Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing

BMC Genomics

Table 4 Reference genome contigs assigned to Atlantic salmon linkage groups

Atlantic salmon linkage group	Atlantic salmon chromosome	No. of genome contigs*	Amount of sequence data (kb)**	Stickleback linkage group	Rainbow trout linkage group
1	2	177	2,030	20	*2/27/* 29/31
2	10	262	3,410	19	6/ 8/27
3	14	156	2,170	3/10	3/ *23/* 29
4	6	230	2,880	11	2/ 9/ 24
5	13	209	2,530	NA	9/22
6	12	211	3,090	17/9	2/29
7	24	94	1,160	13	10
8	15	175	2,220	18	21/ 23
9	11	180	2,160	2	1/ *10/* 18
10	9	298	3,850	1	3/ 4/ 25/26
11	3	232	3,480	11/3	2/ 9/13
12	5	173	2,110	20	3/27/ 31
13	19	110	1,500	21/5	*17/* 19/22
14	21	111	1,570	16	5/ 31
15	27	118	1,330	10/20	16
16	18	159	1,900	6	6/ 21
17	1	254	3,780	14/6	8/14/30
18	23	103	1,300	8	24
19	8	33	454	NA	*14/* 20
20	25	60	809	16	31
21	26	97	1,330	2	10/ 18
22	17	125	1,530	NA	7/12/ 15
23	16	164	2,210	19	6/16/ 27
24	7	109	1,370	4	7/ 15
25	20	196	3,100	13	11/19
28	4	165	2,200	7	14/20
30	29	76	992	21	7/ 17
31	28	84	1,130	5	17/ 22
32	22	120	1,520	17	12
Genome wide	-	4,367	57,402	-	-

Atlantic salmon reference genome contigs were assigned to linkage groups by Blastn alignment against mapped RAD contigs. Column 5 shows the stickleback linkage groups orthologous to the Atlantic salmon linkage groups identified by this study. Column 6 shows the Atlantic salmon - rainbow trout orthologous linkage groups as defined by Phillips et al. [44] (bold) and Danzmann et al. [6] (bold italic) individually, and those identified in both studies (italic). 50% of the stickleback - rainbow trout relationships suggested in this table have been identified in another study comparing rainbow trout and stickleback only [45].
*Grand total includes genome contigs assigned to more than one linkage group only once, thus is less than the sum of genome contigs per linkage group.
**Grand total given includes sequence data of genome contigs assigned to more than one linkage group only once, thus is less than the sum of sequence (kb) assigned per linkage group.

ISSN: 1471-2164