Multiple Genome Alignment for
Identifying the Genomic Core Among
Moderately Related Microbial Genomes
Ikuo Uchiyama
National Institute for Basic Biology
Okazaki, Japan

Species genome concept
Core genome and pan genome
Escherichia coli O157

Escherichia coli
K-12 MG1655

core-genome

727
446

279

pan-genome

2681
1465
O157 Sakai
Shared with E. coli K12 (75%)
Unique to E. coli O157 (25%)

1855
277
CFT073

Core genome concept
Flexible regions(mainly horizontally transferred)

gainlossCore genome(mainly vertically transferred)
Purpose: to identify the core structure of moderately related genomes
using the information of synteny conservation

Genome alignment
based on gene order conservation
gene2
gene1

gene4
gene3

gene6
gene8
gene10
gene5
gene7
gene9

genome1
genome2
genome3
genome4

Neighborhoodgraph

Each edge represents a neighborhood pair of genes that are locatedwithin 20 genes in at least 50% of the genomes

CoreAligner algorithm
Construction of conserved neighborhood graphElimination of loops

Assignment of orientation based on MST
Identification of the optimal path

Conversion to a triplet graph

Conversion to the original graphDatasetBacillaceaeEnterobacteriaceae

Bacillus subtilis 1
Bacillus licheniformis 1
Bacillus halodurans 2
Bacillus clausii 2Bacillus anthrasis Ames 3
Bacills cereus 14579 3
Geobacillus kaustophilus
Oceanobacillus iheyensis(outgroup)
Staphylococcus aureus N315

Escherichia coli K-12 MG1655 4
Salmonella enterica CT18 4Enterobacter sp. 638 4
Erwinia carotovora
Photorhabdus luminescens
Sodalis glossinidius
Serratia proteamaculans
Yersinia pestis CO92
(outgroup)
Viblio cholerae

MBGD (Microbial genome database forcomparative analysis)

Bacillaceae core alignment

Chromosomal location of core genes

1438 orthologous groups

2125 orthologous groups

Ratio of core genes in each functional
category (B. subtilis)

Ratio of core genes in each functional
category (E. coli)

Comparison between the core structures ofBacillaceae and Enterobacteriaceae
Bacillaceae
Enterobacteriaceae
core

Essential genes

593

142

703/682

559

884

26

12211/201

2450

Functional categories of the common core set
Bacillaceae
593

core
142

703/682

Enterobacteriaceae
559

884

Sporulation

Robustness test(50%)

G+C content of the third codon positions

Congruence of phylogenetic trees
Bacillaceae

Phylogenetic tree of concatenated core genes
ML
NeighborNet

Genes in deviated topology
NSH-test, 5% significance levelCore

Non-corep-value

Rejected

Total

RejectedTotal

core<noncore)43 (3.5)85

32 (14.0)228

0.004573

511 (6.2)

176

38 (21.6)

176

2.170e-5617 (5.4)

314

34 (29.6)

115

1.899e-10732 (4.3)739

9 (15.5)58

0.001705

Total

63 (4.8)1314

113 (19.6)

577<2.2e-16

Core genes have more consistent phylogeny than non-core genes

RECOG(Research Environment for Comparative Genomics)
http://mbgd.genome.ad.jp/RECOG
Select organisms
Ortholog groups
DomClust

CoreAligner

Core alignmentConclusion
We have developed a method (CoreAligner) to
extract syntenically conserved regions toconstruct the core genome alignment.
Extracted core set contains most of thefunctionally important genes including theessential genes.
CoreAligner can identify more robust core set
than the method based only on gene conservation.
Indigenousness of the extrated core isdemonstrated by G+C content homogeneity andphylogenetic tree congruence.

The number of deleted core genes
Bacillaceae (1438 core)
Conserved
core

Deleted
core

Total
CDS

Bacillus subtilis

1362

76

4105

Bacillus licheniformis

1387

514152

Bacillus halodurans

1358

80

4066

Bacillus clausii

1296

1424096

Bacillus anthracis

1300

138

5311

Bacillus cereus

1297

1415234

Geobacillus kaustophilus

1356

82

3498

Oceanobacillus iheyensis

1265

173

3500

Staphylococcus aureus

883

555

2588

The number of deleted core genes
Enterobacteriaceae (2125 core)
Conserved
core

Deleted
core

Total
CDS

Escherichia coli

2048

774131

Salmonella enterica

2002123

4395

Enterobacter sp. 638

2057

684115

Erwinia carotovora

2006

119

4472

Photorhabdus luminescens

1769

356

4683

Sodalis glossinidius

1507

618

2432

Serratia proteamaculans

2110

15

4891

Yersinia pestis

2015

110

3885

Vibrio cholerae

1631

494

3835