Table S1. Primers used in this study
Tn-Seq primers
P1 M6 MmeI
Gex PCR Primer 2
AP-A bc-ACACa
AP-B bc-ACACb
CAAGCAGAAGACGGCATACGAAGACCGGGGACTTATCATCCAACCTGT
AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
GTTCAGAGTTCTACAGTCCGACGATCACACNN
5’Phos-GTGTGATCGTCGGACTGTAGAACTCTGAACCTGTC-3’Phos
Construction of deletion vectorsc
GSU1704U1 HindIII
GSU1704U2
GSU1704D1
GSU1704D2 BamHI
GSU2220U1 HindIII
GSU2220U2
GSU2220D1
GSU2220D2 BamHI
GSU2222U1 PstI
GSU2222U2
GSU2222D1
GSU2222D2 BamHI
GSU3376U1 XbaI
GSU3376U2
GSU3376D1
GSU3376D2 EcoRI
GSU2645-2642U1 XbaI
GSU2645-2642U2
GSU2645-2642D1
GSU2645-2642D2 HindIII
GSU2726-2724U1 XbaI
GSU2726-2724U2
GSU2726-2724D1
GSU2726-2724D2 HindIII
GSU2739-2731U1 HindIII
GSU2739-2731U2
GSU2739-2731D1
GSU2739-2731D2 XbaI
GSU2940-2936U1 XbaI
GSU2940-2936U2
GSU2940-2936D1
GSU2940-2936D2 HindIII
GACTAAGCTTAGAGTCACCACCGGGTCATGA
CTGGCTATCTTCTTCATCAGTTCGAGCCCGTACAGACTGCTCCTGTTT
AAACAGGAGCAGTCTGTACGGGCTCGAACTGATGAAGAAGATAGCCAG
GACTGGATCCATGTGGGCCATGACCGGGATG
GACTAAGCTTTGACGTGTTCGATGAGATCAGGC
TACATCAATGCTGAATCGAGCACCTTTGTATCGGAGACAAGGTCTTCCAC
GTGGAAGACCTTGTCTCCGATACAAAGGTGCTCGATTCAGCATTGATGTA
GACTGGATCCCGGTCACGTCATCAACCACGAG
GACTCTGCAGGACGAGATCGTCGGGCTTGGC
GACGAGGATCGTCCTCTGGTCTGATGCGTCGTGCGTGTTGGT
ACCAACACGCACGACGCATCAGACCAGAGGACGATCCTCGTC
GACTGGATCCGGTTGCCAGGATATTGATCTTGCG
AGTCGTCTAGAAAGAGCCGATACTGTAACTACGCG
CTCCACCCTGTTGCGACCGTTGTCGATTACGAGGGCTGTCATCG
CGATGACAGCCCTCGTAATCGACAACGGTCGCAACAGGGTGGAG
AGTCGGAATTCGGAGTACGAAGAGGTAACCGAGGC
ACGTCGTCTAGACTTCAATGTGAGCGATGGTCACC
GCAGGCGGCGTCAACGAACGGCAACCATCGCCACCAAG
CTTGGTGGCGATGGTTGCCGTTCGTTGACGCCGCCTGC
ACGTCGAAGCTTCGCGAACTGCGATGGAAACGTAG
ACGTCGTCTAGACCTCGATGTCACTGATTTCAGCC
CTACCACGTCATGCTTCTCGTATGCTGCAATCGCTGTTTCATTGCTCC
GGAGCAATGAAACAGCGATTGCAGCATACGAGAAGCATGACGTGGTAG
ACGTCGAAGCTTCGTGCTGCTTCGGCAACTC
ACGTCGAAGCTTCGCCACGCCAACCGATATC
TTCACGTTGCTCCGGCAAGCGTTGATCACTTTTGGCGCGTC
GACGCGCCAAAAGTGATCAACGCTTGCCGGAGCAACGTGAA
ACGTCGTCTAGAAGATGGAATCGTATCGGCAACCG
ACGTCGTCTAGAGAACCTGCCGCTTCTGATCC
GTGCTGCGTGGGTGCTACTTCTGTTTCGCCATACAACCTCC
GGAGGTTGTATGGCGAAACAGAAGTAGCACCCACGCAGCAC
ACGTCGAAGCTTCCTCATAGGCGGAATCGGCATT
Confirmation of gene deletion
aseA (GSU1704)
CTGATGGAGACCGATGTCACCT
GCGAGGGCATCCTCCAGCAA
GCTCTACCTGATGCATGCCGA
aseB (GSU2220)
GCTTGATGTCACCCACCTGCA
CCGAGTTCATGAATCGGGCGA
aseC (GSU2222)
CTCCACCAGAGAGGCGTCGAT
ATCGACAACATCGCCCGCATC
aseD (GSU3376)
GAAATACCTCGACGCCCTGGCG
GTGGCGTGTACGGCGATTG
extABCD (GSU2645-2642)
CTGTCGGCAGTGCGCTACTTG
CACGGTCTGCATCACAGCC
extEFG (GSU2726-2724)
CCAGACTGCTCCAGAAGGTGG
omcBC cluster (GSU2739-2731) GCAGGAAGCCGTCTGTCAG
GTGTACCCAGATCGAGAATGCC
GTTCTTGAGGTAGAGCCGCTCC
extHIJKL (GSU2940-2936)
GTTGTGGCAGCGGAAGCAG
a The barcode for the multiplex of samples is underlined, four were used in this study: ACGC, ACTG, ACAC, AGTC.
NN are random nucleotides to ligate to the MmeI generated 2bp overhangs. AP-A bc-ACAC and AP-B bc-ACAC
anneal to form the adaptor used in this study.
primer has 5’ phosphate for the ligation to the dephosphorylated MmeI generated genomic fragments and 3’
phosphate to prevent adaptor to adaptor ligation.
c The (U1, U2) and (D1, D2) primers are used to amplify the upstream and downstream regions of the gene to delete.
The two fragments are combined using overlap PCR and ligated into pK18mobsacB using the indicated restriction
enzymes.
b The