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Table 1 L. monocytogenes genomes analyzed in this study

From: Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification

Strain

Lineage

Serotype

Size (bp)

Contigs1

Genes2

% Identity3

Genbank Accession

Sequencing institution

Note4

EGD-e

II

1/2a

2,944,528

Closed

2931

100

AL591824

European consortium [43]

DSA

R2-561

II

1/2c

2,945,851

37

2993

99.78

AARS00000000

Broad Institute

DS

LO28

II

1/2c

2,675,580

1150

3030

99.6

AARY00000000

Broad Institute/Institut Pasteur

D

Finland 1988

II

3a

2,834,040

49

2740

98.49

AART00000000

Broad Institute

S

10403S

II

1/2a

2,873,541

21

2905

98.48

AARZ00000000

Broad Institute

DS

F2-515

II

1/2a

1,815,995

1728

2710

98.47

AARI00000000

Broad Institute

D

N3-165

II

1/2a

2,884,080

39

2885

98.39

AARQ00000000

Broad Institute

DS

J2-003

II

1/2a

2,741,640

795

2972

98.32

AARM00000000

Broad Institute

D

F6900

II

1/2a

2,968,620

23

3007

98.28

AARU00000000

Broad Institute

DS

F6854

II

1/2a

2,950,285

133

2967

98.26

AADQ00000000

TIGR

DS

J2818

II

1/2a

2,973,040

24

3020

98.24

AARX00000000

Broad Institute

DS

J0161

II

1/2a

3,062,582

25

3114

98.23

AARW00000000

Broad Institute

DS

J1-175

I

1/2b

2,866,484

457

3178

94.39

AARK00000000

Broad Institute

D

J2-064

I

1/2b

2,828,700

545

2968

94.37

AARO00000000

Broad Institute

D

R2-503

I

1/2b

2,991,493

55

2968

94.28

AARR00000000

Broad Institute

S

J1-194

I

1/2b

2,989,818

30

3040

94.27

AARJ00000000

Broad Institute

DS

N1-017

I

4b

3,142,060

79

3253

94.2

AARP00000000

Broad Institute

DS5

Clip 80459

I

4b

2,912,690

Closed

2972

94.17

FM242711

Institut Pasteur

S

F2365

I

4b

2,905,187

Closed

2907

94.14

AE017262

TIGR [85]

DS

H7858

I

4b

2,972,254

181

3195

94.08

AADR00000000

TIGR

DS

HPB2262

I

4b

2,991,120

79

3067

93.98

AATL00000000

Broad Institute/Istituto Superiore di Sanita

DS

HCC23

III

4a

2,976,212

Closed

3059

92.38

CP001175

Mississippi State University

S

F2-524

IIIA

4a

-

-

-

-

-

-

A

F2-501

IIIA

4b

-

-

-

-

-

-

A

J2-071

IIIA

4c

2,851,800

53

2778

92.6

AARN00000000

Broad Institute

DA5

J1-208

IIIB

4a

1,963,740

1660

2809

91.8

AARL00000000

Broad Institute

DA

M1-002

IIIB

4b

-

-

-

-

-

-

A

W1-111

IIIB

4c

-

-

-

-

-

-

A

F2-208

IIIC

4a

-

-

-

-

-

Life Technologies Corporation/Cornell University

A

F2-569

IIIC

4b

-

-

-

-

-

-

A

W1-110

IIIC

4c

-

-

-

-

-

-

A

  1. 1Number of contigs based on GenBank at the time of our study. Strains with > 200 contigs were sequenced only to low coverage and were excluded from analysis.
  2. 2Number of annotated protein coding genes and RNAs based on GenBank.
  3. 3Nucleotide sequence identity in reference to EGD-e.
  4. 4Strains used for array design (D); comparative sequence analysis (S), comparative genomic hybridizations (A).
  5. 5Strains N1-017 and J2-071 were found to be mislabeled in GenBank; this has since been fixed.
  6. - Information not available.
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BMC Genomics

ISSN: 1471-2164

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