pan genomics

8/11/2019 Pan Genomics

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PAN


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full complement of genes in all

species

typically applied to bacteria and

archaea,

union of the gene sets of all the

strains of a species

evolutionary context ->

meta enomics


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Phylogeny

Evolution

Conserved genetics

Mutations

Genetics variations

Environmental effects


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Select the pathogen specie

Select the strains and obtain their

genome sequences

Polygenomic Analyses

Pan Genome, Core Genome and SingletonAnalyses


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Pi


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orynebacterium

pseudotuberculosis

R d h d


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Rod shaped , gram +ive strain

facultative intracellular pathogen

Non motile and poses FIMBRIAE

cause several infectious contagious chron

Lymphadentis , ulcerative lymphangitis , m

edematous skin

Two strains Ovis

Equi


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15 genome sequences

from NCBI

9 OVIS

6 Equi

From the localities ofAustralia, USA, South

Africa, Brazil, Egypt,

Argentine and Kenya


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1. GegeneesSoftware is used

2. Divide the genomes into small sequences

3. All vs. Allsimilarity search -> MinimumShared Content

4. Minimum shared contents were subtracted

from all the genomes to get VARIABLEcontent

5. Comparison between minimum shared

content and variable content -> generate


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1. EDGARSoftware is used

2. Homology analyses based on specific

cutoff

3. Homology analyses was based onBLASTScore Ratio Value (SRV)

4. SRV higher than the specific cutoff

were considered to be orthologous


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1. Subset of genes presenting orthologs in

all selected strains

2. Gene set of strain A is compared with

set of genes of strain B -> orthologs in

both strains were member of CORE

genome AB.

3. Then AB core genome was compared

with genome set of strain C and formed

a CORE genome ABC


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1. Subset of genes presenting non-

orthologs in all selected strains

2. Gene set of strain A is compared with

set of genes of strain B -> non-

orthologs in both strains were member

of PAN genome AB.

3. Then AB core genome was compared

with genome set of strain C and formed

a PAN genome ABC


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Contains only those genes

which were present in only one

strain and have no orthologs in

any other strain


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Pan Genome C. pseudotuberculosis -> 2,782

genes Average Genome of each 15 strains -> 2,078

genes

Pan Genome of OVIS -> 2,403 genes

Average Genome of OVIS -> 2,098 genes

Pan Genome of EQUI -> 2,521 genes

->


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Strain specific genes

GEIs -> evolution by quantum

leaps -> virulence genes

Pathogenicity Islands

Prediction


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case study of Gen

nalysis of Multiple

Pathogenic isolates o

streptococcus

agalactiae


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Definition of Bacterial specie from pre-

genomic era was

Share characteristic phenotypic traits

form one specie

Large genomic info. -> describe the

bacterial species more precisely

But ..

how many genomes are needed to

DEFINE the bacterial species ???


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Comparative analysis of Pan-

Genomes can describe the

BACTERIAL species moreprecisely


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8 genomes of Streptococcus Agalactiae

from GBS (Group B Streptococcus) weresequences

8 strains genomic sequences were

generated by WHOLE-GENOMEshotgunsequencing approach

Genomes of 8 strains were aligned and

were pasted in pseudochomosome


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Accession numbers:

1. A909, BAA-1138;

2. CJB111, BAA-23;

3. H36b, BAA-1174;

4. 18RS21, BAA-1175;

5. COH1, BAA-1176;

6. 515, BAA-1177.


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Each strain was compared by

Smith and Waterman protein search

DNA search of predicted ORFs against

complete DNA sequence

Protein search of all the predicted

proteins of the strain against complete

DNA sequence


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Any method of comparison giving 50 % of

sequence conservation -> Conserved /Strain Specific gene

Core genome is considered with 100 %

similar regions in all the 8 strains or by

subtracting the strain specific genes from

the whole genome of each strain.


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GBS Pan Genome -> comparison of 8strains reveals that Pan-Genome

continue to expand with the inclusion

of strains

At the average of 33 new strain

specific genes are identified for each

new strain sequenced and are added

to the Pan Genome of the specie


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pan genomics

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