Difference between revisions of "Syntenic dotplot"
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| − | [[Image:Dotplot.png|thumb|center|1000px]] | + | [[Image:Dotplot.png|thumb|center|1000px|Syntenic dotplot between two '''Escherichia coli''' genomes: (x-axis) B strain REL606 and (y-axis) strain K-12 substrain DH10B. This dotplot was generated using [[SynMap]] and can be regenerated [http://synteny.cnr.berkeley.edu/CoGe/SynMap.pl?dsgid1=7454;dsgid2=4241;D=20;g=10;A=5;w=0;b=1;ft1=1;ft2=1;dt=geneorder;autogo=1 here].The green line (collection of dots) represent regions of similarity along the two genomes. The arrows point towards the spots where insertion or deletion has occurred in genome of either strains. The numbers correspond to the descriptions in the table below that accounts for these gaps in the dotplots.]] |
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Revision as of 21:54, 6 October 2009
Syntenic dotplot between two Escherichia coli genomes: (x-axis) B strain REL606 and (y-axis) strain K-12 substrain DH10B. This dotplot was generated using SynMap and can be regenerated here.The green line (collection of dots) represent regions of similarity along the two genomes. The arrows point towards the spots where insertion or deletion has occurred in genome of either strains. The numbers correspond to the descriptions in the table below that accounts for these gaps in the dotplots.
| Variation observed in B and K12 |
Description of variation |
Link leading to GEvo |
| 1. Deletion in B strain |
DNA pol II, genes in metabolic pathway, thiamine ABC transporter present in K12 strain Transposase in K12 strain. Prophage CP46 DNA insertion in K12 strain. |
http://tinyurl.com/yexrzpb |
| 2. Insertions in K12 strain |
Transposase in K12 strain. Prophage CP46 DNA insertion in K12 strain. |
http://tinyurl.com/yd2quy7 |
| 3. Deletion in B strain or Insertion in K12 strain |
Presence of lac operon and other metabolic enzymes genes in K12 strain. Pseudogene made by transposon insertion in K12. | http://tinyurl.com/yedn5tb |
| 4. Insertion in B strain and DNA duplication event in K12. |
Prophage DNA insertion in B strain. Recent DNA duplication event in K12 as seen by 100% identity between paralogs. | http://tinyurl.com/yea8bu6 |
| 5. Insertion in B strain |
Bacteriophage DNA insertion in B strain | http://tinyurl.com/yevlb2w |
| 6. Insertion in B strain |
Prophage DNA insertion in B strain | http://tinyurl.com/ybokuag |
| 7. Insertion in K12 strain |
Prophage DNA insertion in K12 | http://tinyurl.com/yaxlh7o |
| 8. Insertion of transposon in K12 and B strain. Deletion of phenylacetic acid genes in B strain or insertion of those in K12. |
Rac prophage DNA insertion in K12. Insertion of IS3 element protein and transposase in B strain. Insertion of IS30 transposon in B strain created pseudogene. Presence of phenylacetic acid degradation genes in K12 | http://tinyurl.com.ye7wcxe |
| 9. Insertion in K12 strains. Flagella synthesizing genes either deleted in B strain or inserted in K12. |
Presence of flagella encoding/regulatory genes in K12. IS5 sequence insertion in K12. CP4-44 prophage DNA insertion in K12. | http://tinyurl.com/ybh84x7
|
| 10. Insertion in B strain. Pili associated genes and metal resistance genes either inserted in K12 or deleted in B strain. |
Bacteriophage DNA insertion in B strain. IS1 sequence insertion in B strain. Presence of pili associated genes in K12 together with genes conferring resistance to Co and Ni. |
http://tinyurl.com/yammj7v |
| 11. Insertion in K12 strain. ParB family protein and recombinase deleted in K12. |
CP4-57 prophage DNA insertion in K12 strain. Presence of ParB family protein gene and recombinase in B strain |
http://tinyurl.com/ycdog2c |
| 12. Insertion in B and K12 strain. Inversion. Insertion of saframycin synthetase in B strain or deletion of that in K12. |
Prophage DNA insertion in B strain. Inversion of prepilin leader peptidase/methylase and M-type protein. Is5 insertion in K12. Presence of saframycin synthetase gene in B strain.
|
http://tinyurl.com/ycoagxh |
| 13. Insertion of transposon, ShiA-like, TrbC-like proteins in B strain. |
IS30 transposon insertion in B strain. Presence of ShiA-like and TrbC-like protein in B strain |
http://tinyurl.com/ydkrcv8 |
| 14. Insertion in B strain |
Insertion of fimbriae synthesis genes, multi drug transporters, Is1 protein gene in B strain. |
http://tinyurl.com/ycwsmsl |
