Table 1. Distribution of repetitive DNA in rice and various GSSs of maize as percent of genome
Details Total BES HindIII BES EcoRI BES MboI BES UF MF HC RescueMu Rice
Total no. of sequences 474,604 309,560 78,313 86,731 50,876 30,000 30,000 30,000 179
Total no. of base pairs 307,169,410 206,221,247 46,673,217 54,274,946 37,621,118 21,649,324 21,637,862 10,074,088 35,800,000
Percent of genome, % 12.99 8.72 1.97 2.29 1.59 0.92 0.91 0.43 8.33
Class I retroelements, % 55.60 58.39 46.77 52.58 57.73 15.70 6.55 4.91 19.28
Ty1/copia-like elements, % 24.54 25.33 20.54 24.97 17.50 8.37 2.54 1.98 3.67
Ty3/gypsy-like elements, % 21.43 23.39 15.69 18.94 31.25 4.32 2.22 1.71 8.90
LINES + SINES, % 0.18 0.23 0.06 0.06 0.04 0.06 0.18 0.13 0.96
Other retroelements, % 9.45 9.44 10.48 8.61 8.94 2.95 1.62 1.09 5.74
Class II DNA transposons, % 0.98 0.94 1.16 0.98 0.92 1.14 1.58 4.84 10.35
hAT superfamily, % 0.03 0.02 0.04 0.03 0.04 0.04 0.09 0.11 0.37
CACTA superfamily, % 0.32 0.31 0.38 0.30 0.21 0.21 0.17 0.76 2.83
Mutator, % 0.01 0.01 0.02 0.02 0.01 0.05 0.05 0.36 0.51
MITEs, % 0.17 0.16 0.20 0.17 0.19 0.39 0.62 1.08 3.96
Other DNA transposons, % 0.45 0.42 0.54 0.48 0.48 0.44 0.65 2.53 2.67
Simple repeats, % 0.40 0.27 0.47 0.83 1.66 1.27 0.19 0.17 1.03
High-copy-number genes, % 0.82 0.12 1.13 3.17 1.95 0.17 0.19 0.15 0.06
Other repeats, % 0.12 0.11 0.12 0.16 0.30 0.09 0.06 0.05 0.43
Total repeats, % 57.91 59.82 49.65 57.72 62.55 18.38 8.57 10.13 31.14
  • Greater than 70% identity limit. UF, The Institute for Genomic Research (TIGR) unfiltered; MF, TIGR MF; HC, TIGR high C0 t; RescueMu, MaizeDB RescueMu; MITE, miniature inverted-repeat TE; LINE, long interspersed nuclear element; SINE, short interspersed nuclear element. Data for Rice comprise 179 pseudo BACs, i.e., 200 kb cut equally from all 12 chromosomes.