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Table 2 Summary statistics of distribution and abundance of detected SSRs in the tested genomic library and SSR frequency estimates for robusta coffee genome

From: Development of new genomic microsatellite markers from robusta coffee (Coffea canephoraPierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies

SSR motif

SSRs detected in the library (% of total SSRs)

Mean no. of repeats/SSR (Range of repeat iterations in the SSR core)

Estimated number/distance of SSRs in the robusta coffee genome

   

Total SSRs/genome (X = n.a/b)*

SSRs/Mb genome (Y = X/a)

SSR spacing in the genome@ (Z = 1000/Y)

Targeted SSRs (DNRsT + TNRsT)

AG

31(26.7)

10.0 (6 to 29)

2057

2.5

393

AC

15 (12.9)

8.4 (6 to 14)

995

1.2

812

DNRs T

46 (39.7)

9.6 (6 to 29)

3053

3.8

265

AGC

9 (7.8)

6.8 (5 to 10)

597

0.7

1354

ATC

4 (3.5)

5.0 (5)

265

0.3

3048

ACG

3 (2.6)

6.7 (5 to 9)

199

0.3

4063

ACC

3 (2.6)

5.7 (5 to 7)

199

0.3

4063

AAT

3 (2.6)

5.3 (5 to 6)

199

0.3

4063

AAC

3 (2.6)

5.0 (5)

199

0.3

4063

AGG

2 (1.7)

6.0 (5 to 7)

133

0.7

6095

AAG

2 (1.7)

5.5 (5 to 6)

133

0.7

6095

CCG

1 (0.9)

6.0 (6)

66

0.1

12190

ACT

0

--

--

--

--

TNRs T

30 (25.9)

5.9 (5 to 10)

1991

2.5

406

SSRs T

76 (65.5)

8.3 (5 to 29)

5044

6.2

160

Non-targeted DNRs (DNRsNT)

AT/AT

10 (8.6)

10.3 (6 to 23)

50563#

62.50

16

Miscellaneous non-targted SSRs

A/T

21 (18.1)

nc

C/G

3 (2.6)

    

Note: Three of these MNRs were detected as part of the compound SSR motifs

AAAT

2 (1.7)

Nc

   

AAGTGG

2 (1.7)

    

AATT

1 (0.7)

    

AAAAAT

1 (0.7)

    

DNRs T+NT

56 (48.3)

11.5 (6 to 29)

53616

66.3

15

DNRs T+NT & TNRs T

86 (74.1)

9.5 (5 to 29)

55607

68.7

15

  1. nc: Not calculated
  2. *: X = estimated number of SSRs in genome; n = No. of detected SSRs in the library; a = 809 Mb -size of the haploid robusta genome [13]; b = 12.19 Mb- size of the screened robusta genome (see table 1)
  3. #: b = 0.16 Mb -size of genome sequenced
  4. @: Distance (in Kb) between two consecutive SSRs
  5. T: Targeted SSRs; NT: Non-targeted SSRs