Table 2. Occurrence and distribution of repetitive DNA in the maize BAC end sequences
Class, subclass, group, clade No. of hits Percentage of hits, % No. of bases, bp Percentage of masked bases, % Percentage of genome,* %
Class I elements (retroelements) 92.65 96.01 55.60
LTR-retrotransposons 90.91 95.65 55.38
Ty1/copia-like elements 133,860 39.74 42.37 24.54
Ji 71,923 21.35 42,306,471 23.78 13.77
Opie 37,451 11.12 22,168,294 12.46 7.22
Prem 14,129 4.19 6,439,116 3.62 2.10
Other copia 10,357 3.07 4,455,318 2.50 1.45
Ty3/gypsy-like elements 116,375 34.55 37.02 21.43
Cinful 40,706 12.08 24,989,484 14.05 8.14
Grande 16,752 4.97 9,772,902 5.49 3.18
Huck 16,892 5.01 9,107,710 5.12 2.97
Tekay 3,116 0.93 1,472,939 0.83 0.48
Zeon 30,305 9.00 17,452,971 9.81 5.68
Other gypsy 8,604 2.55 3,043,159 1.71 0.99
Other LTR-retrotransposons 55,941 16.61 28,912,679 16.25 9.41
Retroposons without LTR 1.75 0.36 0.21
LINEs 1,237 0.37 285,530 0.16 0.09
SINEs 3,802 1.13 256,122 0.14 0.08
Other unclassified retroelements 847 0.25 104,778 0.06 0.03
Class II elements (DNA transposons) 4.12 1.69 0.98
hAT superfamily (hobo-Ac-Tam3) 4,310 0.15 84,656 0.05 0.03
CATA superfamily (En/Spm) 3,140 0.93 981,562 0.55 0.32
MuDR/Mu superfamily 502 0.15 42,734 0.02 0.01
MITEs 1.28 523,368 0.29 0.17
Helitrons 144 0.04 11,174 0.01 0.00
Other unclassified DNA transposons 5,274 1.57 1,366,349 0.77 0.44
Simple repeats 1.42 0.68 0.40
Centromeric repeats 2,348 0.70 598,640 0.34 0.19
Telomeric repeats 465 0.14 131,884 0.07 0.04
VNTR (mini- and microsatellites) 1,030 0.31 85,500 0.05 0.03
Knob-region 956 0.28 402,235 0.23 0.13
High-copy-number genes (ribosomal) 4,908 1.46 2,506,369 1.41 0.82
Other undefined repeats 1,179 0.35 364,729 0.21 0.12
Total 336,840 100 177,871,282 100 57.91
  • Greater than 70% identity limit. MITE, miniature inverted-repeat TE; LINE, long interspersed nuclear element; SINE, short interspersed nuclear element; VNTR, variable number terminal repeat.

  • * Based on 2,365 Mb.