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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.