Table 2.
Survey of bimorphic SINE insertions from random genomic sequence of multiple dogs
|
Breed |
Sequence reads |
SINEC_Cf with unique flanks |
SINEC_Cf absent from CanSS (%) |
SINEC_Cf absent from CanFam1 (%) |
SINEC_Cf absent from both (%) |
|---|---|---|---|---|---|
| Beagle | 99,648 | 990 | 69 (7.0) | 66 (6.7) | 28 (2.8) |
| Labrador Retriever | 99,744 | 942 | 78 (8.3) | 69 (7.3) | 28 (3.0) |
| German Shepherd | 100,743 | 987 | 72 (7.3) | 75 (7.6) | 30 (3.0) |
| Italian Greyhound | 98,208 | 889 | 79 (8.9) | 72 (8.1) | 33 (3.7) |
| English Shepherd | 99,648 | 954 | 88 (9.2) | 81 (8.5) | 38 (4.0) |
| Bedlington Terrier | 102,240 | 969 | 106 (10.9) | 92 (9.5) | 40 (4.1) |
| Portugese Water Dog | 97,728 | 1013 | 95 (9.4) | 94 (9.3) | 42 (4.1) |
| Alaskan Malamute | 100,704 | 932 | 96 (10.3) | 87 (9.3) | 45 (4.8) |
| Rottweiler | 102,143 | 1040 | 106 (10.2) | 120 (11.5) | 52 (5.0) |
| Chinese Gray Wolf | 23,423 | 169 | 16 (9.5) | 17 (10.1) | 7 (4.1) |
| Spanish Gray Wolf | 22,176 | 185 | 18 (9.7) | 15 (8.1) | 9 (4.9) |
| Californian Coyote | 23,790 | 240 | 29 (12.1) | 28 (11.7) | 19 (7.9) |
| Alaskan Gray Wolf | 21,696 | 220 | 34 (15.4) | 36 (16.4) | 20 (9.1) |
| Indian Gray Wolf
|
22,560
|
227
|
32 (14.1)
|
29 (12.8)
|
21 (9.2)
|
-
Whole-genome shotgun reads from the NCBI Trace Archive were derived from nine dogs of different breeds, four wolves, and a coyote. Reads that contained SINEC_Cf sequences with nonrepetitive flanks were searched against CanSS and CanFam1, as described in the Methods section.
