Increased knowledge of Francisellagenus diversity highlights the benefits of optimised DNA-based assays

Ahlinder, Jon; Öhrman, Caroline; Svensson, Kerstin; Lindgren, Petter; Johansson, Anders; Forsman, Mats; Larsson, Pär; Sjödin, Andreas

doi:10.1186/1471-2180-12-220

BMC Microbiology

Table 2 A list of the markers selected to represent published DNA-based markers for molecular PCR detection or phylogenetic identification targeting Francisella

From: Increased knowledge of Francisellagenus diversity highlights the benefits of optimised DNA-based assays

Marker name/ Target gene	Gene locus_tag^a	Amplicon size (bp)^a	Genomic location^a	Reference
01-16S	FTT_r04, FTT_r07, FTT_r10	1139	1311156-2294, 1378275–9413, 1771610-2748	[17, 37, 38, 56]
02-16 s + ItS + 23 s	FTT_r04, FTT_r07, FTT_r10	915	1311470-2371, 1378876–9490, 1771911-2825	[34]
03-16 s + ItS + 23 s	FTT_r03-FTT_r04, FTT_r06-FTT_r07, FTT_r09-FTT_r10	948	1310519-1466, 1377638–8585, 1770973-1920	[34]
04-16 s + ItS + 23 s	FTT_r03, FTT_r06, FTT_r09	925	1309613-10537, 1376732–7656, 1770067-991	[34]
05-aroA	FTT_0588	650	608150-799	[18, 61]
06-atpA	FTT_0062	634	62762-3395	[18, 61]
07-dnaA	FTT_0001	618	303-920	[19]
08-fabH	FTT_1373	1289	1418892-20155	[62]
09-fopA	FTT_0583	886	599105-990	[19]
10-fopA	FTT_0583	1068	599148-600215	[34]
11-fopA-in	FTT_0583	404	599526-929	[15]
12-fopA-out	FTT_0583	708	599428-600135	[15]
13-fopA	FTT_0583	86	599767-852	[9, 16]
14-FtM19	FTT_1472c	250	1524132-381	[56, 58]
15-FtM19	FTT_1472c	316	1524066-381	[65]
16-FTT0376	FTT_0376	107	377718-824	[17]
17-FTT0523	FTT_0523	91	546620.712	[17]
18-groEL	FTT_1696	803	1764659-5461	[34]
19-iglC	FTT_1712c	84	1792514-597	[9, 16]
20-ISFtu2^b	FTT_1311	390	1335726-6115	[56, 59]
21-ISFtu2	FTT_0099^c	97	103438-534^c	[9, 16]
22-lpnA^b	FTT_0901	407	909857-10263	[19, 37, 38, 56, 57]
23-lpnA	FTT_0901	93	910211-301	[9, 16]
24-lpnB	FTT_0904	252	911795-2046	[34]
25-mdh	FTT_0535c	715	556932-7646	[63, 64]
26-mutS	FTT_1499	495	1553224-3718	[19]
27-parC	FTT_0396	643	397063-705	[18, 61]
28-pdpD	FTT_1360c, FTT_1715c	136	1403503-638, 1796838-973	[56, 60]
29-pgm	FTT_0414	650	425033-682	[18, 61]
30-prfB	FTT_0191	376	207686-8061	[19]
31-putA	FTT_1150c	415	1165411-825	[19]
32-rpoA	FTT_0350, FTT_1442c	914	349619-50532	[64]
33-rpoB	FTT_0144	262	156309-570	[34]
34-sdhA	FTT_0074	223	75065-287	[34]
35-tpiA	FTT_0080	484	83679-4162	[19]
36-tpiA	FTT_0080	559	83657-4215	[18, 61]
37-trpE	FTT_1802c	517	1888928-9444	[18, 61]
38-uup	FTT_0445	645	459229-873	[18, 61]

^a Amplicon locus tag, length and location in genome of F. tularensis strain SCHU S4.
^b Primer sequence of primer Tuf1705 in marker 20-ISFtu2 and TUL-435 in marker 22-lpnA seem to be incorrectly specified in [56]. See [37] and [59] for the correct primer sequences.
^c Insertion element present in multiple copies in reference. Only first position and gene specified.

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ISSN: 1471-2180

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