Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

^aGAG and RNase H were not assessed for copia families, and no LTR retrotransposons of rire3 exhibited homology to RNase H.

^bSuperfamily of each LTR retrotransposon family.

^cFamilies were delineated using the program RepMiner (Fig. 1) and the RetrOryza db (http://www.retroryza.org).

^dAverage insertion date of each family, using a substitution rate of 1.3 × 10⁻⁸ per site per year (Ma and Bennetzen 2004).

^eNumber of sequences used per family/gene combination.

^fLength of nucleotide alignment, with gaps.

INT, integrase; RVT, reverse transcriptase; GAG, gag; RH, RNase H.