Difference between revisions of "Syntenic dotplot"

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[[Image:Dotplot.png|thumb|center|983px]]  
 
[[Image:Dotplot.png|thumb|center|983px]]  
  
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<br>  
  
 
{| border="1" cellspacing="1" cellpadding="1" width="1000"
 
{| 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 evidenced by direct repeats.<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&nbsp;&nbsp;  
 
| Recent DNA duplication event&nbsp;&nbsp;  
−
| 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"&nbsp;genes&nbsp;were found near putative prophage tail component gene in REL606. <br>
+
| Possible phage DNA insertion in REL606 as "hypothetical protein"&nbsp;genes&nbsp;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 phage 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 and deletion<br>  
−
| Insertion of IS3 element protein<br>
+
| Insertion of IS3 element protein and deletion of&nbsp;phenylacetic acid degradation genes <br>  
−
| IS insertions along with Rac prophage DNA and phenylacetic acid degradation genes insertion  
+
| IS and Rac prophage DNA insertion
−
| Phage specific genes found in DH10B. Pseudogenes at the site of IS insertions in DH10B<br>
+
| Phage specific genes found in DH10B. IS insertions in REL606 might have created direct repeats and facilitated excision of phenylacetic acid degradation genes.<br>  
−
| No evidence of deletion of phenylacetic acid degradation genes in REL606 as no pseudogenes were found.<br>
+
| none
 
| [http://tinyurl.com/yccbmsq tinyurl.com/yccbmsq]<br>
 
| [http://tinyurl.com/yccbmsq tinyurl.com/yccbmsq]<br>
 
|-
 
|-
−
| 9. Insertion and Inversion. <br><br>
+
| 9. Insertion<br><br>  
−
| none
+
| Deletion of flagella encoding/regulatory genes
−
| Insertion of&nbsp;flagella encoding/regulatory genesIS5 sequence&nbsp;and&nbsp;CP4-44 prophage DNA in DH10B.<br>
+
| &nbsp;flagella encoding/regulatory genesIS5 sequence&nbsp;and&nbsp;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 18:22, 7 October 2009

Dotplot.png


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 evidenced by direct repeats.
 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 phage 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 and deletion
 Insertion of IS3 element protein and deletion of phenylacetic acid degradation genes
IS and Rac prophage DNA insertion Phage specific genes found in DH10B. IS insertions in REL606 might have created direct repeats and facilitated excision of phenylacetic acid degradation genes.
 none tinyurl.com/yccbmsq
9. Insertion

 Deletion of flagella encoding/regulatory genes  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


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