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Table 4 Reference genome contigs assigned to Atlantic salmon linkage groups

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

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 - -
  1. 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].
  2. *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.
  3. **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.