Genomic tools
From Listeriomics Wiki
Genomics webpage
Thanks to Genomics button on the top banner, one can access the genomic webpage which is designed to browse through every complete genome available and access strain name, serotype, lineage, and isolation information, along with a complete phylogram of the Listeria strains. By double clicking on a strain the list of annotated genes will appear in a new summary panel.
| Listeria species reference phylogenomic tree
Nucleic acid alignments of ortholog gene families were concatenated into a single super-alignment. This super-alignment was used to compute a Maximum Likelihood tree using FastTree2, a parallelized and optimized software to build Maximum Likelihood trees. The following parameters were used: the Generalized time-reversible model (GTR) was chosen, the exhaustive search mode was selected to obtain a more accurate reconstruction, NNI and SPR heuristics were used to browse the tree space and BIONJ weighting was chosen to join events during tree space browsing. Support analyses were performed using Shimodaira Hasegawa test (SH) associated with 1000 resampling steps of site likelihood. - |
List of 83 Listeria genomes with strain information available
For each genome, information about serotype, lineage and the origin of strain isolation were retrieved when possible. By double-clicking on a genome in the table, the gene panel will open and show the annotation available for selected genome. |
Genomics database
The following 50 complete Listeria genomes available on NCBI RefSeq and GenBank databases were downloaded and integrated into our database.
| Sequence ID | Release Date | Folder name | Nb chromosome | Chromosome Length | NB Coding element | Chromosome name | Database |
|---|---|---|---|---|---|---|---|
| NC_002973.6 | 28/08/2001 | Listeria monocytogenes serotype 4b str. F2365 | 1 | 2905187 | 2821 | Listeria monocytogenes serotype 4b str. F2365 chromosome, complete genome | RefSeq |
| NC_003210.1 | 08/11/2001 | Listeria monocytogenes EGD-e | 1 | 2944528 | 2867 | Listeria monocytogenes EGD-e chromosome, complete genome | RefSeq |
| NC_003212.1 | 08/11/2001 | Listeria innocua Clip11262 | 2 | 3011208 | 2968 | Listeria innocua Clip11262, complete genome | RefSeq |
| NC_003383.1 | 08/11/2001 | Listeria innocua Clip11262 | 2 | 81905 | 43 | Listeria innocua Clip11262 plasmid pLI100, complete sequence | RefSeq |
| AM263198.1 | 25/10/2006 | Listeria welshimeri serovar 6b str. SLCC5334 | 1 | 2814130 | 2780 | Listeria welshimeri serovar 6b str. SLCC5334 complete genome | RefSeq |
| NC_011660.1 | 12/12/2008 | Listeria monocytogenes HCC23 | 1 | 2976212 | 2974 | Listeria monocytogenes HCC23 chromosome, complete genome | RefSeq |
| FM242711.1 | 30/03/2009 | Listeria monocytogenes Clip80459 serotype 4b | 1 | 2912690 | 1972 | Listeria monocytogenes Clip80459 serotype 4b complete genome | RefSeq |
| NC_013766.1 | 20/01/2010 | Listeria monocytogenes 08-5578 | 2 | 3032288 | 3010 | Listeria monocytogenes 08-5578 chromosome, complete genome | RefSeq |
| NC_013767.1 | 20/01/2010 | Listeria monocytogenes 08-5578 | 2 | 77054 | 78 | Listeria monocytogenes 08-5578 plasmid pLM5578, complete sequence | RefSeq |
| NC_013768.1 | 20/01/2010 | Listeria monocytogenes 08-5923 | 1 | 2999054 | 2966 | Listeria monocytogenes 08-5923, complete genome | GenBank |
| FN557490.1 | 18/02/2010 | Listeria seeligeri serovar 1-2b str. SLCC3954 | 1 | 2797636 | 2722 | Listeria seeligeri serovar 1/2b str. SLCC3954 complete genome | RefSeq |
| NC_017529.1 | 22/09/2010 | Listeria monocytogenes L99 | 1 | 2979198 | 2925 | Listeria monocytogenes L99, complete genome | RefSeq |
| NC_017537.1 | 14/06/2011 | Listeria monocytogenes M7 | 1 | 2976163 | 2977 | Listeria monocytogenes M7 chromosome, complete genome | RefSeq |
| NC_017544.1 | 07/09/2011 | Listeria monocytogenes 10403S | 1 | 2903106 | 2814 | Listeria monocytogenes 10403S chromosome, complete genome | RefSeq |
| NC_017545.1 | 07/09/2011 | Listeria monocytogenes J0161 | 1 | 3000464 | 2955 | Listeria monocytogenes J0161 chromosome, complete genome | RefSeq |
| NC_017546.1 | 13/09/2011 | Listeria monocytogenes FSL R2-561 | 1 | 2973801 | 2910 | Listeria monocytogenes FSL R2-561 chromosome, complete genome | RefSeq |
| NC_017547.1 | 14/09/2011 | Listeria monocytogenes Finland 1998 | 1 | 2874431 | 2762 | Listeria monocytogenes Finland 1998 chromosome, complete genome | RefSeq |
| NC_016011.1 | 15/09/2011 | Listeria ivanovii subsp. ivanovii PAM 55 | 1 | 2928879 | 1911 | Listeria ivanovii subsp. ivanovii PAM 55, complete genome | RefSeq |
| NC_017728.1 | 17/04/2012 | Listeria monocytogenes 07PF0776 | 1 | 2901562 | 2797 | Listeria monocytogenes 07PF0776 chromosome, complete genome | RefSeq |
| NC_014495.1 | 10/09/2012 | Listeria monocytogenes SLCC2755 | 2 | 57780 | 63 | Listeria monocytogenes SLCC2755 plasmid pLM1-2bUG1, complete sequence | RefSeq |
| NC_018584.1 | 10/09/2012 | Listeria monocytogenes ATCC 19117 | 1 | 2951805 | 2868 | Listeria monocytogenes ATCC 19117, complete genome | RefSeq |
| NC_018585.1 | 10/09/2012 | Listeria monocytogenes SLCC2378 | 1 | 2941360 | 2874 | Listeria monocytogenes SLCC2378, complete genome | RefSeq |
| NC_018586.1 | 10/09/2012 | Listeria monocytogenes SLCC2540 | 1 | 2976958 | 2907 | Listeria monocytogenes SLCC2540, complete genome | RefSeq |
| NC_018587.1 | 10/09/2012 | Listeria monocytogenes SLCC2755 | 2 | 2966146 | 2877 | Listeria monocytogenes SLCC2755, complete genome | RefSeq |
| NC_018588.1 | 10/09/2012 | Listeria monocytogenes SLCC2372 | 2 | 2972810 | 2936 | Listeria monocytogenes SLCC2372, complete genome | RefSeq |
| NC_018589.1 | 10/09/2012 | Listeria monocytogenes SLCC2479 | 1 | 2972172 | 2935 | Listeria monocytogenes SLCC2479, complete genome | RefSeq |
| NC_018590.1 | 10/09/2012 | Listeria monocytogenes SLCC2376 | 1 | 2840185 | 2755 | Listeria monocytogenes SLCC2376, complete genome | RefSeq |
| NC_018591.1 | 10/09/2012 | Listeria monocytogenes serotype 7 str. SLCC2482 | 2 | 2936689 | 2874 | Listeria monocytogenes serotype 7 str. SLCC2482, complete genome | RefSeq |
| NC_018592.1 | 10/09/2012 | Listeria monocytogenes SLCC5850 | 1 | 2907142 | 2865 | Listeria monocytogenes SLCC5850, complete genome | RefSeq |
| NC_018593.1 | 10/09/2012 | Listeria monocytogenes SLCC7179 | 1 | 2882234 | 2826 | Listeria monocytogenes SLCC7179, complete genome | RefSeq |
| NC_018642.1 | 10/09/2012 | Listeria monocytogenes L312 | 1 | 2912346 | 2821 | Listeria monocytogenes L312, complete genome | RefSeq |
| NC_018888.1 | 10/09/2012 | Listeria monocytogenes serotype 7 str. SLCC2482 | 2 | 50100 | 55 | Listeria monocytogenes serotype 7 str. SLCC2482 plasmid pLM7UG1, complete sequence | RefSeq |
| NC_018889.1 | 10/09/2012 | Listeria monocytogenes SLCC2372 | 2 | 50100 | 54 | Listeria monocytogenes SLCC2372 plasmid pLM1-2cUG1, complete sequence | RefSeq |
| NC_019556.1 | 21/11/2012 | Listeria monocytogenes serotype 4b str. LL195 | 1 | 2904662 | 2838 | Listeria monocytogenes serotype 4b str. LL195, complete genome | RefSeq |
| NC_020557.1 | 11/01/2013 | Listeria monocytogenes La111 | 1 | 2776517 | 3131 | Listeria monocytogenes La111 complete genome | RefSeq |
| NC_020558.1 | 11/01/2013 | Listeria monocytogenes N53-1 | 1 | 2776847 | 3150 | Listeria monocytogenes N53-1 complete genome | RefSeq |
| NC_021823.1 | 16/07/2013 | Listeria monocytogenes strain C1-387 | 1 | 2988947 | 2953 | Listeria monocytogenes strain C1-387, complete genome | RefSeq |
| NC_021824.1 | 16/07/2013 | Listeria monocytogenes strain J2-064 | 1 | 2943218 | 2865 | Listeria monocytogenes strain J2-064, complete genome | RefSeq |
| NC_021825.1 | 16/07/2013 | Listeria monocytogenes strain J2-1091 | 1 | 2981886 | 2912 | Listeria monocytogenes strain J2-1091, complete genome | RefSeq |
| NC_021826.1 | 16/07/2013 | Listeria monocytogenes strain N1-011A | 2 | 3094342 | 3059 | Listeria monocytogenes strain N1-011A, complete genome | RefSeq |
| NC_021827.1 | 16/07/2013 | Listeria monocytogenes strain J1817 | 2 | 2953716 | 2903 | Listeria monocytogenes strain J1817, complete genome | RefSeq |
| NC_021828.1 | 16/07/2013 | Listeria monocytogenes strain R2-502 | 2 | 57557 | 62 | Listeria monocytogenes strain R2-502 plasmid, complete sequence | RefSeq |
| NC_021829.1 | 16/07/2013 | Listeria monocytogenes J1816 | 1 | 2947460 | 2794 | Listeria monocytogenes J1816, complete genome | RefSeq |
| NC_021830.1 | 16/07/2013 | Listeria monocytogenes J1-220 | 1 | 3032271 | 2985 | Listeria monocytogenes J1-220, complete genome | RefSeq |
| NC_021837.1 | 16/07/2013 | Listeria monocytogenes strain J2-031 | 1 | 2958908 | 2924 | Listeria monocytogenes strain J2-031, complete genome | RefSeq |
| NC_021838.1 | 16/07/2013 | Listeria monocytogenes strain R2-502 | 2 | 3034043 | 2984 | Listeria monocytogenes strain R2-502, complete genome | RefSeq |
| NC_021839.1 | 16/07/2013 | Listeria monocytogenes strain J1776 | 2 | 2953719 | 2902 | Listeria monocytogenes strain J1776, complete genome | RefSeq |
| NC_021840.1 | 16/07/2013 | Listeria monocytogenes strain J1926 | 2 | 2953708 | 2899 | Listeria monocytogenes strain J1926, complete genome | RefSeq |
| NC_022045.1 | 16/07/2013 | Listeria monocytogenes strain N1-011A | 2 | 148959 | 165 | Listeria monocytogenes strain N1-011A plasmid, complete sequence | RefSeq |
| NC_022046.1 | 16/07/2013 | Listeria monocytogenes strain J1776 | 2 | 55804 | 71 | Listeria monocytogenes strain J1776 plasmid, complete sequence | RefSeq |
| NC_022047.1 | 16/07/2013 | Listeria monocytogenes strain J1817 | 2 | 55804 | 71 | Listeria monocytogenes strain J1817 plasmid, complete sequence | RefSeq |
| NC_022051.1 | 16/07/2013 | Listeria monocytogenes strain J1926 | 2 | 55803 | 71 | Listeria monocytogenes strain J1926 plasmid, complete sequence | GenBank |
| NC_022568.1 | 15/09/2013 | Listeria monocytogenes EGD | 1 | 2907193 | 2848 | Listeria monocytogenes EGD chromosome, complete genome | GenBank |
| HG813249.1 | 10/02/2014 | Listeria monocytogenes 6179 | 2 | 3010620 | 3107 | Listeria monocytogenes 6179 chromosome, complete genome | GenBank |
| HG813250.1 | 10/02/2014 | Listeria monocytogenes 6179 | 2 | 62206 | 40 | Listeria monocytogenes 6179 plasmid LM6179, complete genome | GenBank |
| CP007160.1 | 12/02/2014 | Listeria monocytogenes WSLC1001 | 1 | 2951522 | 2916 | Listeria monocytogenes WSLC1001, complete genome | GenBank |
| CP007210.1 | 14/02/2014 | Listeria monocytogenes WSLC1042 | 1 | 2942306 | 2824 | Listeria monocytogenes WSLC1042, complete genome | GenBank |
| HG813247.1 | 23/03/2014 | Listeria monocytogenes R479a | 2 | 2944998 | 3060 | Listeria monocytogenes R479a chromosome, complete genome | GenBank |
| HG813248.1 | 23/03/2014 | Listeria monocytogenes R479a | 2 | 86652 | 40 | Listeria monocytogenes R479a plasmid pLMR479a, complete genome | GenBank |
| CP007492.1 | 25/03/2014 | Listeria monocytogenes NE dc2014 | 1 | 2904662 | 2770 | Listeria monocytogenes strain NE dc2014, complete genome | GenBank |
| CP007600.1 | 06/05/2014 | Listeria monocytogenes CFSAN006122 | 1 | 2908490 | 2776 | Listeria monocytogenes strain CFSAN006122, complete genome | GenBank |
| CP009258.1 | 29/08/2014 | Listeria monocytogenes Lm60 | 1 | 2989687 | 2904 | Listeria monocytogenes strain Lm60, complete genome | GenBank |
