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Table 2 Sequence composition of genome-wide 454 reads and of the sequences adjacent to pSc200 and pSc250 arrays

From: The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements

  All reads Reads with junctions of pSc200 Reads with junctions of pSc250
Type of sequence Cumulative length, bp Proportion to cumulative length, % Cumulative length of non-tandem DNA, bp Proportion, % Cumulative length of non-tandem DNA, bp Proportion, %
Class I TE       
Ty3/Gypsy-like 4 142 315 628 50.84 36542 35.68 65786 40.62
Ty1/Copia-like 799 492 074 9.81 14322 13.99 14677 9.06
solo-LTR 60 362 185 0.74 13119 12.81 37289 23.02
LINE 57 651 280 0.71 483 0.47 1212 0.75
SINE 1 201 224 0.02 0 0.00 0 0.00
Class II TE       
CACTA 454679975 5.58 5544 5.41 5621 3.47
EnSpm 18661838 0.23 984 0.96 23 0.01
Harbinger 20519563 0.25 0 0.00 0 0.00
Mariner 24069442 0.30 370 0.36 147 0.09
Hat 12376913 0.15 0 0.00 268 0.17
Helitron 3779908 0.05 0 0.00 0 0.00
Others 37550591 0.46 124 0.12 307 0.19
Simple repeats, low complexity 27 883 202 0.34 259 0.25 383 0.24
rDNA 8 782 174 0.11 0 0.00 396 0.24
Tandem repeats 16 953 966 0.21 185 0.18 2420 1.49
Unclassified (unknown) 48 627 218 0.60 2348 2.29 2996 1.85
  1. We computed DNA composition of all reads and compared with that in non-tandem DNA adjacent to the pSc200 and pSc250 tandem arrays. Length of all repeats was defined according to annotations that we got in output files of RepeatMasker tool (see “Methods”). Columns “Proportion” denote the ration of the cumulative length of the given non-tandem DNA to the cumulative length of all reads