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Table 3 Distribution of OR into families and subfamilies

From: Inventory of the cichlid olfactory receptor gene repertoires: identification of olfactory genes with more than one coding exon

  Cichlids Fish models
  N. bri. N. bur. P. nye. O. nil. M. zeb. D. rer. G. acu. O. Lat. T. rub. T. nig.
A1 3(e2,p1) 6(e2,p2,f1) 6(e2,p1) 14(e8,p1) 8(e1,p2)    2   
A2 3(e1,p1) 3(e2,p1) 5(e2) 4(e2) 6(e2)      
A3 1(p1) 2(e1) 3 2(e1) 2(e1)      
A4 1(p1) 2 2 2(e2) 2   1 8   
A5 3(e2,p3) 4(e1) 4(p1) 4(e1) 5(pe1)   10 2   
A6 (e1) 1(p1) 1   1    4   
A7          3 3
A8          1  
B1   1 1 1(e1) 1      
C1 1 1 1 (e1) 1     1 1
D1 3(e2) 4(e6) 7(e3,p3) 11(e14) 7(p2)      
D2        6   2 1
E1 7(e3) 12(e1,pe1) 8(e2,pe1) 13(e5,p2) 7(e7,pe1)   5 3   1
E2 (e1) 2 2 3 2   2   1 3
F1       12     
F2       1     
F3          1  
F4 (pe1) 1 1 1 1   1   1 3
F5 1 1 (p1) 1 1   3   1 4
G1 1 1 1 1 1    1   1
H1       6     
H2 1 1 1 1 1   1 1 2  
H3 2(e2) 5 6 6(e3) 3(e1,p1)   1   2  
H4          5 3
H5 2(e1) (e3)   4(e4) 4   4 2   
H6 2(e2,p1,f1) 3(e2,p1) 4(e1,p1) 10(e1,p2) 4(e1)   7    
H7          1 2
I1   1 1 3 1   2 2   1
J1       3     
J2 1 (e1) 1 1 1   1 2 1  
J3 1(e1) (e2) 1(e1) (e1) 1 3 2 1   1
J4       1     
J5 1 1 1 1 1 2 1 1 1  
K1 1 1 1 1 1   1 1   
K2       6     
K3       6     
K4 1 1(e1) 2 2 1(e1)   2 2 1  
K5 (e1) 1(e2) 2(e1,ps1) 4 2(p1)   1 4 3  
K6         3   
K7     1(e2)       
K8 (e1)        1   
L1       12     
L2 5(e2,f1) 4(e6,p1) 5(e4,pe1) 16(e15,p1) 6(e2)      
M1       3     
M2 (e1) (e3) 2 (e2) 1   5 2 2 1
N1       2     
N2 2(e2) 2(e1) 2(e1) 1(e3) 2(p1)   11 9 1 1
N3 1(e3,p2) 1(e5,p1) 2(p1) 3(e4) 6(p1)      
N4       11     
N5       12 1    
N6 3 2(pe1) 2(e1) 7(e2) 1(e3)    1   
O1         1   
O2       1     
O3       2     
O4       5     
O5 2 1(e1) 2(e1) 2(e4) 1(e4)   3    
O6       5     
O7 1(e1) (e1)   (e4) 1   1 2 2 1
O8 1(e1) (e2) 1 1(e1) 1   1    1
O9   (e1) (e1)        
P1       1     
P2 1 1 1 1 1   1 1 1 1
P3 2 2 (e2) 4(e1) 2    2   
P4       3     
Q1          1  
Q2 1 1 1 (p1) 1    1   
R1         1   
R2   1(e1) 1   1      
R3          2 4
R4 (e2,p1) 4(e1) (e2) 9(e8) 3(p1)    3   
R5 1    (e3)       
S1       2     
S2 1(e3,p1) 3(e1) 1(e2) 11(e2) 3(e2,p1)    2   
S3 2 2(e1) 1(e1) 4(e1) 1(e2)    3 1  
S4          1 1
T1       1     
T2       1     
T3       6     
T4   1 (pe1)        
U1 1 1 1 1 1 1     1
V1 1 1 (e2) 1 1      
W1           1
W2         2   
W3 1 1 1   1      
W4           1
W5 1 1(e1)         
W6           1
W7 2 2 2 4(e2) 1    1   1
W8 1 1 1 1 1      
W9 1(e1) 1   (e1) 1    1   
X1   1(e1) (e1) (e2) (e1)      
Y1 1         1  
Z1 1          
Z2         1   
AB1       1     
AB2 (f1) 1   1 (p1)   4    
AC1    (e3)        
AD1           1
AD2       1     
AE1       1     
AE2       2     
AF1       5     
AG1       5     
AG2       3     
AH1       1     
AI1          1  
AJ1       5     
AK       9     
AL       1     
AM       1     
AN           2
Total 69 90 88 158 102 143 78 73 40 42
e36, p13, f3 e50, p9, f1 e33, p12 e101, p7 e28, p13
S/F 49 51 47 47 48 37 26 33 26 25
F 24 26 25 24 25 22 12 16 17 18
  1. ORs were classified into families and subfamilies according to the phylogenetic tree and the percentage of AA identity calculated by MAFFT alignments. Families (F) were named by letters and subfamilies (S/F) by Arabic numbers (left column). For example, A1 (family A subfamily 1) contains 3 complete genes, 2 edge genes (e2) and 1 pseudogene (p1) from N. brichardi. Of the 376 model fish OR (143 zebra fish/D. rerio, 78 stickleback/G. aculeatus, 73 medaka/O. latipes, 40 fugu/T. rubripes and 42 tetraodon/T. nigroviridis – for more details see Additional file 4) 182 were in subfamilies also containing one of more cichlid ORs.
  2. As shown in this Table the 143 zebrafish ORs are distributed into 37 sub-families and 22 families. A similar number of sub-families was reported by Alioto and Ngai [18] analyzing the same set of ORs, however they described height families only, four of them corresponding to several families in our study. Correspondences between the families in [18] and the families described in this work are as follow: Families A, B, C and G described in [18] correspond to families P, AB1, O and L respectively (this work); Families D [18] correspond to AH, M and N; Family E [18] corresponds to families F, H, AD, AE, AF, AG; Family F [18] corresponds to families K and J; Family H [18] corresponds to families S, T, U, AJ, AK, AL and A.