Table 2.

Classification of the 3222 TEs Annotated in the Whole 18.2 Mb of Sequence Produced from the 13-Mb Contigs of Chromosome 3B

Type of TENo. Copies% of TE CopiesNo. Bases% of TE Fraction% of Genome Fraction
LTR retrotransposons
    Gypsy1,21937.837,939,75053.2343.5964.10
        Complete68856.446,264,45378.9034.40
        Solo LTR917.47175,2452.210.96
        Truncated36730.111,195,15715.056.56
        Unknown735.99304,8953.841.67
    Copia50415.643,036,08120.3516.67
        Complete26452.382,374,14478.2013.04
        Solo LTR356.9465,2942.150.36
        Truncated16031.75435,23414.342.39
        Unknown458.93161,4095.320.89
    Unknown1273.94698,0134.683.83
        Complete7559.06583,18983.553.20
        Solo LTR2015.7533,1504.750.18
        Truncated2922.8373,46110.520.40
        Unknown32.368,2131.180.05
Non-LTR retrotransposons
    LINE1705.28317,5982.131.741.75
    SINE30.097160.000.00
Transposons
    CACTA33210.302,479,61816.6213.6114.53
        Complete13741.21,521,87161.388.36
        Truncated15646.99639,25825.783.51
        Unknown3911.75318,48912.841.75
    Harbinger351.0926,4790.180.15
    Mariner2949.1238,5500.260.21
    Mutator742.3043,7240.290.24
    Hat70.229,4440.060.05
    Others1935.9949,1800.330.27
Helitrons
    Helitron50.1613,5620.090.070.07
Unclassified2598.04264,1841.771.451.45
Total3,22214,916,89981.90
  • The distribution of complete, solo LTR, truncated, and unknown (i.e., undefined or partially sequenced) is indicated for the LTR retrotransposons and the CACTA transposons. For these later subcategories, the proportions of copy numbers and TE fraction are expressed as a percentage within each superfamily.