Syntenic dotplot

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Syntenic dotplots are a type of scatter-plot. Each axis represents a sequence laid end-to-end, and each dot in the scatter-plot represents a putative Homologous match between the two sequences. Often, these dotplots are used for whole genome comparisons within the same genome or across two genomes from different taxa in order to identify Synteny. Synteny is defined as two or more genomic regions that are derived from a common ancestral genomic region. The evidence for synteny is the identification of a set of genes in each genome that have a collinear arrangement. When such a pattern of gene-order conservation is discovered, the most parsimonious explanation is that the two regions are related through a common ancestor. While syntenic dotplots are useful for identifying related genomic regions, they are also useful for identifying genomic regions that have undergone an evolutionary change in one of the two genomes being compared. For example, insertions, deletions, duplications, and inversions are readily identifiable from these plots.

Below is an example of comparing two closely related substrains of E. coli strain K12. While their entire genome is highly similar to one another at the nucleotide identity level, there are many "breaks" in the syntenic path through their genomes which reveal a variety of genomic changes (mostly insertions and deletions for this example).

Syntenic dotplot of E-coli B strain REL606(x-axis) and E-coli K12 strain DH10B (y-axis). The "green" line represents the regions of similarities between the two genomes while the discontinuities in the dotplot represent regions of genetic variations at a given locus between the two substrains of E-coli. The numbers correspond to the individual analysis of a break provided in the table below. This dotplot can be regenerated here [1]


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 in REL606 as evidenced by direct repeats.Dotplot shows that the missing genes are present in DH10B but not in this locus. The syntenic region is therefore 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,translocation and inversion
none Prophage DNA insertion and translocation of nitrite reductase 2 genes Phage specific genes found in DH10B
Translocation in DH10B is evident by dotplot. Moreover, the translocated genes in DH10B were found to be inverted. It could not be determined genes on which genomes were inverted as tranposon insertions were found in both genomes.

tinyurl.com/yaxlh7o

http://tinyurl.com/y9cs6ft

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 or transposon 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[2]
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
IS1 insertion at the site of deletion. Another IS1 insertion might have created direct repeats and facilitated deletion.    none tinyurl.com/ykynub2
11. Insertion and deletion 
IS1 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.  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. 

Inversion in DH10B as evidenced by inverted repeats of IS10 transposon.

Deletion of several genes in DH10B is evidenced by IS5  trans-activator transposase and presence of pseudogenes in DH10B,

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 direct repeats. 

tinyurl.com/yhyxgrq

13a. Deletion

13a. none

13a. Deletion of putative adhesin

13a. No direct repeats were found to indicate insertion of putative adhensin in REL606 therefore deletion in DH10B may have happened 13a.none
13a. tinyurl.com/yjojy53

13b. Insertion

13b. IS1 insertion and deletion of lipopolysaccharide genes 

13b. none


13b. IS1 insertion in REL606 indicates that deletion may have occured by formation of directed repeats. 

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. none

13c. Insertion in REL606 is evidenced by direct repeats



13c. direct repeats were found in REL606 which indicates insertion of ShiA-like and TrbC-like genes. 



13c. tinyurl.com/yjzdyum


14a. Insertion

14a. Insertion of several transposons and secondary glycine betaine transporter 14a.Insertion of several transposons. Insertion of Kple2 phage-like element 14a. Direct repeats bordering secondary glycine betaine transporter indicates its insertion 14a. none 14a. tinyurl.com/yzyvunx
14b. Insertion 14b. Insertion of ~15 genes 14b. Phage insertion. Transposon insertions 14b. Insertion in REL606 is evidenced by direct repeats flanking the DNA segment containing several genes. 14b.Phage-like genes were found in DH10B 14b. tinyurl.com/yly2b6u


14c. Deletion

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 direct repeats



14c. Pseudogenes found at the site of deletion and IS10R insertion.



14c. tinyurl.com/yfhhsk6