Table 2 The in silico genome coverages (IgC; %) of 22 species with sequenced genomes (eight plant, 13 animal, and one fungus) by DNA fragments of different ends and lengths (100–600 bp) obtained from in silico digestions with the top 21 restriction enzyme pairs and the GBS reference pair PstI + MspI
PlantaAnimalFungi
Enzyme PairArabidopsisCottonwoodMedicagoWinegrapeSoybeanRiceSorghumMaizeC. elegansFruit flyHoney beeSticklebackPikeZebra fishTurkeyZebra finchDogHousecatHouse mousePigmy chimpOpossumBaker’s yeastMean_allSD_allMean_plants
Genome size (Mb)1203792974269503826592060831582204013771340104010212328241927263152299812
CviAII + Hinfl35.132.527.931.432.531.130.833.831.930.124.635.031.031.030.834.535.935.534.230.035.236.532.32.931.9
CviAII + DdeI34.430.826.630.630.930.331.832.927.029.716.135.132.933.331.935.935.334.933.129.334.535.931.54.431.0
BfaI + HinfI32.532.526.030.931.432.031.834.627.924.517.524.930.227.929.331.836.335.234.630.735.334.830.64.531.5
BfaI + DdeI32.531.425.030.430.431.232.334.223.824.011.825.130.829.128.730.933.632.932.429.033.634.429.45.130.9
CviAII + TfiI33.427.924.327.227.725.826.227.629.325.824.526.623.223.724.726.628.429.725.924.030.833.927.22.927.5
BfaI + TfiI31.829.123.627.928.227.027.329.125.921.417.820.524.022.424.425.830.031.828.025.630.932.726.63.928.0
MluCI + HinfI25.318.014.119.819.224.928.129.113.520.714.133.028.424.225.126.629.629.430.123.524.524.223.95.522.3
MluCI + DdeI24.417.313.619.418.624.027.529.010.219.67.433.330.126.026.528.428.629.429.223.524.122.323.36.721.7
CviAII + ApeKI19.317.212.913.414.225.322.623.818.527.711.033.725.626.628.131.824.923.925.921.020.925.422.46.018.6
HinfI + MseI28.122.018.724.724.328.028.830.627.07.94.310.49.821.68.428.328.828.711.226.17.031.620.79.225.6
HinfI + HpyCH4IV29.422.721.618.023.127.927.227.930.514.311.616.114.824.811.716.019.422.79.315.85.635.420.37.724.7
DdeI + MseI27.120.817.924.123.226.929.330.321.58.33.710.29.322.66.029.529.029.17.525.15.530.019.99.525.0
MluCI + TfiI23.715.011.816.615.919.923.324.611.816.913.124.821.018.419.619.822.725.322.618.520.420.619.44.118.9
DdeI + HpyCH4IV29.222.220.817.522.627.227.227.526.314.99.315.913.826.08.614.618.020.76.514.24.735.219.28.124.3
ApeKI + BfaI19.518.313.114.915.126.323.324.316.812.65.913.814.725.213.529.826.623.914.122.810.524.318.66.319.4
TfiI + HpyCH4IV29.020.719.716.821.524.224.223.728.313.912.315.213.220.210.913.316.820.79.113.86.133.318.56.922.5
NlaIII + MluCI25.719.416.020.219.625.427.029.013.45.22.410.87.727.16.328.729.330.28.024.35.424.318.49.422.8
TfiI + MseI26.519.016.321.520.923.624.326.324.57.85.09.78.516.07.721.422.223.910.121.07.128.317.87.522.3
CviAII + AvaII15.614.012.314.514.618.720.824.712.415.97.022.919.613.414.517.720.420.922.314.920.018.117.14.216.9
ApeKI + MseI17.214.19.913.212.825.122.923.215.87.23.810.09.519.57.026.721.820.410.819.26.221.315.36.817.3
AvaII + BfaI16.115.312.315.815.520.621.826.211.39.03.911.612.313.09.017.322.521.413.416.210.018.115.15.317.9
PstI + MspI3.52.31.61.81.55.66.05.53.14.50.68.94.86.23.35.35.44.63.05.00.84.44.02.03.5
  • IgC values for additional 48 restriction enzyme pairs are shown in Table S3. Three enzyme pairs selected for empirical evaluations in plants are highlighted in red. The number below the organism is its genome size in Mbp (1 × 106 bp). More genome information for these species is shown in Table S2.

  • a The organisms listed are the same as Table S2.