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1 Additional Data File 13. List of 83 disease resistance-related genes that matched the unmapped BESs of On, Or, and Og. BESs that had internal stop codons within the aligned regions are presented in parentheses. Accession # Definition Accession # of BESs O. nivara O. rufipogon O. glaberrima AAX95851 NB-ARC domain, putative [Oryza sativa (japonica CL CW670370,(CW677751),CW ABG22484 retrotransposon protein, putative, - (CL792545),(CL798160) - unclassified,(cl806925),(cl ),(CL829057),(CL ),(CL862603) BAC45136 putative nucleotide-binding - - CW leucine-rich-repeat protein 1 [Oryza sativa Japonica Group] BAC84181 putative stripe rust resistance protein Yr10 [Oryza sativa Japonica Group] - - (CW668819),CW668896,CW BAD23621 blight resistance protein SH20-like - - CW [Oryza sativa Japonica Group] CAD45031 NBS-LRR disease resistance protein - CL homologue [Hordeum vulgare] CAH66367 OSIGBa0130K07.3 [Oryza sativa (indica - CL823783,CL839857,CL

2 CAJ86357 EAY74323 EAY77774 EAY77791 EAY78567 EAY80341 EAY80342 EAY80354 EAY80850 EAY80990 OSIGBa0117N13.1 [Oryza sativa (indica hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ CL805480,CL CL (CL707703),CL (CL811599) CW CW661847,CW852671, CW CL (CW666128) - CL CL611592,CL614106,CL ,CL716481,CL ,CL722882,CL ,CL741613,CL CL614473,CL CL795284,CL

3 EAY80991 EAY81273 EAY81275 EAY81279 EAY81540 EAY81542 EAY81558 EAY81588 EAY81809 hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ CW CL (CW654326),CW CL CL CW CL618156,CL712212,CL ,(CL712765),CL ,CL775801,CL CL CW CL776767,CL783354,CL - CW659764,CW660194, CW678779,(CW680210),CW CL610961,CL628776,CL - CW665546,CW ,CL731498,CL ,CL754979,CL ,CL759929,CL781294

4 EAY82533 EAY83109 EAY83190 EAY83206 EAY83316 EAY83535 EAY83683 EAY83937 EAY85750 EAY85833 EAY85953 hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ CL CL CL CL814175,CL CW657851,CW680471, CW CL CW CL613148,CL617673,CL ,CL757080,CL ,(CL787016) CL CL796834,CL832417,CL CW CL815971,CL (CW679060),CW CW CW761840,CW775279

5 EAY88487 EAY94423 EAY96767 EAY97677 EAY99388 EAZ02190 EAZ03120 EAZ03122 EAZ03692 EAZ03693 hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ CW659494,CW CL743712,CL CL793303,CL814927,CL CW657010,CW685554, ,CL CW685973,CW774749, CW CW CL622853,CL CL CW669415,CW CL630273,CL CL CW658575,(CW681989) - - (CW664493),CW CL CL814662,CL CL611025,CL620245,CL CL819114,CL844980,CL CW ,CL756501,CL ,CL ,CL778428,CL

6 EAZ03865 EAZ06155 EAZ06180 EAZ06896 EAZ07816 EAZ08545 EAZ08556 EAZ08771 EAZ08819 EAZ09172 EAZ11520 hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsI_ hypothetical protein OsJ_ CL798530,CL CL798426,(CL818660) (CW757530) - - CW665209,CW CL CL813643,CL CW CW CL CL720299,CL CW (CL624144),CL721448, CL CL747839,CL CL710360,CL755881,CL CL

7 EAZ17814 EAZ17854 EAZ17877 EAZ18355 EAZ18403 EAZ18867 EAZ19037 EAZ19226 hypothetical protein OsJ_ hypothetical protein OsJ_ hypothetical protein OsJ_ hypothetical protein OsJ_ hypothetical protein OsJ_ hypothetical protein OsJ_ hypothetical protein OsJ_ hypothetical protein OsJ_ CL612832,CL CL823776,CL CL CL CW663785,CW665381, CW669074,CW691226, CW755165,(CW773029) - CL CW (CL800266),(CL852113) - CL CL746564,CL758336,CL - CW754518,CW

8 EAZ39030 EAZ39807 EAZ40863 EAZ41791 EAZ44276 EAZ44473 EAZ44474 hypothetical protein OsJ_ hypothetical protein OsJ_ hypothetical protein OsJ_ hypothetical protein OsJ_ hypothetical protein OsJ_ hypothetical protein OsJ_ hypothetical protein OsJ_ (CW653528),(CW ),(CW764637) - CL815333,CL833700,CL CW687805,CW ,CL CL709211,CL717799,CL - CW (CW660766) - CL CW CL (CW662024) - - CW657610,CW755985, CW772711

9 NP_ Disease resistance protein family CL CW NP_ Transcriptional factor B3 family CL NP_ Disease resistance protein family - - CW660160,CW686461, CW NP_ Disease resistance protein family (CL785928) - - NP_ Similar to NBS-LRR disease - CL854607,CL resistance protein homologue (Fragment). NP_ Similar to NBS-LRR disease - CL796711,CL CW resistance protein homologue (Fragment). NP_ Disease resistance protein family CL NP_ Ras GTPase family - CL

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