Syntenic dotplot

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