Difference between revisions of "Syntenic dotplot"
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| [http://tinyurl.com/yjdqgzr tinyurl.com/yd2quy7]<br> | | [http://tinyurl.com/yjdqgzr tinyurl.com/yd2quy7]<br> | ||
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| − | | 3. | + | | 3. Translocation in REL606 and insertion in DH10B<br> |
| − | | Insertion of IS1 sequence. | + | | Insertion of IS1 sequence. Translocation of ~15 genes including lac operon and other metabolic enzymes genes |
| Insertion of IS3 and IS2 sequences | | Insertion of IS3 and IS2 sequences | ||
| | | | ||
| − | + | Translocation by transposon insertion in REL606 as evidenced by direct repeats and as seen from dotplot that the translocated region in REL606 is syntenic to DH10B but not colinear.<br> | |
| + | |||
| + | | | ||
| + | Pseudogenes of yaiT and yaiX were created in DH10B by transposon insertions. | ||
| + | |||
| + | Insertion by translocation in REL606 was confirmed as lac operon and other metabolic genes were found in DH10B by analyzing the translocated genes on the dotplot | ||
| − | |||
| [http://tinyurl.com/yldc83u http://tinyurl.com/yldc83u]<br> | | [http://tinyurl.com/yldc83u http://tinyurl.com/yldc83u]<br> | ||
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| 9a. Insertion | | 9a. Insertion | ||
| − | | 9a. none<span style="white-space: pre; | + | | 9a. none<span class="Apple-tab-span" style="white-space: pre;"> </span> |
| 9a. Insertion of IS5 sequence | | 9a. Insertion of IS5 sequence | ||
| 9a. none | | 9a. none | ||
| Line 100: | Line 104: | ||
| 10. Insertion and deletion<br><br> | | 10. Insertion and deletion<br><br> | ||
| Bacteriophage DNA insertion and IS1 transposon insertion. Deletion of ~5 genes<br><br> | | Bacteriophage DNA insertion and IS1 transposon insertion. Deletion of ~5 genes<br><br> | ||
| − | | Insertion of IS3<br> | + | | Insertion of IS3<br> |
| − | | Pseudogenes at the site of deletion in REL606 and transposon insertions | + | | Pseudogenes at the site of deletion in REL606 and transposon insertions |
| − | | none | + | | none |
| [http://tinyurl.com/ykynub2 tinyurl.com/ykynub2]<br> | | [http://tinyurl.com/ykynub2 tinyurl.com/ykynub2]<br> | ||
|- | |- | ||
Revision as of 21:11, 28 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 transposon |
Insertion sequences and Prophage CP46 DNA insertion | Prophage specific genes found in DH10B |
Prophage DNA insertion and IS insertions has created pseudogenes in K-12 DH10B |
tinyurl.com/yd2quy7 |
| 3. Translocation in REL606 and insertion in DH10B |
Insertion of IS1 sequence. Translocation of ~15 genes including lac operon and other metabolic enzymes genes | Insertion of IS3 and IS2 sequences |
Translocation by transposon insertion in REL606 as evidenced by direct repeats and as seen from dotplot that the translocated region in REL606 is syntenic to DH10B but not colinear. |
Pseudogenes of yaiT and yaiX were created in DH10B by transposon insertions. Insertion by translocation in REL606 was confirmed as lac operon and other metabolic genes were found in DH10B by analyzing the translocated genes on the dotplot |
http://tinyurl.com/yldc83u |
| 4. Insertion in REL606 and DNA duplication event in DH10B. |
Prophage DNA and transposase insertion |
Recent DNA duplication event | 100% identity between paralogs in DH10B and ~98% identity between syntenic region of DH10B and 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 | 9a. none | 9a. Insertion of IS5 sequence | 9a. none | 9a. none | 9a. http://tinyurl.com/ylllc6u |
| 9b. Insertion | 9b. Insertion of ISI transposon | 9b. none | 9b. none | 9b. none | 9b. tinyurl.com/ygsqg2f |
| 9c. Insertion | 9c. ISI insertion |
9c. Insertion of ABC transporter, flagella encoding genes and few other enzymes | 9c. Inserted DNA segment in DH10B is bordered by direct repeats at both ends. 100% identity was found between the two repeats. |
9c.DR indicates transposon insertion in DH10B. | 9ctinyurl.com/yza4jy3[1] |
| 9d. Insertion | 9d. IS2 insertion |
9d. none | 9d. none | 9d. none | 9d. tinyurl.com/ygfgtqy |
| 10. Insertion and deletion |
Bacteriophage DNA insertion and IS1 transposon insertion. Deletion of ~5 genes |
Insertion of IS3 |
Pseudogenes at the site of deletion in REL606 and transposon insertions | none | tinyurl.com/ykynub2 |
| 11. Insertion and deletion |
IS1 insertion followed by insertion |
CP4-57 prophage DNA insertion and possible deletion of ParB family protein and recombinase |
Phage insertion in DH10B may have created pseudogene of ParB family protein genes and recombinase which later got deleted |
Pseudogenes of yqa, yga and ypj indicated possible formation of pseudogenes of ParB and recombinase at some time prior to their deletion in DH10B. |
tinyurl.com/yg7ybg4 |
| 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 inverted repeats of IS10 transposon. Deletion of several genes in DH10B is evidenced by IS5 trans-activator transposase. |
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 |
tinyurl.com/yhyxgrq |
|
13a. Deletion |
13a. none |
13a. Deletion of putative adhesin |
13a. Insertion of HEAT repeat containing lyase at the site of deletion in DH10B may have created pseudogene of adhensin which later got deleted | 13a.Insertion of HEAT repeat containing lyase is evidenced by its different GC content. Insertion may have created pseudogene of adhesin which later got deleted,in REL606 as evidenced by different GC content of capsule related protein. |
13a. tinyurl.com/yjojy53 |
|
13b, Insertion |
13b. Insertion of IS1, waaL and waaV genes |
13b. Insertion of ~5 rfa genes. |
|
13b. IS1 insertion created pseudogene. | 13b.http://tinyurl.com/yj2yg5s |
|
13c. Insertion and deletion |
13c. Insertion of IS30 transposon and several 'hypothetical protein" genes. |
13c. Deletion of ShiA-like and TrbC-like protein genes |
13c. Insertion in REL606 is evidenced by different GC content of genes.
|
13c. Pseudogene in REL606 and different GC content of genes indicate possible insertion. No DRs were found as to indicate insertion of ShiA-like and TrbC-like gene therefore deletion of these genes in DH10B may have occured |
13c. tinyurl.com/yjzdyum |
|
14a. Insertion |
14a. Inserion of several transposons and secondary glycine betaine transporter | 14a.Insertion of several transposons. Insertion of Kple2 phage-like element | 14a. Insertion of transposons has integreted genes of different GC contents, | 14a. none | 14a. tinyurl.com/yzyvunx |
| 14b. Insertion | 14b. Insertion of ~15 genes | 14b. none | 14b. Insertion in REL606 is evidenced by IR flanking the DNA segment containing several genes. | 14b.Pseudogene created at the site of insertion in DH10B. | 14b. tinyurl.com/yly2b6u |
|
|
14c. none |
14c. Deletion of ~15 genes.
|
14c. Deletion in DH10B is evidenced by insertion of IS10R which may have facilitated excision of DNA by forming DRs |
14c. none |
14c. tinyurl.com/yfhhsk6 |
