Francisella tularensis

Characteristics

• gamma—proteobacterium
• one of the most infectious human intracellular pathogens
• causative agent of tularemia
• category A biodefense concern because of its ability to cause incapacitating, potentially fatal illness

4 subspecies: tularensis, holarctica, novicida, mediasiatica

 Subspecies	        Virulence	Region
 tularensis (Type A)	high	        North America,
 holarctica (Type B)	moderate        North America,Europe, Asia
 novicida               moderate        .
 mediasiatica	        low	        .

Data Sources

NCBI:

• Genome Projects
• SRA BCM
• TA
• TA FTP
• TA OUS18

Broad:

• MSC
• Data Download

Baylor:

• Microbial Genomes
• FTP

JGI:

• Comparative analysis

Univ. of Washington:

• Univ. of Washington Genome Center

Read Counts

• Francisella_tularensis.pdf
• Francisella_tularensis.sxc

Type A

• SCHU_S4 SDRA , Complete (1,892,819 bp) NC_006570
• FSC198 Univ. of Birmingham , Complete ( 1,892,616 bp) NC_008245
• WY96-3418 BioHealthBase , Complete (1,898,476 bp) NC_009257
• FSC033 Broad, Assembly (15 contigs) ***
• ATCC6223 Baylor (88 contigs) ***

Type B

• LVS LLNL, Complete (1,895,994 bp) NC_007880
• OSU18 Baylor, Complete (1,895,727 bp) NC_008369 ***
• KO97 Baylor (126 contigs) ***
• MI001730 Baylor (118 contigs) ***
• OR960246 Baylor (111 contigs) ***
• RC503 Baylor (115 contigs)
• 275 Broad (31 contigs) NZ_AAUD00000000 ***
• FSC022 Broad (19 contigs) NZ_AAYD00000000 ***
• FSC200 Univ of Washington (39 contigs) NZ_AASP00000000
• FTA BioHealthBase/JGI/LANL, Progress
• URFT1 Unite des Rickettsies/CNRS, Progress

Novicida

• U112 Univ. of Washington, Complete (1,910,031 bp) NC_008601
• GA99-3548 Broad (18 contigs) NZ_ABAH00000000 ***
• GA99-3549 Broad (15 contigs) NZ_AAYF00000000 ***

Mediasiatica

• FSC147 DOE, Progress

File Locations on Disk

• /fs/szdata//ncbi/genomes/Bacteria/Francisella_tularensis
• ~dpuiu/Data/F_tularensis/
• /fs/szasmg/Bacteria/F_tularensis

454

Paired End reads:

 * approximately 84-nucleotide DNA fragments 
 * have a 44-mer adaptor sequence in the middle 
 * flanked by a 20-mer sequence on each side. 
 * The two flanking 20-mers are segments of DNA that were originally located approximately 2.5 kb apart in the genome of interest.  
 * The ordering and orienting of contigs generates scaffolds which provide a high-quality draft sequence of the genome.
 pair read article