Table 3.
MapComp Results Using Two Different Intermediate Genomes and Comparison with Results from Reciprocal blast
| Species | Total Markers | Map to Rainbow Trout (RT) Genome: No. (%) | No. Marker Pairs (RT) | Map to Atlantic Salmon (AS) Genome: No. (%) | No. Marker Pairs (AS) | Recip. Best-Hit blast |
|---|---|---|---|---|---|---|
| Lake Whitefish | 3,438 | 1,156 (33%) | 346 | 1,185 (34%) | 609 | 111 |
| Atlantic Salmon | 5,650a | 2,776 (49%) | 619 | 3,434 (60%) | 1,041 | 208 |
| Brook Charr | 3,826 | 2,321 (60%) | N/A | 2,454 (64%) | N/A | N/A |
| Rainbow Trout | 955 | 837 (87%) | 300 | 626 (65%) | 411 | 30 |
| Coho Salmon | 5,377 | 3,873 (72%) | 813 | 2,856 (53%) | 1,068 | 182 |
| Chinook Salmon | 6,352 | 4,663 (73%) | 907 | 3,472 (54%) | 1,162 | 190 |
| Pink Salmon | 7,035 | 4,544 (65%) | 841 | 3,481 (49%) | 1,129 | 210 |
| Chum Salmon | 6,119 | 4,150 (67%) | 795 | 3,139 (51%) | 1,049 | 205 |
| Sockeye Salmon | 6,262 | 4,034 (64%) | 771 | 3,138 (50%) | 1,061 | 209 |
Note.—The number and percentage of markers from each species that map to each genome are shown, along with the number of markers pairs between each species and Brook Charr identified by MapComp. Also shown is the number of homologous markers that would have been found between each species and Brook Charr with a reciprocal best-hit blast approach. Numbers of markers mapping and being paired were similar when tested on the Rainbow Trout (RT) or Atlantic Salmon (AS) genome assemblies. N/A values are present as Brook Charr is not paired against itself.
a
From EST sequences.