Difference between revisions of "Syntenic dotplot"

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9b. Insertion  
 
9b. Insertion  
  
−
9c. Insertion
+
9c. Insertion  
  
−
9d. Insertion
+
9d. Insertion  
  
 
|  
 
|  
Line 82: Line 82:
 
9b. Insertion of ISI transposon  
 
9b. Insertion of ISI transposon  
  
−
9c. none
+
9c. none  
  
−
9d. IS2 insertion 
+
9d. IS2 insertion   
  
 
|  
 
|  
Line 91: Line 91:
 
9b. none  
 
9b. none  
  
−
9c. Insertion of ABC transporter, flagella encoding genes and few other enzymes
+
9c. Insertion of ABC transporter, flagella encoding genes and few other enzymes  
  
−
9d. none
+
9d. none  
  
 
|  
 
|  
Line 100: Line 100:
 
9b. none  
 
9b. none  
  
−
9c. Inserted DNA segment in DH10B is bordered by direct repeats at both ends. 100% identity was found between the two repeats. 
+
9c. Inserted DNA segment in DH10B is bordered by direct repeats at both ends. 100% identity was found between the two repeats.   
  
−
9d. none
+
9d. none  
  
 
|  
 
|  
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9b. none  
 
9b. none  
  
−
9c.DR indicates transposon insertion in DH10B. 
+
9c.DR indicates transposon insertion in DH10B.   
  
−
9d. none
+
9d. none  
  
 
|  
 
|  
 
9a.&nbsp;[http://tinyurl.com/ylllc6u http://tinyurl.com/ylllc6u]<br>  
 
9a.&nbsp;[http://tinyurl.com/ylllc6u http://tinyurl.com/ylllc6u]<br>  
  
−
9b.&nbsp;[http://tinyurl.com/ygsqg2f tinyurl.com/ygsqg2f]
+
9b.&nbsp;[http://tinyurl.com/ygsqg2f tinyurl.com/ygsqg2f]  
  
 
9c.&nbsp;[http://tinyurl.com/ykypc67 tinyurl.com/ykypc67]<br>  
 
9c.&nbsp;[http://tinyurl.com/ykypc67 tinyurl.com/ykypc67]<br>  
  
−
9d.&nbsp;[http://tinyurl.com/ygfgtqy tinyurl.com/ygfgtqy]
+
9d.&nbsp;[http://tinyurl.com/ygfgtqy tinyurl.com/ygfgtqy]  
  
 
|-
 
|-
 
| 10. Insertion and deletion<br><br>  
 
| 10. Insertion and deletion<br><br>  
 
| Bacteriophage DNA insertion and IS1 transposon insertion. Deletion of metal resistance genes<br><br>  
 
| Bacteriophage DNA insertion and IS1 transposon insertion. Deletion of metal resistance genes<br><br>  
−
| Insertion of pili associated genes
+
| Insertion of pili associated genes  
 
| Insertion of pili associated genes in DH10B as evidenced by their different GC codon  
 
| Insertion of pili associated genes in DH10B as evidenced by their different GC codon  
 
| No IR were found as to indicate insertion of genes conferring metal resistance in DH10B. Possible deletion in REL606 of these genes prior to IS1 transposon insertion. &nbsp;  
 
| No IR were found as to indicate insertion of genes conferring metal resistance in DH10B. Possible deletion in REL606 of these genes prior to IS1 transposon insertion. &nbsp;  
 
|  
 
|  
−
[http://tinyurl.com/yammj7v http://tinyurl.com/yammj7v]
+
[http://tinyurl.com/yammj7v http://tinyurl.com/yammj7v]  
  
−
[http://tinyurl.com/ykvvvk2 tinyurl.com/ykvvvk2]
+
[http://tinyurl.com/ykvvvk2 tinyurl.com/ykvvvk2]  
  
 
|-
 
|-
Line 143: Line 143:
 
| 12. Insertion, deletion and Inversion<br>  
 
| 12. Insertion, deletion and Inversion<br>  
 
| IS1 insertion. Insertion of pyrophosphorylase and "hypothetical protein" genes  
 
| IS1 insertion. Insertion of pyrophosphorylase and "hypothetical protein" genes  
−
| IS5 and IS10 transposon insertion. Inversion of ornithine decarboxylase, M-type protein and bifunctional prepilin peptidase/methylase. Deletion of saframycin synthetase, capsule related genes, bio-film formation genes, anti-toxin system and type II secretory apparatus genes.&nbsp;
+
| IS5 and IS10 transposon insertion. Inversion of ornithine decarboxylase, M-type protein and bifunctional prepilin peptidase/methylase. Deletion of saframycin synthetase, capsule related genes, bio-film formation genes, anti-toxin system and type II secretory apparatus genes.&nbsp;  
 
|  
 
|  
−
Insertion of pyrophosphorylase and "hypthetical protein' genes in REL606 as evidenced by their different GC content
+
Insertion of pyrophosphorylase and "hypthetical protein' genes in REL606 as evidenced by their different GC content  
  
 
Inversion in DH10B as evidenced by IR of IS10 transposon.  
 
Inversion in DH10B as evidenced by IR of IS10 transposon.  
  
 
Deletion of several genes in DH10B is evidenced by IS5 transposase transactivator.&nbsp;
 
Deletion of several genes in DH10B is evidenced by IS5 transposase transactivator.&nbsp;
−
 
−
 
  
 
|  
 
|  
−
No evidence of insertion&nbsp;
+
Insertion of IS5 trans-activator transposase indicates possible deletion of several genes in DH10B. Also,No evidence of insertion in REL606 was found such as different GC content or DR
  
 
| [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&nbsp;<br>
−
| IS30 transposon insertion in B strain. Presence of ShiA-like and TrbC-like protein in B strain<br>
+
| Insertion of IS30 transposon and several 'hypothetical protein" genes.&nbsp;<br>  
−
| <br>
+
| Insertion of capsule related proteins
−
| <br>
+
| Insertion of Aec78, TrbC-like and yeeV-like protein  
−
| <br>
+
|  
 +
Insertion in REL606 as evidenced by different GC content of capsule related protein.&nbsp;
 +
 
 +
Insertion of "hypothetical proteins" genes in DH10B as evidenced by their different GC content. &nbsp;
 +
 
 
| [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<br>  
−
| Insertion of fimbriae synthesis genes, multi drug transporters, Is1 protein gene in B strain.<br>  
+
| IS1 transposon insertion. Insertion of fimbriae synthesis genes, multi drug transporters genes and conserved inner membrane protein genes. &nbsp;<br>  
−
| <br>
+
|  
−
| <br>
+
 
 +
 
 +
 
 +
 
 
| <br>  
 
| <br>  
 +
| Insertion in REL606 is evidenced by IR flanking the DNA segment containing several genes.&nbsp;
 
| [http://tinyurl.com/ycwsmsl http://tinyurl.com/ycwsmsl]<br>
 
| [http://tinyurl.com/ycwsmsl http://tinyurl.com/ycwsmsl]<br>
 
|}
 
|}
  
 
<br>
 
<br>

Revision as of 18:23, 14 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
 Transposon insertions 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.
 Rac prophage DNA disrupted by transposon insertion in DH10B tinyurl.com/yccbmsq

9a. Insertion

9b. Insertion

9c. Insertion

9d. Insertion

9a. none

9b. Insertion of ISI transposon

9c. none

9d. IS2 insertion 

9a. Insertion of IS5 sequence

9b. none

9c. Insertion of ABC transporter, flagella encoding genes and few other enzymes

9d. none

9a. none

9b. none

9c. Inserted DNA segment in DH10B is bordered by direct repeats at both ends. 100% identity was found between the two repeats. 

9d. none

9a. none

9b. none

9c.DR indicates transposon insertion in DH10B. 

9d. none

9a. http://tinyurl.com/ylllc6u

9b. tinyurl.com/ygsqg2f

9c. tinyurl.com/ykypc67

9d. tinyurl.com/ygfgtqy

10. Insertion and deletion

 Bacteriophage DNA insertion and IS1 transposon insertion. Deletion of metal resistance genes

 Insertion of pili associated genes Insertion of pili associated genes in DH10B as evidenced by their different GC codon No IR were found as to indicate insertion of genes conferring metal resistance in DH10B. Possible deletion in REL606 of these genes prior to IS1 transposon insertion.  

http://tinyurl.com/yammj7v

tinyurl.com/ykvvvk2

11. Insertion 
 IS1 insertion followed by insertion of ParB family protein genes and recombinase.
 CP4-57 prophage DNA insertion
 Different GC content of ParB family protein and recombinase gene indicates that these genes were acquired by exogenous DNA such as plasmid possibly by homologous crossover as no IR were found.  IS1 insertion probably occured independent of integration of other genes in REL606. http://tinyurl.com/ycdog2c
12. Insertion, deletion and Inversion
 IS1 insertion. Insertion of pyrophosphorylase and "hypothetical protein" genes IS5 and IS10 transposon insertion. Inversion of ornithine decarboxylase, M-type protein and bifunctional prepilin peptidase/methylase. Deletion of saframycin synthetase, capsule related genes, bio-film formation genes, anti-toxin system and type II secretory apparatus genes. 

Insertion of pyrophosphorylase and "hypthetical protein' genes in REL606 as evidenced by their different GC content

Inversion in DH10B as evidenced by IR of IS10 transposon.

Deletion of several genes in DH10B is evidenced by IS5 transposase transactivator. 

Insertion of IS5 trans-activator transposase indicates possible deletion of several genes in DH10B. Also,No evidence of insertion in REL606 was found such as different GC content or DR

http://tinyurl.com/ycoagxh
13. Insertion 
 Insertion of IS30 transposon and several 'hypothetical protein" genes. 
 Insertion of capsule related proteins Insertion of Aec78, TrbC-like and yeeV-like protein

Insertion in REL606 as evidenced by different GC content of capsule related protein. 

Insertion of "hypothetical proteins" genes in DH10B as evidenced by their different GC content.  

http://tinyurl.com/ydkrcv8
14. Insertion
 IS1 transposon insertion. Insertion of fimbriae synthesis genes, multi drug transporters genes and conserved inner membrane protein genes.  




Insertion in REL606 is evidenced by IR flanking the DNA segment containing several genes.  http://tinyurl.com/ycwsmsl


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