Table 1.
Families and genes used in the analyses
[i] aGAG and RNase H were not assessed for copia families, and no LTR retrotransposons of rire3 exhibited homology to RNase H.
[ii] bSuperfamily of each LTR retrotransposon family.
[iii] cFamilies were delineated using the program RepMiner (Fig. 1) and the RetrOryza db (http://www.retroryza.org).
[iv] dAverage insertion date of each family, using a substitution rate of 1.3 × 10−8 per site per year (Ma and Bennetzen 2004).
[v] eNumber of sequences used per family/gene combination.
[vi] fLength of nucleotide alignment, with gaps.
[vii] INT, integrase; RVT, reverse transcriptase; GAG, gag; RH, RNase H.