. 2004 Dec;42(12):5757–5766. doi: 10.1128/JCM.42.12.5757-5766.2004

TABLE 1.

Sequences of primers, amplicon sizes, annealing temperatures, and accession numbers used in this study

DNA target name^a	Forward primer (5′-3′)	Reverse primer (5′-3′)	Amplicon size (bp)	Annealing temp (°C)	GenBank accession no.
Genes conserved in both genomes
16S rDNA	fD1, SFG3, SFG4^b	Rp2, SFG2, SFG5, SFG6^b	1,400	See reference 47	AF541999
gltA	CS1d, CS535d, Rp877p^c	CS428r, CS890r, Rp1258n^c	1,047	See reference 49	U59730
ompB	120M59, 120-607, 120-1378, 120AA2235, 120-2788, 120-3462, 120-4232^d	120-807, 120-1497, 120-2399, 120-2988, 120-3599, 120-4346, 120-4879^d	4,682	See reference 48	AF123721
sca4 (gene D)	D1f, D767f, D1219f, D1738f, D2338f^e	D928r, D1390r, D1876r, D2482r, D3069r^e	2,725	See reference 51	AF163008
Genes degraded in one of the two genomes
ompA	190-70^f	190-701^f	632	52	U43806 (Malish), U45244 (Moroccan), U43798 (M1)
Remnant of Rp352	GCAAAACGGTTGACATTTGA	CTCAAGACAAAATGGGGAAAA	221	50	AY515514
Remnant of Rp543	ATTTTGTTAAAACATATGTAGCGGTAT	TTCAATAGACCTCTTCCCAAGC	250	50	AY515515
Remnant of Rp550	CGGCATTAGATTTTCTGCTTG	CCATGTCATTCTTGCTTTCG	230	50	AY515516
Remnant of Rp723	CTCTACTAAAGCAGATGTCGAAGG	AACGAGCAATACACCTGCAC	250	50	AY515517
Remnant of Rp820	AACCGATGCCTTTTGATTTG	CAACTGCTACATGCCCTGAA	288	50	AY515518
Split Rc148	TCTTTTTGAAGATTGGTGGAAAA	AAGGTTGATGCAAGGGACTTT	166	52	AY518488
Split Rc149	TTTGCAGGTACTGGCTTTATTTC	CCCTGAAAACCGTAACGAAT	159	52	AY518489
Split Rc215	CAAACCGGCTTGAATGATTT	AAGTATCGGCACTTCACATGC	174	52	AY518490
Split Rc217	ATGGAAGCGAGGAGAACCTA	TGCAGAAATATTATCGGTAAAAGC	105	52	AY518491
Split Rc269	CACAGGGGGCTTAAGTAGGTC	ACGGCAAACCAAATACTGTAAA	150	52	AY518492
Split Rc630	GGCATCATTATGCGGGAACAT	CCTCCTACAAGACCGACACC	106	52	AY518493
Split Rc653	AAGCATGCCGATGATTTACC	TGCAATTTCTTGAAGGCTTTT	156	52	AY518494
Split Rc654	TGCAAATCAAGGAGTAATGGTG	TTGCGTTATGCTTTGTATATTCG	157	52	AY518495
Split Rc655	GTCAAAACCGGAAATTGCAC	AAATGAAGGTTCGTTAAAAGCA	103	52	AY518496
Split Rc704	GAGACGATGGAATAGGAGTACTGAA	TTTTCTGCCCCAAATTTTTCC	157	52	AY518497
Split Rc721	TGAGACTCAAAGCCCTTATTTTTC	GGTGTTATTTCTTTATATCGCCAGT	150	52	AY518498
Split Rc776	GGAGGAGCTAAGGGAGCAAT	AAATTTCTTCAAATCGCTCAGG	160	52	AY518499
Split Rc777	TGGCTGATATAAAGGTAAGAAAACA	TCCTGCAATGTTTTTGTTTGA	156	52	AY518500
Split Rc837	GCTTGTGGTCTTGGTGTGG	AGCAAACATTTCGGTAACACC	150	52	AY518501
Split Rc838	GCCGAAAATGACGGTAAAAA	AGTGGAGCATGGTTTGCTGT	156	52	AY518502
Split Rc839	TTGGTTACAGCTGGAAATATGG	CACAAAGATATTTTACAAGAAAGTCA	187	52	AY518503
Split Rc840	GAGAAGCAGTTAATTGGACGTAAA	CAAGAAGCGCATCAAGATCA	150	52	AY518504
Split Rc925	ATTCCGGCATGGATGCTT	CCAAAGCACAAACCATAGAAAA	155	52	AY518505
Split Rc1042	GGTAGGGGCAAACAAAAGCTG	TGCCTTAAGTTTGAGTTGCTTGAA	196	52	AY518506
Split Rc1100	TGCTGTTTCTAGCTTAATGTG	CCTGTTTCTTTTTCCAACTTTTG	159	52	AY518507
Split Rc1101	TGCAGCTCAGGTTATTCATCA	TTAAAAGGTATGGTGCAAATAGAA	160	52	AY518508
Split Rc1102	AGGATTTAATTGGCGTCTTGC	TTTTTGTCGATATTTGCTTTTTCA	150	52	AY518509
Split Rc1137	CGCTTTCGTGAGAATGACAA	TCACCGTAGCTTCTCAAAGTTTC	161	52	AY518510
Intergenic spacers
nusG-rplK	CAGTTGCAATATTGGTAAAGCA	CAGCAGCTGGAATTATCAAGTT	270	54	AY345058
rpoB-rpoC	CAGGCATTCCTGAATCATTT	TCCGTAAAAATTTACTACGCTCA	257	54	AY345057
yqiX-gatB	CTGCGGCAGTACCGACTATT	ATCCGACGCTTGTGAATCAG	258	54	AY345059
rrf-pyrH	GAGCTTTCTCCATCTTTTCTTG	AAAGGGGAATATACGACAATTGAG	238	54	AY345060
RC0241-RC0242	AGCTCAAATTGTGGTGTTTCC	GGGATCCCTATTACAGCAAAA	343	54	AY345061
rne-coxW	CGGAAAAGAATGCAGAGTCTTG	CCATTTTGTAATTAAACTTTTCTGC	244	54	AY345062
RC0432-hsIV	TGTGTGGAGTTAATGTATATTGCGAT	CGAGACTTGTCCATCTGCTG	283	54	AY345063
asmA-rimM	TTAAAGGAATAAAGAAAGGAATAACAA	TTTTCAAATCAAACAACCGAAT	281	54	AY345064
murG-RC0563	GAAGAAAAGAAGGGCATAAGCTA	CAAGCTGAAAGTAAAAACATTCC	293	54	AY345065
dnaN-RC0584	TCGTCATGCCTGTTAAGGTG	TTGGATAATCACCCGCTAAGA	354	54	AY518297
lig-tgt	TTTTTGTGCTTCCTCTTCAGAT	CCAAAATCTCATGAGCCGTA	285	54	AY345066
rpsA-cmk	GCTGCAAGTTGTGGAACAAA	TTACCGGCTTCAGAGATGCTTT	254	54	AY345067
Rho-RC0760	CGGTQTTGTTAAGTTCTGCTGTG	TGCATGCCATTACTTATTACAAATG	385	54	AY345068
folC-bioY	AGGTCGGCACCGGAAAAT	TACGGCGGCGTATTACCTT	269	54	AY354069
tRNA^Leu-mgtE	AGCATTGAGGGTGCTGTTCT	TTCAGCAAATTGATCGTGATG	267	54	AY345072
pth-rplY	TTCCTGGATTACCAAGACCAA	GAAGCTGAAGGGGAACAACA	322	54	AY518299
ntrY-rpsU	AGCTGCTGTTGCTAAAGTAAAAA	CAAGAAGCAGCAAGAAGACAGA	363	54	AY345070
cspA-tRNA^Leu	CGCCATTGTCCTGTTCAATA	TCCGTTATGTCTACCATTCCA	375	54	AY345073
tmk-proP4	TTCCCCTCCCTCAAATGTAA	CGGAGCAAGAAACCCATAAA	258	54	AY354074
msbA2-RC1074	TCGAAATATTTGCAGAGAGCAG	TGAGCTCGCGAAAGTTAGAA	302	54	AY518298
proP5-RC1171	TGCGTGATTTTGTTTGTTTCA	GCACGTAAAATGGGAAAGTGA	261	54	AY345075
dksA-xerC	TCCCATAGGTAATTTAGGTGTTTC	TACTACCGCATATCCAATTAAAAA	416	54	See Fig. 4
serS-virB4	CGGATGTCTTGATAAATTACATGG	TCAAATTTTCGTAAACCACTAAACA	344	54	AY345076
tRNA^Ile-pal	GCGTGCTCTAACCAACTGAG	GAAGAAGCTTTTGCCTATAATCG	307	54	AY345079
pbpA2-RC0856	AGGTTTCCATTTTTCCCAAA	CGAGTAGAGTGZZGGZTZCTCGATG	343	54	AY518300
tRNA^Phe-nifR3	TTGAACCAACGACACAAGGA	CCGTAACACCTGACATTGGA	251	54	AY345080
spo0J-abcT1	AAAGATTTGGAAGAATTAGACTTGAT	TTTGCTTAAACCAACCATTTCA	259	54	AY345081
RC0098-dcd	CCGATGCAAGGCAAATAATA	CGCAAAGGGCCTTATCATAC	288	54	AY345083
RC0102-RC0103	GCGATAAGCGATTTATTAGGC	GAAAGCCTAAAGCCTCCACA	240	54	AY345084
tRNA^fMet-RC0138	GGTCGTTGGTTCAAATCCAG	AAGTCGTCATTGCGAGAAGG	265	54	AY521231
23S rRNA-5S rRNA	GTTGATAGGTCGGGTGTGGA	GGGATCGTGTGTTTCACTCA	200	54	AY345100
mppA-purC	GCAATTATCGGTCCGAATG	TTTCATTTATTTGTCTCAAAATTCA	160	54	AY345089 (type A), AY345087 (type B), AY345086 (type C), AY345085 (type D), AY465118 (type E)
tRNA^Gly-tRNA^Tyr	AGCTTGGAAGGCTGGAACTC	ATCCTTCTCCCTCCACCACT	148	54	AY345097 (type A), AY345099 (type B)
rpmE-tRNA^fMet	TTCCGGAAATGTAGTAAATCAATC	TCAGGTTATGAGCCTGACGA	144	54	AY345091 (type A), AY345092 (type B)
fabZ-lpxD	TGTTAGGATCGATTTTAAGTACTCTATCT	TGGATTGGCATAGACAATCTATTA	195	54	AY518302
fusA-tRNA^Trp	TGATCAAGTGCCGAGTCAAG	GCGCTCTACCAATTGAGCTAC	149	54	AY518303
RC0669-RC0670	TTTAATACCGTTAAACTTATCCAAGTG	TGTTCAACGCCATCATCTTC	295	54	AY518481
RC0280-23S RNA	CAAAAAGCCGACAAAGCCTA	CCTTCATCGCCTTCTAGTGC	258	54	AY518484
acrD-hupA	GGGCGTTTAATACAAATTTTAGACA	CAATTCTCCTTTGATAGGTTAATATGT	388	54	AY518473
RC1137-tlc-5	CGGGATAACGCCGAGTAATA	ATGCCGCTCTGAATTTGTTT	264	54	AY518475
pal-RC1201	TGCAAGCACACATAATGCAA	TCAAAATCGATTCCTCTTTTCC	216	54	AY518472
lgt-RC073	CCTCCGACTATTATGCCTATAACG	ATGACATTTCCTAATATCAATCCAA	244	54	AY518479
udg-RC1213	AATCCCACATATCCGCTACC	AGCCAAAGATAATGAAATCAGAA	248	54	AY518483
secB-czcR	ATGCAGGATTCCAGCCTTTA	GGCTCGCCTTCAATTAACAA	224	54	AY518486
RC0230-RC0231	TGCACCCGCCTAAAACTAAC	ATGGTCGGCCGTAGAAAAA	232	54	AY518480
groES-RC0970	CTTGCATCGGCTTTTCTTTT	AGCTTTGAGCTGATGGGCTA	215	54	AY518487
secA-prsA	GCAGGTTCAAGCGAGTTAATTT	AAAAGCAATACCGGAAAGCA	209	54	AY518485
RC1282-fdxA	CATGCCCTCAGCAAATGATA	GGTTCTGTGAAGATTGCTAATTGA	289	54	AY518482
RC0604-RC0605	AAAGGCAATAACGGCAAAAA	AGCTCGCCAGTTCATTCATC	353	54	AY518474
RC0409-trmU	AACCTTGACGTGCATATTCTAAA	GCCTGACATTGCGACAACTA	270	54	AY518477
RC0272-gyrA	AACAAGAATAGAGCAGCGTTCA	TTTCATCTCATCTTCGATATTTACC	368	54	AY518478
RC1027-xthA2	GGTATGTAAATGAGCCTTATCAATACT	TCAGTAGTATAAGTAGCTCCTGCTGTC	351	54	AY518476

Intergenic spacer designations consist of the name of the 5′ ORF- the name of the 3′ ORF. ORFs encoding putative proteins of unknown function have designations beginning with RC and are numbered with reference to the R. conorii Malish (Seven) genome (GenBank accession no. NC_003103).

See reference 47.

See reference 49.

See reference 48.

See reference 51.

See reference 45.