1. Fig. S1: Fingerprinting of three BAC clones from different accessions of wild rice species with the AA genome constitution. The BAC DNAs were completely digested with the restriction enzyme HindIII and resolved on a 0.8% agarose gel. HindIII- fingerpritings of the BACs were revealed by Southern hybridization following the instructions of the ECL labeling and detection kit (Cat. No. RPN3000, GE, USA). Three Southern hybridizations were done using the whole BAC DNA as the probes: A. OR_BBa0100B19 (Lane 1); B. OR_CBa0092G16 (Lane 2); and C. OR_CBa0094P06 (Lane3). The probe used in the Southern hybridization was marked in asterisk. The extra HindIII-digested band in OR_BBa0100B19 is marked with an arrow to show that OR_BBa0100B19 is the largest clone. 1* 2 3 1 2* 3 1 2 3* ABC

2. OM_Ba0177F21 OM_Ba0178G06 OM_Ba0049B19 OM_Ba0180N01 OM_Ba0165G09 OM_Ba0024C01 NIPPK NBS-LRR cluster Fig. S2: BAC contig covering the Pi2/9 locus in the CC genome of O. minuta. The BAC clones are indicated in rectangles with their names above. Three BACs selected for sequencing are indicated in filled rectangles. The physical relationship between OM_Ba0177F21 and OM_Ba0165G09 in shadow was confirmed by PCR validation and sequencing of the PCR products. Both flanking genes [nitrate inducted protein (NIP) and protein kinase (PK)] are shown in filled boxes. The central NBS-LRR gene cluster is shown in an oval. The figure is not drawn in scale.

3. Nbs12-OM- CC Nbs4-OM-CC Nbs6-OM-CC VG 4 VG 5 VG 7 VG 1 VG 2 VG 6 VG 3 VG 8 Fig. S3: Cladistic analysis of the Pi2/9 gene family members in the Oryza genus. The cladistic tree was constructed based on the sequences of the entire coding sequence (CDS) of the Pi2/9 gene family members in the four wild rice species as well as those in cultivated rice lines. Clustalx and MEGA 4 programs were used for multiple sequence alignment and for tree viewer, respectively. Three genes (Nbs12-OM-CC, Nbs4-OM- CC, and Nbs6-OM-CC) containing large unsequenced gaps are shadowed in their respective clades. The vertical groups (VGs) are shown to the right of their respective clades.

4. Fig. S4: Genomic expansion of the Pi2/9 locus by insertion of transposable elements in the BB subgenome of O. minuta. This figure was modified from Fig. 1 mainly by adding the information of the transposable elements (TEs) in the BB subgenome of O. minuta (A) and O. puncata (B). The TEs are indicated in grey rectangles, and their names are listed above. Detailed information for all the TEs is in Table 3. The shadows linking both genomes indicate the regions that are highly similar to each other, i.e., with ≥90% sequence identity in nucleotides on average. TE1TE3TE4 and TE5TE6 TE7 TE8 TE1TE2TE3 A B TE2 10 kb

5. NBS LRR Pi9 Nbs2-OS-IR31917 Fig. S5: Schematic of the amplification of Nbs2-OS-IR31917. The exons are indicated in red rectangles. The dashed lines in Nbs2-OS-IR31917 indicate the unamplified region. The shadows indicate the amplified and sequenced regions in Nbs2-OS-IR31917.