TABLE 3.

Primers used in this work

PrimerSequenceLocalization in genomeRestriction sitea
A1-hopW1-15′CCCTATAGTGAGTCGAATTCCACTGGAGTCAAGCTTACG3′6121-6139cEcoRI
A2-hopW1-15′GAATTCGACTCACTATAGGGTCTCAGCGGTGTAGCTTTCC3′6711-6730EcoRI
B1-hopW1-15′GTTCTGCTAATGTGGACC3′5607-5624NA
B2-hopW1-15′TAGGATGGGATTGCTGGG3′7232-7249cNA
A1-hopW1-25′CCCTATAGTGAGTCGGATCCGCCTCTATTTGCAACAGC3′63160-63177cBamHI
A2-hopW1-25′GGATCCGACTCACTATAGGGCTATTCCTTCTCTCAGCG3′63471-63488BamHI
B1-hopW1-25′TCCAGGTCGATCATTTGC3′62568-62585NA
B2-hopW1-25′CCGTGATTTCTCTTAGCC3′64178-64195cNA
A1-avrB4-15′CCCTATAGTGAGTCGAATTCGAGCCTTAGTGGTAGTAACC3′3515337-3515356cEcoRI
A2-avrB4-15′GAATTCGACTCACTATAGGGACTAGGTTCATGCATAGGC3′3516388-3516406EcoRI
B1-avrB4-15′CGTGACGAGTGATCATCTGC3′3514781-3514800NA
B2-avrB4-15′ATCCTTTTGCACACCGATCC3′3516888-3516907cNA
A1-avrB4-25′CCCTATAGTGAGTCGGATCCAGAAGCCCGCAGAATTCG3′927554-927571cBamHI
A2-avrB4-25′GGATCCGACTCACTATAGGGTAGATGACGAGCCTTAGG3′928565-928582BamHI
B1-avrB4-25′TTCCAGCACGAAGTATCC3′926946-926963NA
B2-avrB4-25′AAGCGCGAAGAACACGCTG3′929015-929033cNA
A1-hopAB15′CCCTATAGTGAGTCGAATTCAGACAAAGGCTTGATGCC3′107146-107163cEcoRI
A2-hopAB15′GAATTCGACTCACTATAGGGTCCTGATCTCATGGTTGC3′108740-108757EcoRI
B1-hopAB15′TCCATCACCTGTTGAAGC3′106559-106576NA
B2-hopAB15′ATCCGCAACCTCATAGAG3′109299-109316cNA
A1-hopAE15′CCCTATAGTGAGTCGAATTCTCTTGCCTGGCTTACCAC3′4943896-4943913cEcoRI
A2-hopAE15′GAATTCGACTCACTATAGGGTACTGTCGGTGGATATGG3′4946706-4946723EcoRI
B1-hopAE15′AAGCCATGCAGATCCTCG3′4943302-4943319NA
B2-hopAE15′TAATCAGCGCCGAACAGC3′4947287-4947304cNA
A1-avrB25′CCCTATAGTGAGTCGAATTCCGTTCTTACGATCGCGTAGC3′102383-102402cEcoRI
A2-avrB25′GAATTCGACTCACTATAGGGATTCTAGGTGGCATTGCAGG3′103535-103554EcoRI
B1-avrB25′GCCGATAACCTGATCTACG3′101280-101298NA
B2-avrB25′CTTAACTGAGACATCAACGGC3′104481-104501cNA
A1-avrD15′CCCTATAGTGAGTCGGATCCAAACAGCTGCTGATTCCC3′96818-96835cBamHI
A2-avrD15′GGATCCGACTCACTATAGGGTGCTGAAGCTATACAGCC3′97836-97853BamHI
B1-avrD15′TCCGGATGGGGTATACTC3′96266-96283NA
B2-avrD15′TGGCGGCTTTGATCTGTG3′98300-98317cNA
A1-hopD15′CCCTATAGTGAGTCGAATTCCAATGTGTGGTCGCAAGG3′7093-7110cEcoRI
A2-hopD15′GAATTCGACTCACTATAGGGATCATAGTCGACGCGACCT3′9280-9298EcoRI
B1-hopD15′GCATTCAGTTCACCAGACG3′6554-6572NA
B2-hopD15′CGTATAGTGACAAAGGAGG3′9859-9877cNA
A1-hopF35′CCCTATAGTGAGTCGAATTCAGCTTGATGCTGTGCTCC3′4039619-4039636cEcoRI
A2-hopF35′GAATTCGACTCACTATAGGGATGCCCATGGAAGATTCC3′4040252-4040269EcoRI
B1-hopF35′TGCAACTGAACCAGCACC3′4038961-4038978NA
B2-hopF35′ATCTGGCGAGCATTCTCG3′4040823-4040840cNA
A1-hopG15′CCCTATAGTGAGTCGAATTCAGGCAGCATGCGTATTTGC3′897388-897406cEcoRI
A2-hopG15′GAATTCGACTCACTATAGGGTACGTGGTCATCACAAAGC3′899013-899031EcoRI
B1-hopG15′CCTTCATGCCTTGATGACTG3′896841-896860NA
B2-hopG15′ACAGACCGTTGTTAGCCAG3′899582-899600cNA
A1-hopI15′CCCTATAGTGAGTCGAATTCTTTTCGGCGTGAGGAGAC3′4988642-4988659cEcoRI
A2-hopI15′GAATTCGACTCACTATAGGGATGCTTCTCCGGGAACTC3′4989672-4989689EcoRI
B1-hopI15′AGATCACCGGATACATCG3′4988059-4988076NA
B2-hopI15′TTCTGTAGAGCAACACGG3′4990274-4990291cNA
A1-hopQ15′CCCTATAGTGAGTCGAATTCATCTGCGCTTGTCCAGTC3′9414-9431cEcoRI
A2-hopQ15′GAATTCGACTCACTATAGGGCTGGATAGATGAACCTGC3′10751-10768EcoRI
B1-hopQ15′TGTCGGAACAGATACTGC3′8876-8893NA
B2-hopQ15′CGAGACATGGATGTGTGG3′11381-11398cNA
A1-hopR15′CCCTATAGTGAGTCGAATTCAACAAAGGAAGCGACCTG3′198648-198665cEcoRI
A2-hopR15′GAATTCGACTCACTATAGGGGCATCATGCCGAATAGG3′204628-204644EcoRI
B1-hopR15′GCATTCTCAGGTTGTAGATGG3′198090-198110NA
B2-hopR15′CGTCGAGTATCTGTATCGTTGG3′205178-205199cNA
A1-hopX15′CCCTATAGTGAGTCGAATTCTGTTCCTCACTGATTGCG3′1508676-1508693cEcoRI
A2-hopX15′GAATTCGACTCACTATAGGGACAGGTCATAGAGTTCGG3′1509903-1509920EcoRI
B1-hopX15′TGAGCGTGAGAGTTACACG3′1508038-1508056NA
B2-hopX15′GGTCTGACATAATCTGCG3′1510496-1510513cNA
A1-hopAJ15′CCCTATAGTGAGTCGGATCCCTTCATAGGTTTAGCTCGC3′892773-892791cBamHI
A2-hopAJ15′GGATCCGACTCACTATAGGGTGTGAAGTGAAAGTGGCC3′894080-894097BamHI
B1-hopAJ15′TGACAAGCATGCCAAAGC3′892244-892261NA
B2-hopAJ15′CAATCACGGAAGAAGCAC3′894731-894748cNA
A1-hopAK15′CCCTATAGTGAGTCGAATTCAAAAGGGCGACCGAAGTC3′1652010-1652027cEcoRI
A2-hopAK15′GAATTCGACTCACTATAGGGTGAACGATTCGTGATCCG3′1653668-1653685EcoRI
B1-hopAK15′TTGCGTGAAGAGCAACAG3′1651461-1651478NA
B2-hopAK15′CGCCAGCTATAGCAAGAC3′1654216-1654233cNA
A1-hopAS15′CCCTATAGTGAGTCGAATTCGATCAATACAGGTGGTGG3′5376014-5376031cEcoRI
A2-hopAS15′GAATTCGACTCACTATAGGGACGCTGGTCATTCAACTG3′5380168-5380185EcoRI
B1-hopAS15′TGGACGCGTCTTGAATGG3′5375449-5375466NA
B2-hopAS15′TGTCGGATTAGTTCAGGG3′5380661-5380678cNA
A1-hopAT15′CCCTATAGTGAGTCGGATCCACGCTTCTGGATCTTCGG3′894814-894831cBamHI
A2-hopAT15′GGATCCGACTCACTATAGGGTTGAGGATCACAAAGCGC3′895177-895194BamHI
B1-hopAT15′TACATATCCTGTGCGCTG3′894188-894205NA
B2-hopAT15′GGATCTGAATTCCATCGC3′895766-895783cNA
A1-hopAU15′CCCTATAGTGAGTCCTCGAGGGAGGGTTCCAAAGACAG3′26320-26339cXhoI
A2-hopAU15′CTCGAGGACTCACTATAGGGAGCCTGGAGACATTCATGC3′28431-28449XhoI
B1-hopAU15′AGTACCGCAGTCCTTCAC3′25800-25817NA
B2-hopAU15′CTCTGGTGATGTTTTCCG3′28993-29010cNA
A1-hopAV15′CCCTATAGTGAGTCGGATCCCTGCTCCAACTATTAGCC3′45681-45698cBamHI
A2-hopAV15′GGATCCGACTCACTATAGGGATCTCGTCGATGAAGGAC3′48004-48021BamHI
B1-hopAV15′TGTTCAACTACGACCGTC3′45126-45143NA
B2-hopAV15′AACATCCGGCTACTTCAG3′48631-48648cNA
A1-hopAW15′CCCTATAGTGAGTCGAATTCTATGCGTAGTGAACAGGG3′104780-104797cEcoRI
A2-hopAW15′GAATTCGACTCACTATAGGGAGAAACACTGAGTGGTCG3′105491-105508EcoRI
B1-hopAW15′TTCACGTACCTCATCTGC3′104148-104165NA
B2-hopAW15′ATCCAACTGCACATCAGC3′106029-106046cNA
A1-hopAF15′CCCTATAGTGAGTCGGATCCCCGTTGGTTATGTGATGC3′1685066-1685083cBamHI
A2-hopAF15′GGATCCGACTCACTATAGGGCAGCGCTTCGATTTTGCC3′1686077-1686094BamHI
B1-hopAF15′CACTCAAGCCGATCTACC3′1684461-1684478NA
B2-hopAF15′GCTTCATCCCCGATATCC3′1686634-1686651cNA
A1-avrE15′CCCTATAGTGAGTCGAATTCCTGTAGAAATGCGCGAGC3′1477655-1477672cEcoRI
A2-avrE15′GAATTCGACTCACTATAGGGATGTGCCACTGATGGCAG3′1482889-1482906EcoRI
B1-avrE15′GAAGCTCGCGTGTCCGTC3′1477068-1477085NA
B2-avrE15′CGATCATTGGCAACAGC3′1483518-1483534cNA
A1-avrRps45′CCCTATAGTGAGTCGGATCCAACACATCATAGCCCCTG3′75967-75984cBamHI
A2-avrRps45′GGATCCGACTCACTATAGCCTAATGCGCATGAGCAGGC3′76681-76698BamHI
B1-avrRps45′TTTGCCTTCGCCGTACAG3′74923-74940NA
B2-avrRps45′CGTCAAGACGACGGTCAG3′77748-77765cNA
A1-hopAY15′CCCTATAGTGAGTCGAATTCTCTCCGCTTACTGGCTTGC3′110642-110660cEcoRI
A2-hopAY15′GAATTCGACTCACTATAGGGCACCTGCAATTGGAGAGC3′111601-111618EcoRI
B1-hopAY15′CGGTAATAATTGGCATGG3′110198-110215NA
B2-hopAY15′TGCGCAACATCAACGAGG3′112117-112134cNA
P1-EcoRI5′TCAGAATTCGTGTAGGCTGGAGCTGCTTC3′EcoRI
P2-EcoRI5′TCAGAATTCCATATGAATATCCTCCTTAG3′EcoRI
P1-BamHI5′TCAGGATCCGTGTAGGCTGGAGCTGCTTC3′BamHI
P2-BamHI5′TCAGGATCCCATATGAATATCCTCCTTAG3′BamHI
P1-XhoI5′TCACTCGAGGTGTAGGCTGGAGCTGCTTC3′XhoI
P2-XhoI5′TCACTCGAGCATATGAATATCCTCCTTAG3′XhoI
qRT-avrB4-1/2 F5′GGCGATGTTCAATGGCTAAT3′3515731-3515732; 928198-928217
qRT-avrB4-1/2 R5′TTTTGCAAGCTCCCATCAG3′3515842-3515860c; 928070-928088c
qRT-hopW1-1/2 F5′AATCGTCGCAGCAGGTTC3′63361-63378c; 6591-6608c
qRT-hopW1-1/2 R5′CTCTCCAACTCATGCTGAAGG3′63246-63266; 6476-6496
qRT-hopAY1 F5′CGCTAGACCCTCGAACAGTC3′110760-110779
qRT-hopAY1 R5′CCCTGACCTGACCCTTGTT3′110937-110955c
qRT-hopAH2 F5′TTGCTTGCCAGTCAACAGAC3′3525934-3525953
qRT-hopAH2 R5′GCGATGTCATCAGGATTGG3′3526118-3526136c
qRT-hrpA F5′AGGGTATCAACAGCGTCAAG3′1487676-1487695
qRT-hrpA R5′TCAGAACTGGACGACCGAGT3′1487916-1487935c
qRT-16S F5′CAATGGGCGAAAGCCTGAT3′804368-804386
qRT-16S R5′TGCTGGCACAGAGTTAGC3′804502-804519c
hopW1-1/2 F5′GTCAAGCTTTTATGGAAAGCTACACCGC3′6716-6734c; 63486-63504cHindIII
hopW1-1/2 R5′GTCGAATTCCGATTCATTTTGCTGTTGC3′6379-6397; 63149-63167EcoRI
avrB4-1 F5′GTCCTCGAGGAGCGGAACCGAATAAGAGG3′3515319-3515338XhoI
avrB4-2 F5′GTCCTCGAGAGTGCTGAGGACTCGGTAGC3′928612-928631cXhoI
avrB4-1/2 R5′GTCTCTAGATTTGTTACGAATTCTGCGGG3′3516364-3516383c; 927547-927566XbaI
  • a NA, not applicable.