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Table 1 Details of samples and the viruses and viroids detected using the ‘detect viruses and viroids’ workflow using 21–25 nt and 21–22 nt length reads. Additional information can be found on Additional file 6

From: An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids

  

21–25 nt

21–22 nt

24 nt

Host

Viruses detected

Number of contig hits

% Identity

% Coverage of viral genome by contigs

Number of contig hits

% Identity

% Coverage of viral genome by contigs

Number of contig hits

% Identity

% Coverage of viral genome by contigs

Vitis vinifera (S1)

GRSPaV

22

94.03

76.07

21

93.57

74.65

n.a.

n.a.

n.a.

GVBa

13

96.82

70.5

13

97.23

66.54

n.a.

n.a.

n.a.

GFkV

22

92.37

93.2

21

92.12

94.13

n.a.

n.a.

n.a.

GLRaV-3

16

99.7

19.16

14

99.71

19.44

n.a.

n.a.

n.a.

HSVd

2

100

100

1

100

100

2

100

100

Prunus persica (S2)

PNRSV RNA1b

9

98.6

82.63

8

98.68

75.76

n.a.

n.a.

n.a.

PNRSV RNA2b

6

98.63

54.26

5

98.74

49.86

n.a.

n.a.

n.a.

PNRSV RNA3b

2

98.85

100

1

98.66

100

n.a.

n.a.

n.a.

Rubus idaeus (S3)

RBDV RNA1 c

5

97.83

26.41

4

97.89

16.98

n.a.

n.a.

n.a.

RBDV RNA2 c

8

98.77

75.08

6

98.68

60.51

3

99.15

16.76

RYNV

19

98.08

69.14

15

97.23

51.49

1

98.08

0.66

Brassica sp. (S4)

PCV (RdRp)

2

52.12

62.14

2

69.38

41.72

n.a.

n.a.

n.a.

ACV (RT)

2

67.5

57.44

2

52.92

61.08

n.a.

n.a.

n.a.

Ipomoea batatas (S5)

SPSMV-1 MP and CP

1

99.89

98.81

1

100

98.62

n.a.

n.a.

n.a.

Fragaria ananassa (S7)

SMoV RNA1

6

86.67

20.57

4

85.42

11.3

n.a.

n.a.

n.a.

SMoV RNA2

11

87.59

44.62

6

87.13

28.26

n.a.

n.a.

n.a.

Miscanthus sinensis (S9)

SrMV

8

83.43

37.53

7

81.67

37.04

3

90.03

3.16

Citrus medica (S10)

CTVd

26

95.7

56.79

31

97.42

47.8

21

97.96

29.24

CVd-VId

2

99.41

100

2

99.42

100

1

99.36

93.69

HSVd

2

99.09

100

2

99.09

100

2

98.84

100

Citrus sp. (S12)

Citrus endogenous pararetrovirus

42

90.26

77.92

3

91.35

8.87

31

89.07

66.94

Pennisetum advena (S17)

MCDV

29

98.45

72.14

27

98.81

68.35

n.a.

n.a.

n.a.

Citrus latifolia (S18)

CTV

30

98.67

33.03

21

98.69

24.75

n.a.

n.a.

n.a.

Actinidia (S21)

AcVB

33

93.05

41.25

18

94.24

23.21

4

91.75

4.22

Nicotiana tabacum

PVY

3

98.63

100

1

98.65

100

1

98.94

1.94

(S22)

TVCV

5

91.81

14.54

4

89.23

12.23

n.a.

n.a.

n.a.

  1. Virus name: GRSPaV Grapevine rupestris stem pitting-associated virus, GVB Grapevine virus B, GFkV Grapevine fleck virus, GLRaV-3 Grapevine leafroll-associated virus, HSVd Hop stunt viroid, PNRSV Prunus necrotic ringspot virus, RBDV Raspberry bushy dwarf virus, RYNV Rubus yellow net virus, PCV (RdRp) Persimmon cryptic virus (RNA dependent RNA polymerase), ACV (RT) Arisotelia chilensis virus 1 (Reverse transcriptase), SPSMV-1 Sweetpotato symptomless mastrevirus 1, SMoV Strawberry mottle virus, SrMV Sorghum mosaic virus, CTV Citrus tristeza virus, CVd-VI Citrus viroid VI, MCDV Maize chlorotic dwarf virus, AcVB Actinidia virus B, TVCV Tobacco vein-clearing virus, PVY Potato virus Y
  2. aPositive control for GVB identified using biological indexing at Post Entry Quarantine (PEQ)
  3. bPEQ positive control for PNRSV detected using ELISA (Agdia)
  4. cPEQ positive control for RBDV identified using ELISA (Agdia)
  5. dPEQ positive control for CTV and CVd-VI detected using PCR-based assays
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BMC Bioinformatics

ISSN: 1471-2105

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