Figure S1. Frequencies of sequences with continuous undefined nucleotides (Ns) (> 100 bp) adjacent to di-nucleotides repeats (10-100 bp) in the japonica and indica genomes.

Figure S2. Seven japonica-specific insertion (JSI) sites have orthologous and paralogous empty donor sites without JSIs. Each JSI site (JaE) has three homologous sequences that share the same nucleotides (white letters in black) and AT-repeats (ATrs) without a JSI sequence. These consist of paralogous, orthologous and paralogous/orthologous sites in the japonica (Ja chromosome no. Nucleotide positions) and indica genomes (In chromosome no. nucleotide positions).

Figure S3. Confirmation of JSI by PCR primer pairs in a brief rice panel.

Figure S4. The transcripts or predicted genes unique to JSIs within ATs and their counterpart segments in indica.

Table S1. Genomic positions, lengths and detailed ATr sequences of ERTBV segments in the japonica genome.

Table S2. Genomic positions, lengths and details of ATr sequences of ERTBV segments in the indica genome.

Table S3. Characterization of JSPSs that contain ISs on chromosome 10 by manual curation.

Table S4. Features of japonica-specific insertions (JSIs) between ATrs.

Table S5. Characteristics of genes associated with JSI.

Table S6. Characterization of A.thaliana SSR pair sites (AtSPS) by computational analysis on chromosome 1.

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