Table 3 Synteny between lake trout linkage groups and Arctic char, rainbow trout, Atlantic salmon, and brook trout genomes. Arctic char, rainbow trout, and Atlantic salmon chromosomes were recorded if more than 50 RAD contigs from the lake trout linkage group were aligned to a chromosome with a mapping quality of 60. Brook trout linkage groups were recorded if more than 10 aligned markers were detected by MapComp. Graphical depictions of alignment location vs. linkage map position are available in Supplementary Figures S1-S7.
Lake TroutArctic CharRainbow TroutAtlantic SalmonBrook Trout
Sna1Sal15Omy6Ssa24, Ssa26BC6
Sna2Sal1Omy17Ssa12BC3
Sna3Sal20Omy12Ssa03, Ssa13BC8, BC14
Sna4Sal18Omy16, Omy23Ssa01, Ssa19BC1
Sna5Sal6.1, Sal6.2Omy2, Omy14Ssa05BC7
Sna6Sal3Omy21Ssa07BC2
Sna7Sal27Omy15, Omy18Ssa16, Ssa29BC5
Sna8Sal13Omy4, Omy10Ssa04, Ssa23BC4
Sna9Sal26Omy1Ssa16BC20
Sna10Sal16Omy5Ssa10BC17
Sna11Sal32Omy8Ssa14BC22
Sna12Sal23Omy10Ssa04BC9
Sna13Sal2Omy3Ssa25BC24
Sna14Sal7Omy9Ssa15BC30
Sna15Sal9Omy19Ssa01BC12
Sna16Sal17Omy16, Omy20Ssa13, Ssa19BC18
Sna17Sal8Omy25Ssa09BC33
Sna18Sal33Omy11Ssa20BC40
Sna19Sal36Omy22Ssa21BC26
Sna20Sal11Omy7Ssa22BC21
Sna21Sal4q.1:29Omy2Ssa10BC15
Sna22Sal25Omy1Ssa18BC36
Sna23Sal22Omy27Ssa20BC25
Sna24Sal14Omy4Ssa06BC31
Sna25Sal19Omy28Ssa03BC11
Sna26Sal5Omy29Ssa11BC10
Sna27Sal31Omy18Ssa27BC23
Sna28Sal4q.2Omy25Ssa09BC35
Sna29Sal28Omy8Ssa15BC19
Sna30Sal10Omy26Ssa11BC28
Sna31Sal4q.1:29Omy5Ssa01BC13
Sna32Sal30Omy14Ssa14BC34
Sna33Sal14Omy11Ssa19BC16
Sna34Sal4pOmy24Ssa09BC38
Sna35Sal8Omy20Ssa28BC27
Sna36Sal37Omy9Ssa18BC32
Sna37Sal35Omy3Ssa02BC29
Sna38Sal24Omy15Ssa17BC37
Sna39Sal21Omy13Ssa02BC42
Sna40Sal12Omy7Ssa17BC39
Sna41Sal20Omy13Ssa06BC14
Sna42Sal34aOmy19Ssa08BC41
  • a Sal34 appears to be homologous with Sna42, however fewer than 50 RAD contigs mapped to this chromosome.