Table 1. Amount of DNA involved in small DNA arrangements
Subspecies Small DNA rearrangements* Number Total size, bp
indica Insertions 41 81,202
    Insertions of LTR-retrotransposons 13 56,775
    Insertions of MITEs 16 4,353
    Insertions of other DNA transposons 2 15,627
    Insertions (unknown) 10 4,447
Deletions 51 19814
Unclear indels§ 92 38,735
Tandem duplications 8 298
Amplification of SSRs 9 563
japonica Insertions 42 111,127
    Insertions of LTR-retrotransposons 15 95,065
    Insertions of MITEs 16 4,085
    Insertions of other DNA transposons 1 11,480
    Insertions (unknown) 10 4,431
Deletions 38 2487
Unclear indels 84 40,885
Tandem duplications 9 309
Amplification of SSRs 19 611
  • * A total of 604 and 590 small indels <10 bp are excluded from this table, accounting for 1,502 and 1,509 bp of indica and japonica genomic sequences, respectively.

  • Thirteen of 28 insertions of LTR-retrotransposons and 8 of 32 insertions of MITEs were judged by structural analysis.

  • Loss of 5,135 bp of DNA from a LTR-retrotransposon by homologous recombination and a deletion of a 12,749-bp fragment from a LTR-retrotransposon were identified based on sequence alignments relative to known LTR-retrotransposons.

  • § Insertions in indica relative to japonica.

  • Insertions in japonica relative to indica.