Syntenic dotplot

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).

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[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	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 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.	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 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. 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. Insertion in both is evideneced by different GC content of the 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. 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 DRs	14c. none	14c. tinyurl.com/yfhhsk6