Table 1 Statistics of the LTR retrotransposons in the eight AA-genome Oryza species
TotalSATRUFNIVGLABARGLULONMER
Assembled lengtha373394307312308305298311
Estimated lengthb389473395370376366344388
Numbers of LTR retrotransposon families
 Total790582733641643606634698649
 Ty1-copia126104123113108107116114113
 Ty3-gypsy166132155131136125133149138
 Unclassified498346455397399374385435398
Sequence lengths of retrotransposons in the genomesc
 Total124.0297.3276.8878.1374.9774.7362.8380.67
 Ty1-copia12.6510.948.868.978.598.926.619.49
 Ty3-gypsy66.6339.0130.0230.8228.7529.1420.8733.43
 Unclassified44.7347.3738.0038.3437.6236.6735.3537.75
  • SAT, O. sativa ssp. japonica. cv. Nipponbare (Release 7); RUF, O. rufipogon; NIV, O. nivara; GLA, O. glaberrima; BAR, O. barthii; GLU, O. glumaepatula; LON, O. longistaminata; MER, O. meridionalis; LTR, long terminal repeat.

  • a Assembled length (Mb) stands for total contig length.

  • b Estimated length (Mb) was assessed by reads at 17 k-mer.

  • c Sequence lengths of LTR retrotransposons in genomes (Mb) were calculated based on the annotation using RepeatMasker.