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Table 1 Characteristics of genomic islands (GIs) and islets (Gis) identified in this study

From: Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans

Elementa

Size (kb)

Number of ORFs

% GC Contentb

Average CAI (Percent genes with low CAI)c

tRNA in Vicinity

Flanking Direct Repeats

Mobile Genetic Elements

Chromosome left end; SCO0001-0081

69.6

81

69.5

0.58 (59%)

-

-

8 transposon related genes

Gi-1; SCO0090-0099

6.6

10

67.1

0.56 (67%)

-

-

6 transposon related genes

GI-1; SCO0979-1000

25.9

22

70.7

0.67 (23%)

-

-

1 phage related integrase

Gi-2; SCO2381-2384

6.4

4

68.4

0.57 (75%)

-

-

-

Gi-3; SCO2862-2871

8.6

10

65.9

0.54 (78%)

-

-

1 gene similar to phage replication regulator

Gi-4; SCO3250-3270

14.0

21

66.2

0.54 (80%)

Arg-tRNA CCT

43 bp perfect repeat

Mostly plasmid (pSAM2) related genes

GI-2; SCO3437-3506

75.0

70

68.7

0.60 (55%)

-

61 bp repeat (6 mismatches)

5 transposon related genes

Gi-5; SCO3929-3937

9.2

8

68.0

0.59 (50%)

-

-

pSAM2 integration site, some plasmid functions

Gi-6; SCO3980-3998

10.7

19

65.8

0.44 (100%)

Ser-tRNA TGA

106 bp repeat (8 mismatches)

pSAM2 insertion element

Gi-7; SCO4060-4066

5.2

7

66.1

0.43 (100%)

Ser-tRNA GGA

88 bp repeat (4 mismatches)

2 transposon related genes

Gi-8; SCO4210-4213

3.8

4

66.8

0.50 (75%)

-

19 bp perfect repeat

Some phage related genes

Gi-9; SCO4346-4350

7.0

5

66.9

0.55 (75%)

-

-

-

Gi-10; SCO4533-4537

4.3

5

72.1

0.70 (0%)

-

-

-

Gi-11; SCO4615-4631

15.9

17

68.3

0.62 (31%)

Tyr-tRNA GTA

112 bp repeat (1 mismatch)

Possible SLP1 insertion

Gi-12; SCO5327-5350

21.3

24

65.3

0.67 (55%)

Arg-tRNA CCG

114 bp repeat (4 mismatches)

pSAM2 integration, plasmid/phage related genes

Gi-13; SCO5605-5620

12.9

16

67.0

0.58 (67%)

-

-

All phage related genes

Gi-14; SCO5632-5644

10.4

13

63.8

0.44 (100%)

-

52 bp repeat (5 mismatches)

Some plasmid related functions

Gi-15; SCO5718-5735

21.8

18

68.1

0.56 (72%)

-

-

-

Gi-16; SCO6120-6124

2.9

5

70.0

0.67 (25%)

-

-

-

Gi-17; SCO6314-6338

23.6

23

70.2

0.59 (70%)

-

-

2 transposon related genes

GI-3; SCO6353-6405

56.6

53

68.6

0.56 (61%)

-

-

4 transposon related genes

GI-4; SCO6625-6642

30.4

18

68.6

0.56 (65%)

-

-

Few phage related genes

GI-5; SCO6806-6953

153.3

148

69.0

0.60 (53%)

Pro-tRNA GGG

44 bp perfect repeat

1 transposon related gene at end

Gi-18; SCO7795-7802

4.2

8

65.2

0.48 (86%)

-

-

3 transposon related genes

Chromosome right end; SCO7827-7845

20.4

19

70.1

0.55 (83%)

-

-

1 transposon related gene;

  1. aLarge genomic islands (≥25 kb) are in bold face
  2. bPercentage GC content within each genomic island; compare with 72.1% average GC content of whole genome
  3. cCompare the average CAI of ORFs within each segment with 0.73, the average CAI of all genes in S. coelicolor. Percent genes with low CAI is the fraction of genes in each island with CAI values lower than global mean – standard deviation (= 0.625)
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BMC Genomics

ISSN: 1471-2164

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