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Table 1 Distribution of perfect microsatellites with ≥3 repeats and minimum 15 bp length in genomic and EST sequences of cucumber and selected plant species#

From: Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

 

Cucumber

Microsatellite density (SSR/Mbp)

  

Sequence type

Count

Rel. freq. (%)

Mean repeat number

Density (SSR/Mb)

Mt

Gm

Pt

At

Vv

Oz

Sb

All species mean

T-test statistics ( T , P )§

   SSR type

             

Genomic

             

   Dinucleotide

29,651

26.5

9.6

146.0

61.5

74.6

132.6

78.7

117.2

100.1

51.6

95.3*

(2.57, 0.022)

   Trinucleotide

28,645

25.6

4.9

141.1

97.0

103.1

132.2

146.6

115.8

220.1

108.5

133.0*

(2.27, 0.039)

   Tetranucleotide

33,348

29.8

3.2

164.2

102.8

97.5

144.9

93.2

171.3

132.7

105.4

126.5*

(2.86, 0.013)

   Pentanucleotide

11,038

9.8

3.2

54.4

40.0

27.2

62.1

32.0

58.0

45.8

22.5

42.8

n.s.

   Hexanucleotide

6,290

5.6

3.3

31.0

14.4

16.8

26.9

13.6

29.3

27.4

27.5

23.4

n.s.

   Heptanucleotide

2,337

2.1

3.3

11.5

2.5

7.1

7.3

5.8

12.4

2.5

1.9

6.3

n.s.

   Octanucleotide

764

0.7

3.2

3.8

0.3

0.4

1.0

0.7

2.8

0.8

0.2

1.2

n.s.

   Total/mean

112,073

100

5.3

551.9

318.4

326.7

508.3

370.5

506.9

529.4

317.6

428.5

n.s.

   Total seq. (Mbp)‡

   

203.1

109.5

242.8

307.8

119.2

303.1

370.8

738.5

  

   GC content (%)

   

32.3

35.2

36.6

33.3

36.0

34.4

43.6

43.9

  

EST-clustered †

             

   Dinucleotide

1,413/2,305

16.3/14.8

7.6/8.3

75.0/54.8

36.6

81.1

86.6

47.8

40.7

57.9

52.1

59.7

 

   Trinucleotide

3,685/7,560

42.6/48.5

4.9/5.0

195.5/179.7

160.0

179.9

177.4

231.8

108.4

485.7

366.3

238.1

 

   Tetranucleotide

1,892/2,916

21.9/18.7

3.2/3.3

100.4/69.3

74.5

81.2

91.6

50.9

53.3

107.3

125.5

85.6

 

   Pentanucleotide

807/978

9.3/6.3

3.3/3.4

42.8/23.3

25.9

27.5

30.2

12.4

17.4

41.6

44.1

30.2

 

   Hexanucleotide

635/1,519

7.3/9.7

3.3/3.4

33.7/36.1

25.9

29.2

34.1

13.4

22.1

44.6

56.5

32.4

 

   Heptanucleotide

162/230

1.9/1.5

3.3/3.3

8.6/5.5

1.7

3.6

4.0

0.9

4.2

1.9

1.4

3.3

 

   Octanucleotide

52/95

0.6/0.6

3.3/3.2

2.8/2.3

0.2

0.4

0.8

0.7

1.0

0.2

0.2

0.8

 

   Total/mean

8,646/15,603

100/100

4.7/4.7

458.7/370.9

324.9

403.0

424.7

357.8

247.3

739.3

646.1

450.2

 

   Total seq. (Mbp)‡

   

18.8/42.1

51.9

51.3

67.6

74.8

81.4

158.2

32.4

  

   GC content (%)

   

39.5/41.4

39.6

41.5

42.4

42.7

43.9

51.5

52.0

  

EST-bulked

             

   Dinucleotide

3,515

12.9

7.5

55.2

         

   Trinucleotide

12,151

44.6

4.8

190.9

         

   Tetranucleotide

5,798

21.3

3.2

91.1

         

   Pentanucleotide

3,037

11.1

3.2

47.7

         

   Hexanucleotide

2,155

7.9

3.2

33.9

         

   Heptanucleotide

447

1.6

3.6

7.0

         

   Octanucleotide

155

0.6

3.2

2.4

         

   Total/mean

27,258

100

4.5

428.2

         

   Total seq. (Mbp)‡

   

63.7

         

   GC content (%)

   

40.3

         
  1. # Mt = Medicago truncatula, Gm = Glycine max, Pt = Populus trichocarpa, At = Arabidopsis thaliana, Vv = Vitis vinifera, Oz = Oryza sativa, Sb = Sorghum bicolor. Data for highest frequencies and totals are denoted with boldface typed numbers. † Two clustered EST data sets from cucumber lines WI 1983 and Gy14 (WI 1983/Gy14) were analyzed. ‡ Total length of sequences analyzed.* Value is significantly higher than its EST counterpart, at P ≤ 0.05. n.s. Value not significantly different from its EST counterpart. §T = t-test statistic, P = probability value. Only SSRs with 3 or more repeat units and a minimum 12 bp were considered.
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