Table 1 Results of de novo genome assembly for PacBio sequence data of 23 NCTC Clostridium perfringens strains.

From: Comparative in silico genome analysis of Clostridium perfringens unravels stable phylogroups with different genome characteristics and pathogenic potential

 

Extrachromosomal elements

 

Chromosome

A

B

C

D

E

F

Strain

SRA Run

Toxin-type

Toxin genes

Status

Size (Mb)

Status

Size (Kb)

Status

Size (Kb)

Status

Size (Kb)

Status

Size (Kb)

Status

Size (Kb)

Status

Size (Kb)

NCTC8678

ERR1377187

A

cpa

●

2.9

◐

38

◐

4.7

        

NCTC8797

ERR1377188

F

cpa, cpe

●?

2.9

◐

25.3

◐

19

        

NCTC13170

ERR1377189

A

cpa

●

3.29

–

–

          

NCTC8503

ERR1407347

D

cpa, etx

◐

3.4 (6 ctgs*)

●§ (etx)

54.6

●

19.3

        

NCTC2544

ERR1456745

A

cpa

●

3.18

–

–

          

NCTC8799

ERR1466824

F

cpa, cpe

●

2.9

◐

63.1

◐

10.2

◐

7.8

      

NCTC10612

ERR1588634

F

cpa, cpe

●

3.0

●

13.6

◐

8.8

        

NCTC3182

ERR1599940

C

cpa, cpb

◐

3.5 (1ctg*)

●

49.4

●§ (cpb)

59.1

●

37.2

      

NCTC8238

ERR1656456

F

cpa, cpe

●

2.9

●

56.6

          

NCTC8246

ERR1656458

A

cpa, cpb2

●

3.3

●

54.3

          

NCTC2837

ERR1656459

A

cpa

●

3.3

–

–

          

NCTC8081

ERR1656460

C

cpa, cpb, cpe

●

3.1

●§ (cpe)

116.6

●

73.5

●§ (cpb)

67.9

●

58.1

●

53.7

◐

20.7

NCTC8247

ERR1674568

F

cpa, cpe

●

2.9

◐

57.02

          

NCTC8239

ERR1681948

F

cpa, cpe

●

2.9

●

56.6

          

NCTC9851

ERR1681949

F

cpa, cpe

●

2.9

●

56.6

●

12.3

        

NCTC10239

ERR1681950

F

cpa, cpe

●

2.9

●

57.9

●

12.4

●

12.2

      

NCTC10240

ERR1681951

F

cpa, cpe

●

2.9

●

56.6

◐

9.7

        

NCTC8679

ERR1787549

F

cpa, cpe

●

2.9

●

54.4

●

12.1

        

NCTC10578

ERR1787550

A

cpa

●

3.3

–

–

          

NCTC10613

ERR1787552

F

cpa, cpe

◐

2.94 (ctgs)

●

56.6

●

38.1

●

12.2

●

12.3

◐

8.9

  

NCTC10614

ERR1800584

F

cpa, cpe

●

2.9

●

56.6

●

12.2

        

NCTC8359

ERR1805687

F

cpa, cpe

●?

2.9

●

56.6

●

13.4

●

12.2

      

NCTC11144

ERR1954484

F

cpa, cpe

●

3.2

●§ (cpe)

78

●

58.6

●

50.9

      
  1. *ctg; contig: a contiguous fragment of DNA.
  2. ● Circularized finished genetic element.
  3. ●? The genome is circularized but there is uncertainty about its finished status as deep valleys (assembly area with little support of PacBio reads) were noticed in the coverage plot of the genome of strain NCTC8797 that may indicate a misassembly issue. Also, the genome of strain NCTC8359 showed a large spike in the coverage plot which may indicate collapsed repeats.
  4. ◐ Draft genetic element.
  5. ●§; indicates possible conjugative plasmids carrying known significant toxin genes (epsilon, beta, entero-toxin genes) and the species conjugation locus.
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