8
0.2
0.4
+
HD AX22 JN14 QQ63306 QQ63319 QQ63307 JN16 JX21
NMDS2
++JN2BH931 +
0.0
ZS48
-0.2
B
NY140
-0.4
+MN20 + MN7_M
++
HN1
NY9172 -0.6
+
-1.5
-1.0
0.04
0.02
PC1 (10.9%)
0.6
-0.08
-0.5
0.0
NMDS1
HN2
+ + JX19
+ + + BH803 JX1
+
LC12 + + + NY236 LC14 WN
+
0.5
Figure S2 PCA and NMDS of CNVRs on Chinese bulls. A. PCA of CNVRs on all Chinese bulls. B. NMDS of CNVRs on all Chinese bulls. Taurine, blue; Yak, green; Buffalo, red.
1.0
cell pcell e x tr a e e maxctrracelluacellulanrvelopret mem omol lar re regio n bran ecula gion e-en r com part close plex d lum orga organeel n nelle le p synasynapasrt pse p e art v i auxil r virion ion iary t a rans ntioxidpart port protaent bindi in chem cata ng electoattractlytic enzy ron c ant mole me r arrie c egula r u l a r s t t r r u a trans ctura nsdu tor cripti l mol cer t r on re ecule a n anat s l a t ion r gulato omic egula r al str t r a t u n biolocture fo sporteorr biolo gical a rmatio cellu gical dhes n regu ion cellu lar com la n lar co pon mpo ent bcell kiltliio nent ioge ng orga nesis cellu nizat l a r d p e estab velo roceion p ss lishm men ent o tal pr death f loca ocess immu lizati ne sy stem growon locaplrocesths izatio multi mul meta locom n cellu ti\-or bolic lar o ganis prooction rgan m p ess isma roce pigml processss repro rep entati on resp ductiveroductio onse p oc n ess rhyth to strim m viral ic pr ulus repro oces ducti s on
Percent of genes 10
1
Cellular Component 6
0.1
0.01
Molecular Function Biological Process
Figure S3 Gene ontology (GO) annotations for genes covered by CNVRs. 647 genes are annotated with GO IDs out of 716 genes covered by CNVRs. Gene annotations with Refgene IDs were done based on genome assemblies of Btau_4.0, Btau_4.6, and Btau_4.6.1, and GO IDs were retrieved in R package biomaRt.
0
Number of genes
100 647
Relatived mRNA expression level of PLA2G2D
A
10 9 8 7 6 5 4 3 2 1 0
heart
liver
spleen
lung
10
B
intestine
stomach
muscle
adipose
23563.6
9 Relatived mRNA expression level of MYH3
kidney Tissues
fetal bovine
8
newborn bovine
7 6 5 4 3 2 1 0
heart
liver
lung
kidney Tissues
spleen
muscle
Figure S4 Expression pattern analysis of PLA2G2D gene and MYH3 gene. A. Expression pattern analysis of PLA2G2D gene in several tissues of adult bovine. B. Expression pattern analysis of MYH3 gene in several tissues of fetal and newborn bovine. The expression in muscle of fetal bovine was discontinued because it was far out of the others’ ranges. Relative mRNA expression levels of PLA2G2D gene and MYH3 gene in different tissues were analyzed by qPCR. mRNA expression were normalized against that of GAPDH gene. Error bars represent standard error of the mean (SE). Each column value represents the Means±SE of three replicates.
