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Table 2 Regions of genomic plasticity (RGP-Cy#) identified in N. cyriacigeorgica by ACT comparisons with the N. farcinica genome

From: The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen’s lifestyle

RGP

GI position

Virulence gene (in or around GI)

ORF begin

ORF end

Length (kb)

Nb. of genes

Gene class

Putative role of GI

tRNA

Cy1

61471..73200

 

nocyr_0048

nocyr_0063

11.7

14

Unknown

Unknown

0

Cy2

213775..239600

 

nocyr_0182

nocyr_0205

25.8

21

Enzymes, transporters, histidine degradation, CSP

Unknown

3

Cy3

343550..357558

nocyr_0300

nocyr_0300

nocyr_0309

14

10

Enzymes, regulators, transporters, catalase

Adaptation to atypical conditions

1

Cy4

387100..424100

 

nocyr_0340

nocyr_0383

37

43

Recombinase, integrase, topisomerase, ADN pol III, cadmium inductible protein

Plasticity, adaptation

1

Cy5

512800..526200

 

nocyr_0472

nocyr_0488

13.4

17

regulators, transporters

Unknown

0

Cy6

594300..599228

0547 → 0555, 0566 → 0567

nocyr_0557

nocyr_0561

4.9

5

Regulators, ISNcy5

Plasticity

1

Cy7

1045000..1055000

 

nocyr_0920

nocyr_0925

10

6

Unknown

Unknown

1

Cy8

1098658..1109690

 

nocyr_0967

nocyr_0978

11.3

11

Integrase, endoribonuclease

Plasticity

0

Cy9

1480355..1548800

 

nocyr_1341

nocyr_1391

69.3

51

Enzymes, regulators, mycosin

Virulence

2

Cy10

1937100..2016932

nocyr_1792

nocyr_1739

nocyr_1800

79.8

68

Enzymes, regulators, C31 phage resistance genes

Defense

1

Cy11

2164650..2173100

 

nocyr_1932

nocyr_1940

8.4

9

Unknown

Unknown

0

Cy12

2273150..2315500

 

nocyr_2044

nocyr_2082

42.4

36

Enzymes, transporters, regulators, integrases

Plasticity

1

Cy13

3131000..3204200

 

nocyr_2827

nocyr_2884

73.2

58

Enzymes, regulators, ISNcy2-b, ISNcy4, integrases, PBP

Plasticity, adaptation

0

Cy14

3265400..3337600

 

nocyr_2933

nocyr_2985

72.2

61

Enzymes, Nitrate reduction/expulsion, ISNcy1-d, regulators, recombinase

Nitrite/Nitrate metabolism, plasticity

1

Cy15

4299671..4308500

 

nocyr_3906

nocyr_3911

8.8

6

Cobalamin and citrate metabolism

Vit B12, energy metabolism

0

Cy16

4339344..4363500

 

nocyr_3940

nocyr_3962

24.2

23

Enzymes, regulators, limonene-momooxygenase

Unknown, Adaptation

0

Cy17

4409577..4447497

 

nocyr_4002

nocyr_4035

37.9

34

Enzymes, regulators, transporters

Unknown

0

Cy18

4523400..4592400

nocyr_4112, nocyr_4128

nocyr_4097

nocyr_4162

69

66

Enzymes, regulators, NRPS, transporters, fatty acid synthesis, spermidin, sigma factor, DHB

Fatty acid and peptide synthesis, adaptation, virulence, plasticity

1

Cy19

5338862..5361100

 

nocyr_4801

nocyr_4818

22.2

14

Enzymes, regulators

Unknown, vitamine métabolism

0

Cy20

5611900..5622135

 

nocyr_5027

nocyr_5036

10.2

10

Unknown

Unknown

0

Cy21

5720300..5758400

nocyr_5135, nocyr_5136

nocyr_5133

nocyr_5170

38.1

38

Enzymes, transporters, regulators, sulfur metabolism

Energy metabolism, virulence, adaptation

0

Cy22

5992000..6012890

 

nocyr_5383

nocyr_5404

20.9

21

Enzymes

Unknown

0