KIT 8A

BAC clones of S. Typhimurium LT2 (SGSC1412)

Clones and kit description were provided by Washington University Genome Sequencing Center. For further information see sequencing and construction of the physical map of S. typhimurium.

Sequence published in: McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Stoneking T, Nhan M, Waterston R, Wilson RK. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature. 2001 Oct 25;413(6858):852-6.

The physical map of Salmonella enterica serovar Typhimurium strain LT2 (STM) was constructed by Dan Layman, Mandeep Sekhon and the Washington University Genome Sequencing Center Fingerprinting Group by generating fingerprints from a BAC library supplied by Rod Wing and Jeff Tompkins at the Clemson University Genomics Institute (http://www.genome.clemson.edu). The library was constructed using a modified pBeloBAC11. The pBeloBAC11 vector was derived from the bacterial F factor and carries a chloramphenicol resistance marker. It is a modified version of pBAC108L with the polylinker replaced by the lacZ multiple cloning site region of pGEM3Z. The DNA of Typhimurium strain LT2 was SauIIIA digested, cloned into a BamHI site, and transformed into E. coli K12 with selection for chloramphenicol resistance (25 ug/ml). For details on the vector see Kim et. al. 1996. Genomics 34:213-214. The original library consisted of 4608 BAC clones with an average insert size of 100kb. 4285 clones were sucessfully fingerprinted using PstI, analyzed with Image (http://www.sanger.ac.uk/Software/Image) and assembled in an FPC database (http://www.sanger.ac.uk/Software/fpc). The assembled contigs were manually edited to achieve proper order and were then merged with one another to generate the largest contigs possible.

To facilitate the final assembly of the physical map, a tiling path of 239 100kb in silico fragments was created(with overlap of 20 kb) from the finished STM-meld sequence and added to the FPC database. This allowed for contiguous assembly of the genome as well as verified the proper correlation between the physical and sequence maps.

A minimal tiling path of BAC clones was selected from the map for end-sequencing and generation of STS markers. These clones formed the tiling path that is represented in the table below and are available from the SGSC.

The clones are maintained as cells of E. coli K12 carrying the pBeloBAC11 vector with inserts of Typhimurium DNA. All clones were grown in LB + 25 ug/ml chloramphenicol and are stored at -70 degrees C in 30% glycerol.


For additional information on BAC library construction and sequencing see:
McClelland M, et. al. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature. 2001 Oct 25;413(6858):852-6.

Typhimurium pBeloBAC11 Tiling Path Clones:
BAC Clones containing Typhimurium inserts from a region of the Typhimurium genome (starting and ending positions of the genome section represented are listed in the table) located by blasting BAC end-sequence against the finished STM and pSLT sequences.

 


Insertion of Salmonella Typhimurium DNA

 STM BAC Clone
(also Strain Number)

 SGSC Number

 Starting Position (in bp)*
(Approximate value relative to finished STM sequence)

 
Ending Position (in bp)*
(Approximate value relative to finished STM sequence)
B_STM02H12  SGSC4001 4781490  62083
B_STM06F20  SGSC4002  4823949 129179 
B_STM03I04  SGSC4003  4844110 139729
 B_STM06G03  SGSC4004  129418 247179
 B_STM03G17  SGSC4005  206312  302750
 B_STM01E04  SGSC4006  263438  365741
 B_STM01H10  SGSC4007  303082  401685
STM_Gap1

 -
 N/A  N/A
B_STM02C03  SGSC4008  421645  494991
 B_STM10P10  SGSC4009  454220  586182
 B_STM09K05  SGSC4010  573580  719946
 B_STM01I17  SGSC4011  692347  801457
 B_STM07L19  SGSC4012  720215  826102
 B_STM02G07  SGSC4013  801902  941492
 B_STM02P01  SGSC4014  837453  941863
 B_STM07I11  SGSC4015  842866 963545
 STM_Gap2

 -
 N/A  N/A
 B_STM11C02  SGSC4016  973962  1071996
 B_STM08B15  SGSC4017  977466  1096889
 B_STM10G24  SGSC4018  977691  1104267
 STM_Gap3

 -
 N/A  N/A
 B_STM10C07  SGSC4019  1104380  1229937
 B_STM04J20  SGSC4020  1193163  1282754
 B_STM10L12  SGSC4021  1230271  1326612
B_STM07A09   SGSC4022  1283306  1400368
 B_STM05H15  SGSC4023  1379597  1496842
 B_STM07H21  SGSC4024  1464540  1562427
 B_STM01K19  SGSC4025  1555262  1651617
 B_STM08J17  SGSC4026  1635398  1735994
 B_STM07J05  SGSC4027  1722437  1852497
 B_STM12G09  SGSC4028  1788374  1897924
 B_STM02G22  SGSC4029  1855053  2011442
 B_STM02M15  SGSC4030  1958388  2061674
 B_STM07E15  SGSC4031  2021725  2140735
 B_STM10K13  SGSC4032  2089807  2203449
 B_STM12E18  SGSC4033  2140852  2252845
 B_STM06J01  SGSC4034  2203790  2333414
 B_STM06B16  SGSC4035  2256263  2368548
 B_STM01G16  SGSC4036  2336838  2455145
 B_STM02P20  SGSC4037  2400808  2529068
 B_STM11M01  SGSC4038  2457220  2569511
 B_STM01G19  SGSC4039  2529288  2657104
 B_STM11H17  SGSC4040  2621676  2729630
 B_STM06C08  SGSC4041  2712480  2812744
 B_STM02J22  SGSC4042  2770956  2869656
 B_STM09F10  SGSC4043  2851142  2955174
 B_STM03H05  SGSC4044  2931599  3045762
 B_STM10F09  SGSC4045  2993524  3117268
 B_STM02N13  SGSC4046  3046187  3167176
 B_STM07O19 SGSC4047  3124448 3227450
 B_STM02G15 SGSC4048  3117828  3245925
  STM_Gap4

 -
 N/A  N/A
 B_STM05O18 SGSC4049   3267377  3372703
 B_STM09M24  SGSC4050  3341535  3474489
 B_STM07I01  SGSC4051  3438714  3546476
 B_STM01J17  SGSC4052  3494556  3600798
 B_STM12L10  SGSC4053  3584493  3701578
 B_STM10N08  SGSC4054  3648068  3784895
 B_STM03J14  SGSC4055  3716426  3821129
 B_STM08I08  SGSC4056  3785148  3921564
 B_STM02F04  SGSC4057  3873414  3982178
 B_STM11E18  SGSC4058  3937670  4045939
 B_STM06F02  SGSC4059  3982493  4093453
 B_STM08J11  SGSC4060  4076157  4220418
 B_STM02D09  SGSC4061  4138460  4249026
 B_STM06J05  SGSC4062  4225050  4343456
 B_STM07G02  SGSC4063  4253730  4391655
 B_STM09P09  SGSC4064  4343795  4464564
 B_STM04H17  SGSC4065  4392042  4499407
 B_STM06C06  SGSC4066  4464831  4565839
 B_STM05B18  SGSC4067  4558813  4677586
B_STM12I02   SGSC4068  4634372  4748330
 B_STM11N19  SGSC4069  4720258  4852300

 pSLT BAC Clone

 SGSC Number

 Starting Position*
(Approximate value relative to finished pSLT sequence)

 
Ending Position*
(Approximate value relative to finished pSLT sequence)
B_STM05C22  SGSC4070  1545  1497
 B_STM07D15  SGSC4071  28530  28456

* Starting and ending positions derived from blasting BAC end-sequence against the finished STM and pSLT sequences.

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