Difference between revisions of "Syntenic dotplot"
From CoGepedia
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− | [[Image:Dotplot.png|thumb|center| | + | [[Image:Dotplot.png|thumb|center|983px]] |
− | <br> | + | <br> |
− | {| | + | {| border="1" cellspacing="1" cellpadding="1" width="1000" |
|- | |- | ||
− | | Variation type<br> | + | | Variation type<br> |
− | | Difference in strain B REL606<br> | + | | Difference in strain B REL606<br> |
− | | Difference in strain K-12 DH10B<br> | + | | Difference in strain K-12 DH10B<br> |
− | | Evidence<br> | + | | Evidence<br> |
− | | Notes<br> | + | | Notes<br> |
| Link leading to GEvo <br> | | Link leading to GEvo <br> | ||
|- | |- | ||
− | | 1. Deletion<br> | + | | 1. Deletion<br> |
− | | none<br> | + | | none<br> |
− | | Deletion of ~18 genes including DNA <br>pol II, genes in metabolic pathway, thiamine ABC transporter<br><br> | + | | Deletion of ~18 genes including DNA <br>pol II, genes in metabolic pathway, thiamine ABC transporter<br><br> |
− | | pseudogenes in DH10B at deletion site.<br><br> | + | | pseudogenes in DH10B at deletion site.<br><br> |
− | | Possible additional insertion in DH10B as evidenced by <br>pseudogenes of yabP, RNA pol associated helicase and FruR, that are not present in REl606<br><br> | + | | Possible additional insertion in DH10B as evidenced by <br>pseudogenes of yabP, RNA pol associated helicase and FruR, that are not present in REl606<br><br> |
| [http://tinyurl.com/yexrzpb tinyurl.com/yexrzpb]<br> | | [http://tinyurl.com/yexrzpb tinyurl.com/yexrzpb]<br> | ||
|- | |- | ||
− | | 2. Insertion<br> | + | | 2. Insertion<br> |
− | | Insertion of IS1 sequence and a "predicted" transposase<br> | + | | Insertion of IS1 sequence and a "predicted" transposase<br> |
| Insertion sequences and Prophage CP46 DNA insertion | | Insertion sequences and Prophage CP46 DNA insertion | ||
− | | Prophage specific genes found<br> | + | | Prophage specific genes found<br> |
− | | Prophage DNA insertion created pseudogenes in K-12 DH10B<br> | + | | Prophage DNA insertion created pseudogenes in K-12 DH10B<br> |
| [http://tinyurl.com/yd2quy7 tinyurl.com/yd2quy7]<br> | | [http://tinyurl.com/yd2quy7 tinyurl.com/yd2quy7]<br> | ||
|- | |- | ||
− | | 3. Deletion in B strain or Insertion in K12 strain<br> | + | | 3. Deletion in B strain or Insertion in K12 strain<br> |
| Insertion of IS1 sequence. Insertion of ~15 genes including lac operon and other metabolic enzymes genes | | Insertion of IS1 sequence. Insertion of ~15 genes including lac operon and other metabolic enzymes genes | ||
| Insertion of IS3 and IS2 sequence | | Insertion of IS3 and IS2 sequence | ||
− | | Pseudogene made in DH10B by IS sequence and transposon insertion<br> | + | | Pseudogene made in DH10B by IS sequence and transposon insertion<br> |
− | | Possible insertion in B REL606 as no evidence of pseudogene is seen in DH10B to account for gene loss in DH10B<br> | + | | Possible insertion in B REL606 as no evidence of pseudogene is seen in DH10B to account for gene loss in DH10B<br> |
| [http://tinyurl.com/yedn5tb http://tinyurl.com/yedn5tb]<br> | | [http://tinyurl.com/yedn5tb http://tinyurl.com/yedn5tb]<br> | ||
|- | |- | ||
− | | 4. Insertion in B strain and DNA duplication event in K12. <br> | + | | 4. Insertion in B strain and DNA duplication event in K12. <br> |
− | | Prophage DNA and transposase insertion <br> | + | | Prophage DNA and transposase insertion <br> |
| Recent DNA duplication event | | Recent DNA duplication event | ||
− | | 100% identity between paralogs and ~98% identity between syntenic region in REL606<br> | + | | 100% identity between paralogs and ~98% identity between syntenic region in REL606<br> |
− | | Possible phage DNA insertion in REL606 as "hypothetical protein" were found near putative prophage tail component gene in REL606. <br> | + | | Possible phage DNA insertion in REL606 as "hypothetical protein" genes were found near putative prophage tail component gene in REL606. <br> |
| [http://tinyurl.com/yea8bu6 tinyurl.com/yea8bu6]<br> | | [http://tinyurl.com/yea8bu6 tinyurl.com/yea8bu6]<br> | ||
|- | |- | ||
− | | 5. Insertion<br> | + | | 5. Insertion<br> |
− | | Bacteriophage DNA insertion <br> | + | | Bacteriophage DNA insertion <br> |
− | | IS2 sequence insertion<br> | + | | IS2 sequence insertion<br> |
− | | Pseudogenes at IS2 insertion site in DH10B. Phage specific genes were found in REL606<br> | + | | Pseudogenes at IS2 insertion site in DH10B. Phage specific genes were found in REL606<br> |
− | | Possible page DNA insertion in REL606 as "Hypothetical proteins" were found near phage specific genes <br> | + | | Possible page DNA insertion in REL606 as "Hypothetical proteins" were found near phage specific genes <br> |
| [http://tinyurl.com/yevlb2w tinyurl.com/yevlb2w]<br> | | [http://tinyurl.com/yevlb2w tinyurl.com/yevlb2w]<br> | ||
|- | |- | ||
− | | 6. Insertion<br> | + | | 6. Insertion<br> |
− | | Prophage DNA insertion <br> | + | | Prophage DNA insertion <br> |
− | | none<br> | + | | none<br> |
− | | Phage specific genes were found in REL606<br> | + | | Phage specific genes were found in REL606<br> |
− | | none<br> | + | | none<br> |
| [http://tinyurl.com/ybokuag tinyurl.com/ybokuag]<br> | | [http://tinyurl.com/ybokuag tinyurl.com/ybokuag]<br> | ||
|- | |- | ||
− | | 7. Insertion<br> | + | | 7. Insertion<br> |
| none | | none | ||
| Prophage DNA insertion | | Prophage DNA insertion | ||
− | | Phage specific genes found in DH10B<br> | + | | Phage specific genes found in DH10B<br> |
− | | none<br> | + | | none<br> |
| [http://tinyurl.com/yaxlh7o tinyurl.com/yaxlh7o]<br> | | [http://tinyurl.com/yaxlh7o tinyurl.com/yaxlh7o]<br> | ||
|- | |- | ||
− | | 8. Insertion<br> | + | | 8. Insertion<br> |
− | | Insertion of IS3 element protein<br> | + | | Insertion of IS3 element protein<br> |
| IS insertions along with Rac prophage DNA and phenylacetic acid degradation genes insertion | | IS insertions along with Rac prophage DNA and phenylacetic acid degradation genes insertion | ||
− | | Phage specific genes found in DH10B. Pseudogenes at the site of IS insertions in DH10B<br> | + | | Phage specific genes found in DH10B. Pseudogenes at the site of IS insertions in DH10B<br> |
− | | No evidence of deletion of phenylacetic acid degradation genes in REL606 as no pseudogenes were found.<br> | + | | No evidence of deletion of phenylacetic acid degradation genes in REL606 as no pseudogenes were found.<br> |
| [http://tinyurl.com/yccbmsq tinyurl.com/yccbmsq]<br> | | [http://tinyurl.com/yccbmsq tinyurl.com/yccbmsq]<br> | ||
|- | |- | ||
− | | 9. Insertion | + | | 9. Insertion and Inversion. <br><br> |
− | | | + | | none |
− | + | | Insertion of flagella encoding/regulatory genesIS5 sequence and CP4-44 prophage DNA in DH10B.<br> | |
− | | <br> | + | | <br> |
− | | <br> | + | | <br> |
− | | [http://tinyurl.com/ybh84x7 http://tinyurl.com/ybh84x7 ] | + | | [http://tinyurl.com/ybh84x7 http://tinyurl.com/ybh84x7 ] |
− | <br> | + | <br> |
|- | |- | ||
− | | 10. Insertion in B strain. <br>Pili associated genes and metal resistance genes either inserted in K12 or deleted in B strain.<br><br> | + | | 10. Insertion in B strain. <br>Pili associated genes and metal resistance genes either inserted in K12 or deleted in B strain.<br><br> |
− | | Bacteriophage DNA insertion in B strain. <br>IS1 sequence insertion in B strain. <br>Presence of pili associated genes in K12 together with genes conferring resistance to Co and Ni.<br><br> | + | | Bacteriophage DNA insertion in B strain. <br>IS1 sequence insertion in B strain. <br>Presence of pili associated genes in K12 together with genes conferring resistance to Co and Ni.<br><br> |
− | | <br> | + | | <br> |
− | | <br> | + | | <br> |
− | | <br> | + | | <br> |
| [http://tinyurl.com/yammj7v http://tinyurl.com/yammj7v]<br> | | [http://tinyurl.com/yammj7v http://tinyurl.com/yammj7v]<br> | ||
|- | |- | ||
− | | 11. Insertion in K12 strain. ParB family protein and recombinase deleted in K12. <br> | + | | 11. Insertion in K12 strain. ParB family protein and recombinase deleted in K12. <br> |
− | | CP4-57 prophage DNA insertion in K12 strain. Presence of ParB family protein gene and recombinase in B strain<br> | + | | CP4-57 prophage DNA insertion in K12 strain. Presence of ParB family protein gene and recombinase in B strain<br> |
− | | <br> | + | | <br> |
− | | <br> | + | | <br> |
− | | <br> | + | | <br> |
| [http://tinyurl.com/ycdog2c http://tinyurl.com/ycdog2c]<br> | | [http://tinyurl.com/ycdog2c http://tinyurl.com/ycdog2c]<br> | ||
|- | |- | ||
− | | 12. Insertion in B and K12 strain. Inversion. Insertion of saframycin synthetase in B strain or deletion of that in K12. <br> | + | | 12. Insertion in B and K12 strain. Inversion. Insertion of saframycin synthetase in B strain or deletion of that in K12. <br> |
| Prophage DNA insertion in B strain. <br>Inversion of prepilin leader peptidase/methylase and M-type protein. Is5 insertion in K12. Presence of saframycin synthetase gene in B strain. | | Prophage DNA insertion in B strain. <br>Inversion of prepilin leader peptidase/methylase and M-type protein. Is5 insertion in K12. Presence of saframycin synthetase gene in B strain. | ||
− | <br> | + | <br> |
− | | <br> | + | | <br> |
− | | <br> | + | | <br> |
− | | <br> | + | | <br> |
| [http://tinyurl.com/ycoagxh http://tinyurl.com/ycoagxh]<br> | | [http://tinyurl.com/ycoagxh http://tinyurl.com/ycoagxh]<br> | ||
|- | |- | ||
− | | 13. Insertion of transposon, ShiA-like, TrbC-like proteins in B strain. <br> | + | | 13. Insertion of transposon, ShiA-like, TrbC-like proteins in B strain. <br> |
− | | IS30 transposon insertion in B strain. Presence of ShiA-like and TrbC-like protein in B strain<br> | + | | IS30 transposon insertion in B strain. Presence of ShiA-like and TrbC-like protein in B strain<br> |
− | | <br> | + | | <br> |
− | | <br> | + | | <br> |
− | | <br> | + | | <br> |
| [http://tinyurl.com/ydkrcv8 http://tinyurl.com/ydkrcv8]<br> | | [http://tinyurl.com/ydkrcv8 http://tinyurl.com/ydkrcv8]<br> | ||
|- | |- | ||
− | | 14. Insertion in B strain<br> | + | | 14. Insertion in B strain<br> |
− | | Insertion of fimbriae synthesis genes, multi drug transporters, Is1 protein gene in B strain.<br> | + | | Insertion of fimbriae synthesis genes, multi drug transporters, Is1 protein gene in B strain.<br> |
− | | <br> | + | | <br> |
− | | <br> | + | | <br> |
− | | <br> | + | | <br> |
| [http://tinyurl.com/ycwsmsl http://tinyurl.com/ycwsmsl]<br> | | [http://tinyurl.com/ycwsmsl http://tinyurl.com/ycwsmsl]<br> | ||
|} | |} | ||
<br> | <br> |
Revision as of 11:43, 7 October 2009
Variation type |
Difference in strain B REL606 |
Difference in strain K-12 DH10B |
Evidence |
Notes |
Link leading to GEvo |
1. Deletion |
none |
Deletion of ~18 genes including DNA pol II, genes in metabolic pathway, thiamine ABC transporter |
pseudogenes in DH10B at deletion site. |
Possible additional insertion in DH10B as evidenced by pseudogenes of yabP, RNA pol associated helicase and FruR, that are not present in REl606 |
tinyurl.com/yexrzpb |
2. Insertion |
Insertion of IS1 sequence and a "predicted" transposase |
Insertion sequences and Prophage CP46 DNA insertion | Prophage specific genes found |
Prophage DNA insertion created pseudogenes in K-12 DH10B |
tinyurl.com/yd2quy7 |
3. Deletion in B strain or Insertion in K12 strain |
Insertion of IS1 sequence. Insertion of ~15 genes including lac operon and other metabolic enzymes genes | Insertion of IS3 and IS2 sequence | Pseudogene made in DH10B by IS sequence and transposon insertion |
Possible insertion in B REL606 as no evidence of pseudogene is seen in DH10B to account for gene loss in DH10B |
http://tinyurl.com/yedn5tb |
4. Insertion in B strain and DNA duplication event in K12. |
Prophage DNA and transposase insertion |
Recent DNA duplication event | 100% identity between paralogs and ~98% identity between syntenic region in REL606 |
Possible phage DNA insertion in REL606 as "hypothetical protein" genes were found near putative prophage tail component gene in REL606. |
tinyurl.com/yea8bu6 |
5. Insertion |
Bacteriophage DNA insertion |
IS2 sequence insertion |
Pseudogenes at IS2 insertion site in DH10B. Phage specific genes were found in REL606 |
Possible page DNA insertion in REL606 as "Hypothetical proteins" were found near phage specific genes |
tinyurl.com/yevlb2w |
6. Insertion |
Prophage DNA insertion |
none |
Phage specific genes were found in REL606 |
none |
tinyurl.com/ybokuag |
7. Insertion |
none | Prophage DNA insertion | Phage specific genes found in DH10B |
none |
tinyurl.com/yaxlh7o |
8. Insertion |
Insertion of IS3 element protein |
IS insertions along with Rac prophage DNA and phenylacetic acid degradation genes insertion | Phage specific genes found in DH10B. Pseudogenes at the site of IS insertions in DH10B |
No evidence of deletion of phenylacetic acid degradation genes in REL606 as no pseudogenes were found. |
tinyurl.com/yccbmsq |
9. Insertion and Inversion. |
none | Insertion of flagella encoding/regulatory genesIS5 sequence and CP4-44 prophage DNA in DH10B. |
|
|
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 |