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Supplementary Table S4: Oligonucleotide primers used in this work
Primer name
Sequence (5' to 3')
gibfrag01_fwd
ACACAAAAGAACCCCCAGA
gibfrag01_rev
gibfrag02_fwd
gibfrag02_rev
0347US_fwd
0347US_rev
gibfrag03_fwd
gibfrag03_rev
gibfrag04_fwd
gibfrag04_rev
0347DS_fwd
0347DS_rev
insrt_cnfirm_fwd
insrt_cnfirm_rev
hmuV_F
hmuV_R
hmuU_F
hmuU_R
hmuT_F
hmuT_R
hmuS_F
hmuS_R
hmuR_F
hmuR_R
hyp_F
hyp_R
exbB_F
exbB_R
exbD1_F
exbD1_R
exbD1a_F
exbD1a_R
Description
Amplify fragment 01 from pPY17a for first
Gibson construction
CAGGAAAGAACATGTGAGCAAA
Amplify fragment 01 from pPY17a for first
Gibson construction
CCTTTTGCTGGCCTTTTG
Amplify fragment 02 from pPY17a for first
Gibson construction
GTTAAGGGATGCAGGTCG
Amplify fragment 02 from pPY17a for first
Gibson construction
CGACCTGCATCCCTTAACAACCAAAAGG Amplify upstream region of hmuR from TM1040
TCCAGATCC
genomic DNA and add overhangs. Used in first
Gibson construction
TCTGGGGGTTCTTTTGTGTCTCGATGTAT Amplify upstream region of hmuR from TM1040
TGATCCGCAT
genomic DNA and add overhangs. Used in first
Gibson construction
AAATAATAGTGAACGGCAGG
Amplify fragment 03 from pLH01 for second
Gibson construction
AGAGCTTTGTTGTAGGTG
Amplify fragment 03 from pLH01 for second
Gibson construction
TACGATACACTTCCGCTC
Amplify fragment 04 from pLH01 for second
Gibson construction
ACCCATCACATATACCTG
Amplify fragment 04 from pLH01 for second
Gibson construction
CACCTACAACAAAGCTCTCCCAGACTGA Amplify downstream region of hmuR from
AAAAGCGG
TM1040 genomic DNA and add overhangs. Used
in second Gibson construction
GAGCGGAAGTGTATCGTATTGCGTCTGA Amplify downstream region of hmuR from
TATTGCTTGT
TM1040 genomic DNA and add overhangs. Used
in second Gibson construction
AGAGGCCGCAAGAGTGAA
Used to confirm double cross-over event in R.
LH02
GAGGGAGGTGAGGACAGCAA
Used to confirm double cross-over event in R.
LH02
ATCAACGCCTGTCAGAGGTC
(B4) – used in RT-qPCR
GTTTGCGGCAGAACAAAGAC
(A1) – used in RT-qPCR
TCATCAGCCGTACCATCATC
(B5) – used in RT-qPCR
CGTTTCAGCAAGATCCACAG
(A2) – used in RT-qPCR
TATCCGTGAACCCAAACCTG
(B6) – used in RT-qPCR
GTTGATCTTGTCGACGATGC
(A3) – used in RT-qPCR
GATTCTGCAGCCAGAAATCG
(B7) – used in RT-qPCR
TGTCGGTGTCTTCATTCAGG
(A4) – used in RT-qPCR
AATTGACGACCGATCCTGAG
(A5) – used in RT-qPCR
CGGAGCCATATTCAAACGAC
(B8) – used in RT-qPCR
GATGCTTCTGACGCTCTTTG
(A6) – used in RT-qPCR
ACACCAGCAACATCGAACTG
(B9) – used in RT-qPCR
GTTCTGGACGGCAATAAAGG
(A7) – used in RT-qPCR
CGATCGACAGTCCAATAAGC
(B10) – used in RT-qPCR
TGCTCTCTTCGACGTTTTCG
(A8) – used in RT-qPCR
CTTCACCATTCAGCGACATC
(C1) – used in RT-qPCR
GATGGTAGCCTGCATTTTCG
(A9) – used in RT-qPCR
TTCCTCTTCCCAGATGATGC
(C2) – used in RT-qPCR
tonB_F
tonB_R
rpoD_F
rpoD_R
gyrA_F
gyrA_R
gmkA_F
gmkA_R
kmR_F_compete
kmR_R_compete
hmuR_F_compete
hmuR_R_compete
AAGAGACCGCTGTGGAAATC
CTGAACAAGGTCCGCAAAAC
CGCCAAGAAATACACCAACC
TTATAGCCGCGACGGTATTC
ACGCTCTTTGTGGCGAATAC
GGGATTGGCAGAATGTTGAC
TGCTCTTTGACATCGACTGG
AGATCGACAGCGTGTGTTTG
ATTCTCACCGGATTCAGTCG
ATTCCGACTCGTCCAACATC
AAAGGAACGGTTGAATGCGG
GATCTCCTGGCGTTCGTAGC
(A10) – used in RT-qPCR
(C3) – used in RT-qPCR
- used in RT-qPCR
- used in RT-qPCR
- used in RT-qPCR
- used in RT-qPCR
- used in RT-qPCR
- used in RT-qPCR
- used for TM1040 + LH02 competition exp
- used for TM1040 + LH02 competition exp
- used for TM1040 + LH02 competition exp
- used for TM1040 + LH02 competition exp
Letters in parentheses in the “Description” column indicate shorthand names for primers as
designated in the figures